%%bash
date
Mon May 23 09:57:56 PDT 2016
%%bash
system_profiler SPSoftwareDataType
Software:
System Software Overview:
System Version: OS X 10.9.5 (13F34)
Kernel Version: Darwin 13.4.0
Boot Volume: Hummingbird
Boot Mode: Normal
Computer Name: hummingbird
User Name: Sam (Sam)
Secure Virtual Memory: Enabled
Time since boot: 35 days 2 minutes
%%bash
#Uses grep to exclude lines that display serial number and hardware UUID
system_profiler SPHardwareDataType | grep -v [SH][ea]
Model Name: Xserve
Model Identifier: Xserve3,1
Processor Name: Quad-Core Intel Xeon
Processor Speed: 2.26 GHz
Number of Processors: 2
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache (per Processor): 8 MB
Memory: 24 GB
Processor Interconnect Speed: 5.86 GT/s
Boot ROM Version: XS31.0081.B06
SMC Version (system): 1.43f4
LOM Revision: 1.1.8
Since this all required the use of 'sudo' the following was run outside of this notebook:
cd /Volumes/usr/local/bioinformatics
sudo wget http://catchenlab.life.illinois.edu/stacks/source/stacks-1.40.tar.gz
sudo tar -zxvf stacks-1.40.tar.gz
sudo rm stacks-1.40.tar.gz
cd /Volumes/usr/local/bioinformatics/stacks-1.40
sudo ./configure --enable-sparsehash --enable-bam --with-bam-include-path=/usr/local/bioinformatics/samtools-0.1.19 --with-bam-lib-path=/usr/local/bioinformatics/samtools-0.1.19
sudo make -j 8
sudo make install
cd /Volumes/toaster/sam/stacks/oly_BGI_GBS
/Volumes/toaster/sam/stacks/oly_BGI_GBS
ls
160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz 1NF_25A_1.fq.gz* 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz 1NF_25A_2.fq.gz* 1HL_10A_1.fq.gz* 1NF_26A_1.fq.gz* 1HL_10A_2.fq.gz* 1NF_26A_2.fq.gz* 1HL_11A_1.fq.gz* 1NF_27A_1.fq.gz* 1HL_11A_2.fq.gz* 1NF_27A_2.fq.gz* 1HL_12A_1.fq.gz* 1NF_28A_1.fq.gz* 1HL_12A_2.fq.gz* 1NF_28A_2.fq.gz* 1HL_13A_1.fq.gz* 1NF_29A_1.fq.gz* 1HL_13A_2.fq.gz* 1NF_29A_2.fq.gz* 1HL_14A_1.fq.gz* 1NF_2A_1.fq.gz* 1HL_14A_2.fq.gz* 1NF_2A_2.fq.gz* 1HL_15A_1.fq.gz* 1NF_30A_1.fq.gz* 1HL_15A_2.fq.gz* 1NF_30A_2.fq.gz* 1HL_16A_1.fq.gz* 1NF_31A_1.fq.gz* 1HL_16A_2.fq.gz* 1NF_31A_2.fq.gz* 1HL_17A_1.fq.gz* 1NF_32A_1.fq.gz* 1HL_17A_2.fq.gz* 1NF_32A_2.fq.gz* 1HL_19A_1.fq.gz* 1NF_33A_1.fq.gz* 1HL_19A_2.fq.gz* 1NF_33A_2.fq.gz* 1HL_1A_1.fq.gz* 1NF_4A_1.fq.gz* 1HL_1A_2.fq.gz* 1NF_4A_2.fq.gz* 1HL_20A_1.fq.gz* 1NF_5A_1.fq.gz* 1HL_20A_2.fq.gz* 1NF_5A_2.fq.gz* 1HL_21A_1.fq.gz* 1NF_6A_1.fq.gz* 1HL_21A_2.fq.gz* 1NF_6A_2.fq.gz* 1HL_22A_1.fq.gz* 1NF_7A_1.fq.gz* 1HL_22A_2.fq.gz* 1NF_7A_2.fq.gz* 1HL_23A_1.fq.gz* 1NF_8A_1.fq.gz* 1HL_23A_2.fq.gz* 1NF_8A_2.fq.gz* 1HL_24A_1.fq.gz* 1NF_9A_1.fq.gz* 1HL_24A_2.fq.gz* 1NF_9A_2.fq.gz* 1HL_25A_1.fq.gz* 1SN_10A_1.fq.gz* 1HL_25A_2.fq.gz* 1SN_10A_2.fq.gz* 1HL_26A_1.fq.gz* 1SN_11A_1.fq.gz* 1HL_26A_2.fq.gz* 1SN_11A_2.fq.gz* 1HL_27A_1.fq.gz* 1SN_12A_1.fq.gz* 1HL_27A_2.fq.gz* 1SN_12A_2.fq.gz* 1HL_28A_1.fq.gz* 1SN_13A_1.fq.gz* 1HL_28A_2.fq.gz* 1SN_13A_2.fq.gz* 1HL_29A_1.fq.gz* 1SN_14A_1.fq.gz* 1HL_29A_2.fq.gz* 1SN_14A_2.fq.gz* 1HL_2A_1.fq.gz* 1SN_15A_1.fq.gz* 1HL_2A_2.fq.gz* 1SN_15A_2.fq.gz* 1HL_31A_1.fq.gz* 1SN_16A_1.fq.gz* 1HL_31A_2.fq.gz* 1SN_16A_2.fq.gz* 1HL_33A_1.fq.gz* 1SN_17A_1.fq.gz* 1HL_33A_2.fq.gz* 1SN_17A_2.fq.gz* 1HL_34A_1.fq.gz* 1SN_18A_1.fq.gz* 1HL_34A_2.fq.gz* 1SN_18A_2.fq.gz* 1HL_35A_1.fq.gz* 1SN_19A_1.fq.gz* 1HL_35A_2.fq.gz* 1SN_19A_2.fq.gz* 1HL_3A_1.fq.gz* 1SN_1A_1.fq.gz* 1HL_3A_2.fq.gz* 1SN_1A_2.fq.gz* 1HL_4A_1.fq.gz* 1SN_20A_1.fq.gz* 1HL_4A_2.fq.gz* 1SN_20A_2.fq.gz* 1HL_5A_1.fq.gz* 1SN_21A_1.fq.gz* 1HL_5A_2.fq.gz* 1SN_21A_2.fq.gz* 1HL_6A_1.fq.gz* 1SN_22A_1.fq.gz* 1HL_6A_2.fq.gz* 1SN_22A_2.fq.gz* 1HL_7A_1.fq.gz* 1SN_23A_1.fq.gz* 1HL_7A_2.fq.gz* 1SN_23A_2.fq.gz* 1HL_8A_1.fq.gz* 1SN_24A_1.fq.gz* 1HL_8A_2.fq.gz* 1SN_24A_2.fq.gz* 1HL_9A_1.fq.gz* 1SN_25A_1.fq.gz* 1HL_9A_2.fq.gz* 1SN_25A_2.fq.gz* 1NF_10A_1.fq.gz* 1SN_26A_1.fq.gz* 1NF_10A_2.fq.gz* 1SN_26A_2.fq.gz* 1NF_11A_1.fq.gz* 1SN_27A_1.fq.gz* 1NF_11A_2.fq.gz* 1SN_27A_2.fq.gz* 1NF_12A_1.fq.gz* 1SN_28A_1.fq.gz* 1NF_12A_2.fq.gz* 1SN_28A_2.fq.gz* 1NF_13A_1.fq.gz* 1SN_29A_1.fq.gz* 1NF_13A_2.fq.gz* 1SN_29A_2.fq.gz* 1NF_14A_1.fq.gz* 1SN_2A_1.fq.gz* 1NF_14A_2.fq.gz* 1SN_2A_2.fq.gz* 1NF_15A_1.fq.gz* 1SN_30A_1.fq.gz* 1NF_15A_2.fq.gz* 1SN_30A_2.fq.gz* 1NF_16A_1.fq.gz* 1SN_31A_1.fq.gz* 1NF_16A_2.fq.gz* 1SN_31A_2.fq.gz* 1NF_17A_1.fq.gz* 1SN_32A_1.fq.gz* 1NF_17A_2.fq.gz* 1SN_32A_2.fq.gz* 1NF_18A_1.fq.gz* 1SN_3A_1.fq.gz* 1NF_18A_2.fq.gz* 1SN_3A_2.fq.gz* 1NF_19A_1.fq.gz* 1SN_4A_1.fq.gz* 1NF_19A_2.fq.gz* 1SN_4A_2.fq.gz* 1NF_1A_1.fq.gz* 1SN_5A_1.fq.gz* 1NF_1A_2.fq.gz* 1SN_5A_2.fq.gz* 1NF_20A_1.fq.gz* 1SN_6A_1.fq.gz* 1NF_20A_2.fq.gz* 1SN_6A_2.fq.gz* 1NF_21A_1.fq.gz* 1SN_7A_1.fq.gz* 1NF_21A_2.fq.gz* 1SN_7A_2.fq.gz* 1NF_22A_1.fq.gz* 1SN_8A_1.fq.gz* 1NF_22A_2.fq.gz* 1SN_8A_2.fq.gz* 1NF_23A_1.fq.gz* 1SN_9A_1.fq.gz* 1NF_23A_2.fq.gz* 1SN_9A_2.fq.gz* 1NF_24A_1.fq.gz* index.lst 1NF_24A_2.fq.gz*
process_radtags command for matching the paired FASTQ files.¶%%bash
seq1=( 1HL_10A_1.fq.gz 1HL_11A_1.fq.gz 1HL_12A_1.fq.gz 1HL_13A_1.fq.gz 1HL_14A_1.fq.gz 1HL_15A_1.fq.gz 1HL_16A_1.fq.gz 1HL_17A_1.fq.gz 1HL_19A_1.fq.gz 1HL_1A_1.fq.gz 1HL_20A_1.fq.gz 1HL_21A_1.fq.gz 1HL_22A_1.fq.gz 1HL_23A_1.fq.gz 1HL_24A_1.fq.gz 1HL_25A_1.fq.gz 1HL_26A_1.fq.gz 1HL_27A_1.fq.gz 1HL_28A_1.fq.gz 1HL_29A_1.fq.gz 1HL_2A_1.fq.gz 1HL_31A_1.fq.gz 1HL_33A_1.fq.gz 1HL_34A_1.fq.gz 1HL_35A_1.fq.gz 1HL_3A_1.fq.gz 1HL_4A_1.fq.gz 1HL_5A_1.fq.gz 1HL_6A_1.fq.gz 1HL_7A_1.fq.gz 1HL_8A_1.fq.gz 1HL_9A_1.fq.gz 1NF_10A_1.fq.gz 1NF_11A_1.fq.gz 1NF_12A_1.fq.gz 1NF_13A_1.fq.gz 1NF_14A_1.fq.gz 1NF_15A_1.fq.gz 1NF_16A_1.fq.gz 1NF_17A_1.fq.gz 1NF_18A_1.fq.gz 1NF_19A_1.fq.gz 1NF_1A_1.fq.gz 1NF_20A_1.fq.gz 1NF_21A_1.fq.gz 1NF_22A_1.fq.gz 1NF_23A_1.fq.gz 1NF_24A_1.fq.gz 1NF_25A_1.fq.gz 1NF_26A_1.fq.gz 1NF_27A_1.fq.gz 1NF_28A_1.fq.gz 1NF_29A_1.fq.gz 1NF_2A_1.fq.gz 1NF_30A_1.fq.gz 1NF_31A_1.fq.gz 1NF_32A_1.fq.gz 1NF_33A_1.fq.gz 1NF_4A_1.fq.gz 1NF_5A_1.fq.gz 1NF_6A_1.fq.gz 1NF_7A_1.fq.gz 1NF_8A_1.fq.gz 1NF_9A_1.fq.gz 1SN_10A_1.fq.gz 1SN_11A_1.fq.gz 1SN_12A_1.fq.gz 1SN_13A_1.fq.gz 1SN_14A_1.fq.gz 1SN_15A_1.fq.gz 1SN_16A_1.fq.gz 1SN_17A_1.fq.gz 1SN_18A_1.fq.gz 1SN_19A_1.fq.gz 1SN_1A_1.fq.gz 1SN_20A_1.fq.gz 1SN_21A_1.fq.gz 1SN_22A_1.fq.gz 1SN_23A_1.fq.gz 1SN_24A_1.fq.gz 1SN_25A_1.fq.gz 1SN_26A_1.fq.gz 1SN_27A_1.fq.gz 1SN_28A_1.fq.gz 1SN_29A_1.fq.gz 1SN_2A_1.fq.gz 1SN_30A_1.fq.gz 1SN_31A_1.fq.gz 1SN_32A_1.fq.gz 1SN_3A_1.fq.gz 1SN_4A_1.fq.gz 1SN_5A_1.fq.gz 1SN_6A_1.fq.gz 1SN_7A_1.fq.gz 1SN_8A_1.fq.gz 1SN_9A_1.fq.gz )
seq2=( 1HL_10A_2.fq.gz 1HL_11A_2.fq.gz 1HL_12A_2.fq.gz 1HL_13A_2.fq.gz 1HL_14A_2.fq.gz 1HL_15A_2.fq.gz 1HL_16A_2.fq.gz 1HL_17A_2.fq.gz 1HL_19A_2.fq.gz 1HL_1A_2.fq.gz 1HL_20A_2.fq.gz 1HL_21A_2.fq.gz 1HL_22A_2.fq.gz 1HL_23A_2.fq.gz 1HL_24A_2.fq.gz 1HL_25A_2.fq.gz 1HL_26A_2.fq.gz 1HL_27A_2.fq.gz 1HL_28A_2.fq.gz 1HL_29A_2.fq.gz 1HL_2A_2.fq.gz 1HL_31A_2.fq.gz 1HL_33A_2.fq.gz 1HL_34A_2.fq.gz 1HL_35A_2.fq.gz 1HL_3A_2.fq.gz 1HL_4A_2.fq.gz 1HL_5A_2.fq.gz 1HL_6A_2.fq.gz 1HL_7A_2.fq.gz 1HL_8A_2.fq.gz 1HL_9A_2.fq.gz 1NF_10A_2.fq.gz 1NF_11A_2.fq.gz 1NF_12A_2.fq.gz 1NF_13A_2.fq.gz 1NF_14A_2.fq.gz 1NF_15A_2.fq.gz 1NF_16A_2.fq.gz 1NF_17A_2.fq.gz 1NF_18A_2.fq.gz 1NF_19A_2.fq.gz 1NF_1A_2.fq.gz 1NF_20A_2.fq.gz 1NF_21A_2.fq.gz 1NF_22A_2.fq.gz 1NF_23A_2.fq.gz 1NF_24A_2.fq.gz 1NF_25A_2.fq.gz 1NF_26A_2.fq.gz 1NF_27A_2.fq.gz 1NF_28A_2.fq.gz 1NF_29A_2.fq.gz 1NF_2A_2.fq.gz 1NF_30A_2.fq.gz 1NF_31A_2.fq.gz 1NF_32A_2.fq.gz 1NF_33A_2.fq.gz 1NF_4A_2.fq.gz 1NF_5A_2.fq.gz 1NF_6A_2.fq.gz 1NF_7A_2.fq.gz 1NF_8A_2.fq.gz 1NF_9A_2.fq.gz 1SN_10A_2.fq.gz 1SN_11A_2.fq.gz 1SN_12A_2.fq.gz 1SN_13A_2.fq.gz 1SN_14A_2.fq.gz 1SN_15A_2.fq.gz 1SN_16A_2.fq.gz 1SN_17A_2.fq.gz 1SN_18A_2.fq.gz 1SN_19A_2.fq.gz 1SN_1A_2.fq.gz 1SN_20A_2.fq.gz 1SN_21A_2.fq.gz 1SN_22A_2.fq.gz 1SN_23A_2.fq.gz 1SN_24A_2.fq.gz 1SN_25A_2.fq.gz 1SN_26A_2.fq.gz 1SN_27A_2.fq.gz 1SN_28A_2.fq.gz 1SN_29A_2.fq.gz 1SN_2A_2.fq.gz 1SN_30A_2.fq.gz 1SN_31A_2.fq.gz 1SN_32A_2.fq.gz 1SN_3A_2.fq.gz 1SN_4A_2.fq.gz 1SN_5A_2.fq.gz 1SN_6A_2.fq.gz 1SN_7A_2.fq.gz 1SN_8A_2.fq.gz 1SN_9A_2.fq.gz )
time for pair in "${!seq1[@]}"; do
i=${seq1[$pair]}
j=${seq2[$pair]}
/usr/local/bioinformatics/stacks-1.40/process_radtags \
-1 $i \
-2 $j \
-o /Volumes/toaster/sam/stacks/oly_BGI_GBS/radtags_out/ \
-e apeKI \
-c \
-q \
-i gzfastq \
-t 90 \
>>radtags.stdout 2>>radtags.stderr
done
real 363m13.851s user 358m15.349s sys 1m54.588s
cd radtags_out/
/Volumes/toaster/sam/stacks/oly_BGI_GBS/radtags_out
process_radtags output files into single FASTQ file¶Creates four lists of each fastq file and processes them using arrays. Uses a for loop to precess each value (i.e. index) of the four arrays is assigned to four different variables. The contents of the four variables are concatentated into a single file. The output file is named utilizing parameter substitution: ${i/_1.1/}. This takes the file stored in the variable "i", matches the text "_1.1" in that file name and replaces it with nothing "/" (i.e. deletes it).
%%bash
list1=( 1HL_10A_1.1.fq.gz 1HL_11A_1.1.fq.gz 1HL_12A_1.1.fq.gz 1HL_13A_1.1.fq.gz 1HL_14A_1.1.fq.gz 1HL_15A_1.1.fq.gz 1HL_16A_1.1.fq.gz 1HL_17A_1.1.fq.gz 1HL_19A_1.1.fq.gz 1HL_1A_1.1.fq.gz 1HL_20A_1.1.fq.gz 1HL_21A_1.1.fq.gz 1HL_22A_1.1.fq.gz 1HL_23A_1.1.fq.gz 1HL_24A_1.1.fq.gz 1HL_25A_1.1.fq.gz 1HL_26A_1.1.fq.gz 1HL_27A_1.1.fq.gz 1HL_28A_1.1.fq.gz 1HL_29A_1.1.fq.gz 1HL_2A_1.1.fq.gz 1HL_31A_1.1.fq.gz 1HL_33A_1.1.fq.gz 1HL_34A_1.1.fq.gz 1HL_35A_1.1.fq.gz 1HL_3A_1.1.fq.gz 1HL_4A_1.1.fq.gz 1HL_5A_1.1.fq.gz 1HL_6A_1.1.fq.gz 1HL_7A_1.1.fq.gz 1HL_8A_1.1.fq.gz 1HL_9A_1.1.fq.gz 1NF_10A_1.1.fq.gz 1NF_11A_1.1.fq.gz 1NF_12A_1.1.fq.gz 1NF_13A_1.1.fq.gz 1NF_14A_1.1.fq.gz 1NF_15A_1.1.fq.gz 1NF_16A_1.1.fq.gz 1NF_17A_1.1.fq.gz 1NF_18A_1.1.fq.gz 1NF_19A_1.1.fq.gz 1NF_1A_1.1.fq.gz 1NF_20A_1.1.fq.gz 1NF_21A_1.1.fq.gz 1NF_22A_1.1.fq.gz 1NF_23A_1.1.fq.gz 1NF_24A_1.1.fq.gz 1NF_25A_1.1.fq.gz 1NF_26A_1.1.fq.gz 1NF_27A_1.1.fq.gz 1NF_28A_1.1.fq.gz 1NF_29A_1.1.fq.gz 1NF_2A_1.1.fq.gz 1NF_30A_1.1.fq.gz 1NF_31A_1.1.fq.gz 1NF_32A_1.1.fq.gz 1NF_33A_1.1.fq.gz 1NF_4A_1.1.fq.gz 1NF_5A_1.1.fq.gz 1NF_6A_1.1.fq.gz 1NF_7A_1.1.fq.gz 1NF_8A_1.1.fq.gz 1NF_9A_1.1.fq.gz 1SN_10A_1.1.fq.gz 1SN_11A_1.1.fq.gz 1SN_12A_1.1.fq.gz 1SN_13A_1.1.fq.gz 1SN_14A_1.1.fq.gz 1SN_15A_1.1.fq.gz 1SN_16A_1.1.fq.gz 1SN_17A_1.1.fq.gz 1SN_18A_1.1.fq.gz 1SN_19A_1.1.fq.gz 1SN_1A_1.1.fq.gz 1SN_20A_1.1.fq.gz 1SN_21A_1.1.fq.gz 1SN_22A_1.1.fq.gz 1SN_23A_1.1.fq.gz 1SN_24A_1.1.fq.gz 1SN_25A_1.1.fq.gz 1SN_26A_1.1.fq.gz 1SN_27A_1.1.fq.gz 1SN_28A_1.1.fq.gz 1SN_29A_1.1.fq.gz 1SN_2A_1.1.fq.gz 1SN_30A_1.1.fq.gz 1SN_31A_1.1.fq.gz 1SN_32A_1.1.fq.gz 1SN_3A_1.1.fq.gz 1SN_4A_1.1.fq.gz 1SN_5A_1.1.fq.gz 1SN_6A_1.1.fq.gz 1SN_7A_1.1.fq.gz 1SN_8A_1.1.fq.gz 1SN_9A_1.1.fq.gz )
list2=( 1HL_10A_1.rem.1.fq.gz 1HL_11A_1.rem.1.fq.gz 1HL_12A_1.rem.1.fq.gz 1HL_13A_1.rem.1.fq.gz 1HL_14A_1.rem.1.fq.gz 1HL_15A_1.rem.1.fq.gz 1HL_16A_1.rem.1.fq.gz 1HL_17A_1.rem.1.fq.gz 1HL_19A_1.rem.1.fq.gz 1HL_1A_1.rem.1.fq.gz 1HL_20A_1.rem.1.fq.gz 1HL_21A_1.rem.1.fq.gz 1HL_22A_1.rem.1.fq.gz 1HL_23A_1.rem.1.fq.gz 1HL_24A_1.rem.1.fq.gz 1HL_25A_1.rem.1.fq.gz 1HL_26A_1.rem.1.fq.gz 1HL_27A_1.rem.1.fq.gz 1HL_28A_1.rem.1.fq.gz 1HL_29A_1.rem.1.fq.gz 1HL_2A_1.rem.1.fq.gz 1HL_31A_1.rem.1.fq.gz 1HL_33A_1.rem.1.fq.gz 1HL_34A_1.rem.1.fq.gz 1HL_35A_1.rem.1.fq.gz 1HL_3A_1.rem.1.fq.gz 1HL_4A_1.rem.1.fq.gz 1HL_5A_1.rem.1.fq.gz 1HL_6A_1.rem.1.fq.gz 1HL_7A_1.rem.1.fq.gz 1HL_8A_1.rem.1.fq.gz 1HL_9A_1.rem.1.fq.gz 1NF_10A_1.rem.1.fq.gz 1NF_11A_1.rem.1.fq.gz 1NF_12A_1.rem.1.fq.gz 1NF_13A_1.rem.1.fq.gz 1NF_14A_1.rem.1.fq.gz 1NF_15A_1.rem.1.fq.gz 1NF_16A_1.rem.1.fq.gz 1NF_17A_1.rem.1.fq.gz 1NF_18A_1.rem.1.fq.gz 1NF_19A_1.rem.1.fq.gz 1NF_1A_1.rem.1.fq.gz 1NF_20A_1.rem.1.fq.gz 1NF_21A_1.rem.1.fq.gz 1NF_22A_1.rem.1.fq.gz 1NF_23A_1.rem.1.fq.gz 1NF_24A_1.rem.1.fq.gz 1NF_25A_1.rem.1.fq.gz 1NF_26A_1.rem.1.fq.gz 1NF_27A_1.rem.1.fq.gz 1NF_28A_1.rem.1.fq.gz 1NF_29A_1.rem.1.fq.gz 1NF_2A_1.rem.1.fq.gz 1NF_30A_1.rem.1.fq.gz 1NF_31A_1.rem.1.fq.gz 1NF_32A_1.rem.1.fq.gz 1NF_33A_1.rem.1.fq.gz 1NF_4A_1.rem.1.fq.gz 1NF_5A_1.rem.1.fq.gz 1NF_6A_1.rem.1.fq.gz 1NF_7A_1.rem.1.fq.gz 1NF_8A_1.rem.1.fq.gz 1NF_9A_1.rem.1.fq.gz 1SN_10A_1.rem.1.fq.gz 1SN_11A_1.rem.1.fq.gz 1SN_12A_1.rem.1.fq.gz 1SN_13A_1.rem.1.fq.gz 1SN_14A_1.rem.1.fq.gz 1SN_15A_1.rem.1.fq.gz 1SN_16A_1.rem.1.fq.gz 1SN_17A_1.rem.1.fq.gz 1SN_18A_1.rem.1.fq.gz 1SN_19A_1.rem.1.fq.gz 1SN_1A_1.rem.1.fq.gz 1SN_20A_1.rem.1.fq.gz 1SN_21A_1.rem.1.fq.gz 1SN_22A_1.rem.1.fq.gz 1SN_23A_1.rem.1.fq.gz 1SN_24A_1.rem.1.fq.gz 1SN_25A_1.rem.1.fq.gz 1SN_26A_1.rem.1.fq.gz 1SN_27A_1.rem.1.fq.gz 1SN_28A_1.rem.1.fq.gz 1SN_29A_1.rem.1.fq.gz 1SN_2A_1.rem.1.fq.gz 1SN_30A_1.rem.1.fq.gz 1SN_31A_1.rem.1.fq.gz 1SN_32A_1.rem.1.fq.gz 1SN_3A_1.rem.1.fq.gz 1SN_4A_1.rem.1.fq.gz 1SN_5A_1.rem.1.fq.gz 1SN_6A_1.rem.1.fq.gz 1SN_7A_1.rem.1.fq.gz 1SN_8A_1.rem.1.fq.gz 1SN_9A_1.rem.1.fq.gz )
list3=( 1HL_10A_2.2.fq.gz 1HL_11A_2.2.fq.gz 1HL_12A_2.2.fq.gz 1HL_13A_2.2.fq.gz 1HL_14A_2.2.fq.gz 1HL_15A_2.2.fq.gz 1HL_16A_2.2.fq.gz 1HL_17A_2.2.fq.gz 1HL_19A_2.2.fq.gz 1HL_1A_2.2.fq.gz 1HL_20A_2.2.fq.gz 1HL_21A_2.2.fq.gz 1HL_22A_2.2.fq.gz 1HL_23A_2.2.fq.gz 1HL_24A_2.2.fq.gz 1HL_25A_2.2.fq.gz 1HL_26A_2.2.fq.gz 1HL_27A_2.2.fq.gz 1HL_28A_2.2.fq.gz 1HL_29A_2.2.fq.gz 1HL_2A_2.2.fq.gz 1HL_31A_2.2.fq.gz 1HL_33A_2.2.fq.gz 1HL_34A_2.2.fq.gz 1HL_35A_2.2.fq.gz 1HL_3A_2.2.fq.gz 1HL_4A_2.2.fq.gz 1HL_5A_2.2.fq.gz 1HL_6A_2.2.fq.gz 1HL_7A_2.2.fq.gz 1HL_8A_2.2.fq.gz 1HL_9A_2.2.fq.gz 1NF_10A_2.2.fq.gz 1NF_11A_2.2.fq.gz 1NF_12A_2.2.fq.gz 1NF_13A_2.2.fq.gz 1NF_14A_2.2.fq.gz 1NF_15A_2.2.fq.gz 1NF_16A_2.2.fq.gz 1NF_17A_2.2.fq.gz 1NF_18A_2.2.fq.gz 1NF_19A_2.2.fq.gz 1NF_1A_2.2.fq.gz 1NF_20A_2.2.fq.gz 1NF_21A_2.2.fq.gz 1NF_22A_2.2.fq.gz 1NF_23A_2.2.fq.gz 1NF_24A_2.2.fq.gz 1NF_25A_2.2.fq.gz 1NF_26A_2.2.fq.gz 1NF_27A_2.2.fq.gz 1NF_28A_2.2.fq.gz 1NF_29A_2.2.fq.gz 1NF_2A_2.2.fq.gz 1NF_30A_2.2.fq.gz 1NF_31A_2.2.fq.gz 1NF_32A_2.2.fq.gz 1NF_33A_2.2.fq.gz 1NF_4A_2.2.fq.gz 1NF_5A_2.2.fq.gz 1NF_6A_2.2.fq.gz 1NF_7A_2.2.fq.gz 1NF_8A_2.2.fq.gz 1NF_9A_2.2.fq.gz 1SN_10A_2.2.fq.gz 1SN_11A_2.2.fq.gz 1SN_12A_2.2.fq.gz 1SN_13A_2.2.fq.gz 1SN_14A_2.2.fq.gz 1SN_15A_2.2.fq.gz 1SN_16A_2.2.fq.gz 1SN_17A_2.2.fq.gz 1SN_18A_2.2.fq.gz 1SN_19A_2.2.fq.gz 1SN_1A_2.2.fq.gz 1SN_20A_2.2.fq.gz 1SN_21A_2.2.fq.gz 1SN_22A_2.2.fq.gz 1SN_23A_2.2.fq.gz 1SN_24A_2.2.fq.gz 1SN_25A_2.2.fq.gz 1SN_26A_2.2.fq.gz 1SN_27A_2.2.fq.gz 1SN_28A_2.2.fq.gz 1SN_29A_2.2.fq.gz 1SN_2A_2.2.fq.gz 1SN_30A_2.2.fq.gz 1SN_31A_2.2.fq.gz 1SN_32A_2.2.fq.gz 1SN_3A_2.2.fq.gz 1SN_4A_2.2.fq.gz 1SN_5A_2.2.fq.gz 1SN_6A_2.2.fq.gz 1SN_7A_2.2.fq.gz 1SN_8A_2.2.fq.gz 1SN_9A_2.2.fq.gz )
list4=( 1HL_10A_2.rem.2.fq.gz 1HL_11A_2.rem.2.fq.gz 1HL_12A_2.rem.2.fq.gz 1HL_13A_2.rem.2.fq.gz 1HL_14A_2.rem.2.fq.gz 1HL_15A_2.rem.2.fq.gz 1HL_16A_2.rem.2.fq.gz 1HL_17A_2.rem.2.fq.gz 1HL_19A_2.rem.2.fq.gz 1HL_1A_2.rem.2.fq.gz 1HL_20A_2.rem.2.fq.gz 1HL_21A_2.rem.2.fq.gz 1HL_22A_2.rem.2.fq.gz 1HL_23A_2.rem.2.fq.gz 1HL_24A_2.rem.2.fq.gz 1HL_25A_2.rem.2.fq.gz 1HL_26A_2.rem.2.fq.gz 1HL_27A_2.rem.2.fq.gz 1HL_28A_2.rem.2.fq.gz 1HL_29A_2.rem.2.fq.gz 1HL_2A_2.rem.2.fq.gz 1HL_31A_2.rem.2.fq.gz 1HL_33A_2.rem.2.fq.gz 1HL_34A_2.rem.2.fq.gz 1HL_35A_2.rem.2.fq.gz 1HL_3A_2.rem.2.fq.gz 1HL_4A_2.rem.2.fq.gz 1HL_5A_2.rem.2.fq.gz 1HL_6A_2.rem.2.fq.gz 1HL_7A_2.rem.2.fq.gz 1HL_8A_2.rem.2.fq.gz 1HL_9A_2.rem.2.fq.gz 1NF_10A_2.rem.2.fq.gz 1NF_11A_2.rem.2.fq.gz 1NF_12A_2.rem.2.fq.gz 1NF_13A_2.rem.2.fq.gz 1NF_14A_2.rem.2.fq.gz 1NF_15A_2.rem.2.fq.gz 1NF_16A_2.rem.2.fq.gz 1NF_17A_2.rem.2.fq.gz 1NF_18A_2.rem.2.fq.gz 1NF_19A_2.rem.2.fq.gz 1NF_1A_2.rem.2.fq.gz 1NF_20A_2.rem.2.fq.gz 1NF_21A_2.rem.2.fq.gz 1NF_22A_2.rem.2.fq.gz 1NF_23A_2.rem.2.fq.gz 1NF_24A_2.rem.2.fq.gz 1NF_25A_2.rem.2.fq.gz 1NF_26A_2.rem.2.fq.gz 1NF_27A_2.rem.2.fq.gz 1NF_28A_2.rem.2.fq.gz 1NF_29A_2.rem.2.fq.gz 1NF_2A_2.rem.2.fq.gz 1NF_30A_2.rem.2.fq.gz 1NF_31A_2.rem.2.fq.gz 1NF_32A_2.rem.2.fq.gz 1NF_33A_2.rem.2.fq.gz 1NF_4A_2.rem.2.fq.gz 1NF_5A_2.rem.2.fq.gz 1NF_6A_2.rem.2.fq.gz 1NF_7A_2.rem.2.fq.gz 1NF_8A_2.rem.2.fq.gz 1NF_9A_2.rem.2.fq.gz 1SN_10A_2.rem.2.fq.gz 1SN_11A_2.rem.2.fq.gz 1SN_12A_2.rem.2.fq.gz 1SN_13A_2.rem.2.fq.gz 1SN_14A_2.rem.2.fq.gz 1SN_15A_2.rem.2.fq.gz 1SN_16A_2.rem.2.fq.gz 1SN_17A_2.rem.2.fq.gz 1SN_18A_2.rem.2.fq.gz 1SN_19A_2.rem.2.fq.gz 1SN_1A_2.rem.2.fq.gz 1SN_20A_2.rem.2.fq.gz 1SN_21A_2.rem.2.fq.gz 1SN_22A_2.rem.2.fq.gz 1SN_23A_2.rem.2.fq.gz 1SN_24A_2.rem.2.fq.gz 1SN_25A_2.rem.2.fq.gz 1SN_26A_2.rem.2.fq.gz 1SN_27A_2.rem.2.fq.gz 1SN_28A_2.rem.2.fq.gz 1SN_29A_2.rem.2.fq.gz 1SN_2A_2.rem.2.fq.gz 1SN_30A_2.rem.2.fq.gz 1SN_31A_2.rem.2.fq.gz 1SN_32A_2.rem.2.fq.gz 1SN_3A_2.rem.2.fq.gz 1SN_4A_2.rem.2.fq.gz 1SN_5A_2.rem.2.fq.gz 1SN_6A_2.rem.2.fq.gz 1SN_7A_2.rem.2.fq.gz 1SN_8A_2.rem.2.fq.gz 1SN_9A_2.rem.2.fq.gz )
time for index in "${!list1[@]}"; do
i=${list1[$index]}
j=${list2[$index]}
k=${list3[$index]}
l=${list4[$index]}
cat $i $j $k $l > ${i/_1.1/}
done
real 19m58.597s user 0m2.011s sys 1m23.679s
%%bash
echo *A.fq.gz
1HL_10A.fq.gz 1HL_11A.fq.gz 1HL_12A.fq.gz 1HL_13A.fq.gz 1HL_14A.fq.gz 1HL_15A.fq.gz 1HL_16A.fq.gz 1HL_17A.fq.gz 1HL_19A.fq.gz 1HL_1A.fq.gz 1HL_20A.fq.gz 1HL_21A.fq.gz 1HL_22A.fq.gz 1HL_23A.fq.gz 1HL_24A.fq.gz 1HL_25A.fq.gz 1HL_26A.fq.gz 1HL_27A.fq.gz 1HL_28A.fq.gz 1HL_29A.fq.gz 1HL_2A.fq.gz 1HL_31A.fq.gz 1HL_33A.fq.gz 1HL_34A.fq.gz 1HL_35A.fq.gz 1HL_3A.fq.gz 1HL_4A.fq.gz 1HL_5A.fq.gz 1HL_6A.fq.gz 1HL_7A.fq.gz 1HL_8A.fq.gz 1HL_9A.fq.gz 1NF_10A.fq.gz 1NF_11A.fq.gz 1NF_12A.fq.gz 1NF_13A.fq.gz 1NF_14A.fq.gz 1NF_15A.fq.gz 1NF_16A.fq.gz 1NF_17A.fq.gz 1NF_18A.fq.gz 1NF_19A.fq.gz 1NF_1A.fq.gz 1NF_20A.fq.gz 1NF_21A.fq.gz 1NF_22A.fq.gz 1NF_23A.fq.gz 1NF_24A.fq.gz 1NF_25A.fq.gz 1NF_26A.fq.gz 1NF_27A.fq.gz 1NF_28A.fq.gz 1NF_29A.fq.gz 1NF_2A.fq.gz 1NF_30A.fq.gz 1NF_31A.fq.gz 1NF_32A.fq.gz 1NF_33A.fq.gz 1NF_4A.fq.gz 1NF_5A.fq.gz 1NF_6A.fq.gz 1NF_7A.fq.gz 1NF_8A.fq.gz 1NF_9A.fq.gz 1SN_10A.fq.gz 1SN_11A.fq.gz 1SN_12A.fq.gz 1SN_13A.fq.gz 1SN_14A.fq.gz 1SN_15A.fq.gz 1SN_16A.fq.gz 1SN_17A.fq.gz 1SN_18A.fq.gz 1SN_19A.fq.gz 1SN_1A.fq.gz 1SN_20A.fq.gz 1SN_21A.fq.gz 1SN_22A.fq.gz 1SN_23A.fq.gz 1SN_24A.fq.gz 1SN_25A.fq.gz 1SN_26A.fq.gz 1SN_27A.fq.gz 1SN_28A.fq.gz 1SN_29A.fq.gz 1SN_2A.fq.gz 1SN_30A.fq.gz 1SN_31A.fq.gz 1SN_32A.fq.gz 1SN_3A.fq.gz 1SN_4A.fq.gz 1SN_5A.fq.gz 1SN_6A.fq.gz 1SN_7A.fq.gz 1SN_8A.fq.gz 1SN_9A.fq.gz
%%bash
#Runs ustacks and appends sql ID to each file for downstream analysis.
sql_id=0
time for i in *A.fq.gz; do
((sql_id++))
/usr/local/bioinformatics/stacks-1.40/ustacks \
-t gzfastq \
-f $i \
-o /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/ \
-i $sql_id \
-d \
-r \
-p 16
done
ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_10A.fq.gz Loaded 6009115 RAD-Tags; inserted 2673528 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.9361; Std Dev: 46.477; Max: 11579 Deleveraging trigger: 58; Removal trigger: 105 284534 initial stacks were populated; 2388994 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 14108 stacks. 271362 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.3279; Std Dev: 101.886; Max: 105 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 271362 stacks merged into 191105 stacks; deleveraged 6205 stacks; removed 7009 stacks. After merging, coverage depth Mean: 12.4659; Std Dev: 125.276; Max: 187 Merging remainder radtags 2612887 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1570227 remainder reads; unable to match 1042660 remainder reads. After remainders merged, coverage depth Mean: 21.0389; Std Dev: 126.003; Max: 664 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4966455 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_10A.fq.gz... read 6009115 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_11A.fq.gz Loaded 6730383 RAD-Tags; inserted 2979538 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.0862; Std Dev: 46.7618; Max: 13020 Deleveraging trigger: 59; Removal trigger: 106 315491 initial stacks were populated; 2664047 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 16193 stacks. 300368 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.4723; Std Dev: 104.995; Max: 106 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 300368 stacks merged into 210026 stacks; deleveraged 6906 stacks; removed 8141 stacks. After merging, coverage depth Mean: 12.5965; Std Dev: 129.557; Max: 215 Merging remainder radtags 2917285 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1747418 remainder reads; unable to match 1169867 remainder reads. After remainders merged, coverage depth Mean: 21.2981; Std Dev: 130.31; Max: 743 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5560516 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_11A.fq.gz... read 6730383 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_12A.fq.gz Loaded 4761703 RAD-Tags; inserted 2301544 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.5713; Std Dev: 50.1431; Max: 8662 Deleveraging trigger: 61; Removal trigger: 111 238415 initial stacks were populated; 2063129 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 10006 stacks. 229014 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.10072; Std Dev: 92.8984; Max: 111 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 229014 stacks merged into 174716 stacks; deleveraged 4183 stacks; removed 4003 stacks. After merging, coverage depth Mean: 10.4463; Std Dev: 109.961; Max: 165 Merging remainder radtags 2241342 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1291328 remainder reads; unable to match 950014 remainder reads. After remainders merged, coverage depth Mean: 18.0375; Std Dev: 110.688; Max: 449 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3811689 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_12A.fq.gz... read 4761703 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_13A.fq.gz Loaded 5047958 RAD-Tags; inserted 2294928 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.6398; Std Dev: 54.0414; Max: 10729 Deleveraging trigger: 66; Removal trigger: 120 241272 initial stacks were populated; 2053656 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 10375 stacks. 231511 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.9893; Std Dev: 106.12; Max: 120 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 231511 stacks merged into 167294 stacks; deleveraged 4853 stacks; removed 5207 stacks. After merging, coverage depth Mean: 11.7656; Std Dev: 128.999; Max: 179 Merging remainder radtags 2239589 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1350554 remainder reads; unable to match 889035 remainder reads. After remainders merged, coverage depth Mean: 20.1296; Std Dev: 129.718; Max: 564 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4158923 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_13A.fq.gz... read 5047958 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_14A.fq.gz Loaded 3801103 RAD-Tags; inserted 1786525 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.6073; Std Dev: 40.0115; Max: 8719 Deleveraging trigger: 51; Removal trigger: 91 194916 initial stacks were populated; 1591609 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 9383 stacks. 186177 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.1716; Std Dev: 81.9224; Max: 91 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 186177 stacks merged into 140358 stacks; deleveraged 3576 stacks; removed 3445 stacks. After merging, coverage depth Mean: 10.752; Std Dev: 97.084; Max: 145 Merging remainder radtags 1733567 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1024052 remainder reads; unable to match 709515 remainder reads. After remainders merged, coverage depth Mean: 18.2669; Std Dev: 97.864; Max: 554 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3091588 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_14A.fq.gz... read 3801103 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_15A.fq.gz Loaded 4142411 RAD-Tags; inserted 1957244 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.7212; Std Dev: 36.9228; Max: 8117 Deleveraging trigger: 48; Removal trigger: 85 208698 initial stacks were populated; 1748546 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 10195 stacks. 199253 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.36043; Std Dev: 81.3102; Max: 85 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 199253 stacks merged into 150277 stacks; deleveraged 4011 stacks; removed 3722 stacks. After merging, coverage depth Mean: 11.05; Std Dev: 96.294; Max: 135 Merging remainder radtags 1904922 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1139698 remainder reads; unable to match 765224 remainder reads. After remainders merged, coverage depth Mean: 18.8666; Std Dev: 97.1684; Max: 605 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3377187 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_15A.fq.gz... read 4142411 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_16A.fq.gz Loaded 4400190 RAD-Tags; inserted 2034412 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.0772; Std Dev: 44.2637; Max: 9496 Deleveraging trigger: 55; Removal trigger: 100 218506 initial stacks were populated; 1815906 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 9919 stacks. 209248 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.61055; Std Dev: 88.5534; Max: 100 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 209248 stacks merged into 155273 stacks; deleveraged 4164 stacks; removed 4245 stacks. After merging, coverage depth Mean: 11.3348; Std Dev: 105.833; Max: 170 Merging remainder radtags 1979764 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1180923 remainder reads; unable to match 798841 remainder reads. After remainders merged, coverage depth Mean: 19.1884; Std Dev: 106.644; Max: 510 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3601349 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_16A.fq.gz... read 4400190 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_17A.fq.gz Loaded 6889027 RAD-Tags; inserted 3000022 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.7314; Std Dev: 50.2483; Max: 14226 Deleveraging trigger: 63; Removal trigger: 113 309756 initial stacks were populated; 2690266 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 15952 stacks. 294895 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.9875; Std Dev: 114.394; Max: 113 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 294895 stacks merged into 201665 stacks; deleveraged 7171 stacks; removed 8469 stacks. After merging, coverage depth Mean: 13.4389; Std Dev: 143.144; Max: 250 Merging remainder radtags 2945388 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1805337 remainder reads; unable to match 1140051 remainder reads. After remainders merged, coverage depth Mean: 22.8365; Std Dev: 143.884; Max: 505 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5748976 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_17A.fq.gz... read 6889027 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_19A.fq.gz Loaded 6823890 RAD-Tags; inserted 3002794 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.5466; Std Dev: 52.7725; Max: 12963 Deleveraging trigger: 65; Removal trigger: 118 308934 initial stacks were populated; 2693860 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 14750 stacks. 295126 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.8155; Std Dev: 111.871; Max: 118 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 295126 stacks merged into 203742 stacks; deleveraged 7310 stacks; removed 8218 stacks. After merging, coverage depth Mean: 13.0204; Std Dev: 139.363; Max: 220 Merging remainder radtags 2947805 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1788848 remainder reads; unable to match 1158957 remainder reads. After remainders merged, coverage depth Mean: 22.2137; Std Dev: 140.096; Max: 456 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5664933 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_19A.fq.gz... read 6823890 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_1A.fq.gz Loaded 4264748 RAD-Tags; inserted 2026387 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.8146; Std Dev: 41.6286; Max: 8654 Deleveraging trigger: 52; Removal trigger: 94 211855 initial stacks were populated; 1814532 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 10221 stacks. 202333 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.37924; Std Dev: 85.4842; Max: 94 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 202333 stacks merged into 153444 stacks; deleveraged 3917 stacks; removed 3591 stacks. After merging, coverage depth Mean: 10.975; Std Dev: 101.096; Max: 155 Merging remainder radtags 1973620 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1177434 remainder reads; unable to match 796186 remainder reads. After remainders merged, coverage depth Mean: 18.8691; Std Dev: 101.944; Max: 444 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3468562 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_1A.fq.gz... read 4264748 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_20A.fq.gz Loaded 5487343 RAD-Tags; inserted 2439789 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.0695; Std Dev: 48.6613; Max: 11949 Deleveraging trigger: 61; Removal trigger: 109 256767 initial stacks were populated; 2183022 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 12204 stacks. 245337 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.4314; Std Dev: 104.3; Max: 109 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 245337 stacks merged into 173087 stacks; deleveraged 5529 stacks; removed 6366 stacks. After merging, coverage depth Mean: 12.5132; Std Dev: 128.385; Max: 176 Merging remainder radtags 2388286 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1437772 remainder reads; unable to match 950514 remainder reads. After remainders merged, coverage depth Mean: 21.1772; Std Dev: 129.14; Max: 529 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4536829 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_20A.fq.gz... read 5487343 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_21A.fq.gz Loaded 4888590 RAD-Tags; inserted 2268948 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.3321; Std Dev: 41.9239; Max: 9954 Deleveraging trigger: 53; Removal trigger: 95 235852 initial stacks were populated; 2033096 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11682 stacks. 224993 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.8362; Std Dev: 87.0389; Max: 95 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 224993 stacks merged into 165321 stacks; deleveraged 4837 stacks; removed 4759 stacks. After merging, coverage depth Mean: 11.6864; Std Dev: 104.549; Max: 155 Merging remainder radtags 2215893 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1324104 remainder reads; unable to match 891789 remainder reads. After remainders merged, coverage depth Mean: 19.9756; Std Dev: 105.441; Max: 650 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3996801 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_21A.fq.gz... read 4888590 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_22A.fq.gz Loaded 3912844 RAD-Tags; inserted 1953542 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.2814; Std Dev: 38.9718; Max: 9034 Deleveraging trigger: 49; Removal trigger: 88 195317 initial stacks were populated; 1758225 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 8909 stacks. 187053 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 8.95263; Std Dev: 81.5536; Max: 88 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 187053 stacks merged into 146470 stacks; deleveraged 3154 stacks; removed 2728 stacks. After merging, coverage depth Mean: 10.2707; Std Dev: 95.0062; Max: 158 Merging remainder radtags 1904708 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1100666 remainder reads; unable to match 804042 remainder reads. After remainders merged, coverage depth Mean: 17.9624; Std Dev: 95.8838; Max: 697 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3108802 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_22A.fq.gz... read 3912844 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_23A.fq.gz Loaded 6807463 RAD-Tags; inserted 2926995 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.5871; Std Dev: 48.7711; Max: 13434 Deleveraging trigger: 61; Removal trigger: 110 313577 initial stacks were populated; 2613418 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 16044 stacks. 298593 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.9091; Std Dev: 106.461; Max: 110 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 298593 stacks merged into 205560 stacks; deleveraged 6889 stacks; removed 8348 stacks. After merging, coverage depth Mean: 13.3355; Std Dev: 132.8; Max: 205 Merging remainder radtags 2860452 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1781931 remainder reads; unable to match 1078521 remainder reads. After remainders merged, coverage depth Mean: 22.4199; Std Dev: 133.49; Max: 582 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5728942 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_23A.fq.gz... read 6807463 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_24A.fq.gz Loaded 5133729 RAD-Tags; inserted 2312782 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.817; Std Dev: 45.4401; Max: 11107 Deleveraging trigger: 57; Removal trigger: 103 243244 initial stacks were populated; 2069538 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11840 stacks. 232207 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.2512; Std Dev: 99.822; Max: 103 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 232207 stacks merged into 167057 stacks; deleveraged 5057 stacks; removed 5407 stacks. After merging, coverage depth Mean: 12.2681; Std Dev: 121.436; Max: 184 Merging remainder radtags 2259318 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1374675 remainder reads; unable to match 884643 remainder reads. After remainders merged, coverage depth Mean: 20.8146; Std Dev: 122.252; Max: 733 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4249086 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_24A.fq.gz... read 5133729 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_25A.fq.gz Loaded 5579934 RAD-Tags; inserted 2483765 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.837; Std Dev: 45.2394; Max: 10741 Deleveraging trigger: 57; Removal trigger: 102 266859 initial stacks were populated; 2216906 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 12886 stacks. 254840 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.2774; Std Dev: 95.553; Max: 102 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 254840 stacks merged into 181786 stacks; deleveraged 5651 stacks; removed 6325 stacks. After merging, coverage depth Mean: 12.3219; Std Dev: 116.774; Max: 166 Merging remainder radtags 2421111 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1489729 remainder reads; unable to match 931382 remainder reads. After remainders merged, coverage depth Mean: 20.8545; Std Dev: 117.579; Max: 649 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4648552 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_25A.fq.gz... read 5579934 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_26A.fq.gz Loaded 5926543 RAD-Tags; inserted 2649553 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.0342; Std Dev: 53.0557; Max: 11006 Deleveraging trigger: 65; Removal trigger: 118 277320 initial stacks were populated; 2372233 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 12476 stacks. 265606 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.4039; Std Dev: 101.925; Max: 118 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 265606 stacks merged into 189119 stacks; deleveraged 5799 stacks; removed 6461 stacks. After merging, coverage depth Mean: 12.4482; Std Dev: 124.892; Max: 225 Merging remainder radtags 2589223 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1574008 remainder reads; unable to match 1015215 remainder reads. After remainders merged, coverage depth Mean: 21.1016; Std Dev: 125.682; Max: 730 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4911328 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_26A.fq.gz... read 5926543 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_27A.fq.gz Loaded 6034261 RAD-Tags; inserted 2732378 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.8481; Std Dev: 48.057; Max: 9988 Deleveraging trigger: 60; Removal trigger: 108 284152 initial stacks were populated; 2448226 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13823 stacks. 271225 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.2574; Std Dev: 98.3367; Max: 108 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 271225 stacks merged into 197274 stacks; deleveraged 5813 stacks; removed 5909 stacks. After merging, coverage depth Mean: 12.2337; Std Dev: 119.043; Max: 194 Merging remainder radtags 2667602 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1654664 remainder reads; unable to match 1012938 remainder reads. After remainders merged, coverage depth Mean: 20.921; Std Dev: 119.833; Max: 1108 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5021323 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_27A.fq.gz... read 6034261 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_28A.fq.gz Loaded 7110060 RAD-Tags; inserted 2640660 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.6062; Std Dev: 43.7415; Max: 13545 Deleveraging trigger: 54; Removal trigger: 98 436207 initial stacks were populated; 2204453 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 15345 stacks. 422188 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.13787; Std Dev: 80.7291; Max: 98 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 422188 stacks merged into 268127 stacks; deleveraged 8120 stacks; removed 18217 stacks. After merging, coverage depth Mean: 12.2374; Std Dev: 106.034; Max: 242 Merging remainder radtags 2483566 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1372037 remainder reads; unable to match 1111529 remainder reads. After remainders merged, coverage depth Mean: 17.7568; Std Dev: 106.285; Max: 452 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5998531 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_28A.fq.gz... read 7110060 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_29A.fq.gz Loaded 5791410 RAD-Tags; inserted 2585520 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.983; Std Dev: 49.7092; Max: 11040 Deleveraging trigger: 62; Removal trigger: 111 272474 initial stacks were populated; 2313046 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13123 stacks. 260195 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.3287; Std Dev: 102.214; Max: 111 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 260195 stacks merged into 184662 stacks; deleveraged 5879 stacks; removed 6397 stacks. After merging, coverage depth Mean: 12.3606; Std Dev: 125.401; Max: 206 Merging remainder radtags 2526364 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1538777 remainder reads; unable to match 987587 remainder reads. After remainders merged, coverage depth Mean: 21.0336; Std Dev: 126.173; Max: 777 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4803823 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_29A.fq.gz... read 5791410 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_2A.fq.gz Loaded 5201616 RAD-Tags; inserted 2345384 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.6279; Std Dev: 43.0716; Max: 11524 Deleveraging trigger: 55; Removal trigger: 98 250601 initial stacks were populated; 2094783 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 12987 stacks. 238524 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.1056; Std Dev: 97.7063; Max: 98 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 238524 stacks merged into 171801 stacks; deleveraged 5202 stacks; removed 5747 stacks. After merging, coverage depth Mean: 12.0665; Std Dev: 118.654; Max: 175 Merging remainder radtags 2287661 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1391487 remainder reads; unable to match 896174 remainder reads. After remainders merged, coverage depth Mean: 20.4924; Std Dev: 119.439; Max: 749 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4305442 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_2A.fq.gz... read 5201616 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_31A.fq.gz Loaded 4627425 RAD-Tags; inserted 2151765 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.9906; Std Dev: 42.2053; Max: 8047 Deleveraging trigger: 53; Removal trigger: 95 230360 initial stacks were populated; 1921405 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 10914 stacks. 220209 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.52767; Std Dev: 81.9655; Max: 95 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 220209 stacks merged into 163555 stacks; deleveraged 4470 stacks; removed 4453 stacks. After merging, coverage depth Mean: 11.2307; Std Dev: 98.4678; Max: 167 Merging remainder radtags 2095633 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1242901 remainder reads; unable to match 852732 remainder reads. After remainders merged, coverage depth Mean: 19.0803; Std Dev: 99.3295; Max: 579 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3774693 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_31A.fq.gz... read 4627425 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_33A.fq.gz Loaded 5109315 RAD-Tags; inserted 2306469 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.5723; Std Dev: 41.521; Max: 10110 Deleveraging trigger: 53; Removal trigger: 95 247205 initial stacks were populated; 2059264 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 12606 stacks. 235513 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.0534; Std Dev: 87.5977; Max: 95 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 235513 stacks merged into 169926 stacks; deleveraged 5195 stacks; removed 5644 stacks. After merging, coverage depth Mean: 12.0436; Std Dev: 106.369; Max: 182 Merging remainder radtags 2248592 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1365171 remainder reads; unable to match 883421 remainder reads. After remainders merged, coverage depth Mean: 20.4; Std Dev: 107.259; Max: 941 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4225894 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_33A.fq.gz... read 5109315 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_34A.fq.gz Loaded 5469267 RAD-Tags; inserted 2457470 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.6096; Std Dev: 42.3012; Max: 11293 Deleveraging trigger: 54; Removal trigger: 96 264614 initial stacks were populated; 2192856 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13876 stacks. 251723 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.0932; Std Dev: 93.6932; Max: 96 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 251723 stacks merged into 180647 stacks; deleveraged 5576 stacks; removed 6062 stacks. After merging, coverage depth Mean: 12.129; Std Dev: 114.268; Max: 192 Merging remainder radtags 2397196 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1461442 remainder reads; unable to match 935754 remainder reads. After remainders merged, coverage depth Mean: 20.5474; Std Dev: 115.046; Max: 408 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4533513 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_34A.fq.gz... read 5469267 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_35A.fq.gz Loaded 4960955 RAD-Tags; inserted 2298040 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.976; Std Dev: 40.0148; Max: 9333 Deleveraging trigger: 51; Removal trigger: 91 248167 initial stacks were populated; 2049873 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 12273 stacks. 236758 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.56257; Std Dev: 88.8155; Max: 91 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 236758 stacks merged into 175175 stacks; deleveraged 4680 stacks; removed 4930 stacks. After merging, coverage depth Mean: 11.3244; Std Dev: 106.265; Max: 161 Merging remainder radtags 2237064 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1335047 remainder reads; unable to match 902017 remainder reads. After remainders merged, coverage depth Mean: 19.2063; Std Dev: 107.08; Max: 516 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4058938 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_35A.fq.gz... read 4960955 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_3A.fq.gz Loaded 4170141 RAD-Tags; inserted 2008646 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.3369; Std Dev: 37.2197; Max: 7913 Deleveraging trigger: 48; Removal trigger: 85 214441 initial stacks were populated; 1794205 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 10579 stacks. 204601 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.01124; Std Dev: 78.544; Max: 85 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 204601 stacks merged into 156062 stacks; deleveraged 3894 stacks; removed 3536 stacks. After merging, coverage depth Mean: 10.5321; Std Dev: 92.8761; Max: 165 Merging remainder radtags 1953476 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1115119 remainder reads; unable to match 838357 remainder reads. After remainders merged, coverage depth Mean: 17.8787; Std Dev: 93.6657; Max: 719 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3331784 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_3A.fq.gz... read 4170141 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_4A.fq.gz Loaded 4848328 RAD-Tags; inserted 2208506 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.2637; Std Dev: 45.5099; Max: 9710 Deleveraging trigger: 57; Removal trigger: 102 239789 initial stacks were populated; 1968717 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11601 stacks. 228929 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.73427; Std Dev: 91.4183; Max: 102 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 228929 stacks merged into 167822 stacks; deleveraged 4722 stacks; removed 4846 stacks. After merging, coverage depth Mean: 11.5455; Std Dev: 110.08; Max: 210 Merging remainder radtags 2147423 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1299661 remainder reads; unable to match 847762 remainder reads. After remainders merged, coverage depth Mean: 19.5564; Std Dev: 110.83; Max: 624 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4000566 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_4A.fq.gz... read 4848328 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_5A.fq.gz Loaded 3735433 RAD-Tags; inserted 1781328 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.3573; Std Dev: 41.2232; Max: 7983 Deleveraging trigger: 52; Removal trigger: 93 193661 initial stacks were populated; 1587667 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 8888 stacks. 185339 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 8.97561; Std Dev: 81.5712; Max: 93 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 185339 stacks merged into 142386 stacks; deleveraged 3364 stacks; removed 3122 stacks. After merging, coverage depth Mean: 10.3537; Std Dev: 95.7157; Max: 147 Merging remainder radtags 1729635 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1005364 remainder reads; unable to match 724271 remainder reads. After remainders merged, coverage depth Mean: 17.6023; Std Dev: 96.4637; Max: 643 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3011162 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_5A.fq.gz... read 3735433 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_6A.fq.gz Loaded 3904377 RAD-Tags; inserted 1905778 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.2571; Std Dev: 39.0144; Max: 8636 Deleveraging trigger: 49; Removal trigger: 88 199099 initial stacks were populated; 1706679 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 8518 stacks. 191232 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 8.91493; Std Dev: 78.2575; Max: 88 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 191232 stacks merged into 145730 stacks; deleveraged 3847 stacks; removed 3333 stacks. After merging, coverage depth Mean: 10.3897; Std Dev: 92.2068; Max: 134 Merging remainder radtags 1862199 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1075563 remainder reads; unable to match 786636 remainder reads. After remainders merged, coverage depth Mean: 17.9777; Std Dev: 93.0097; Max: 615 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3117741 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_6A.fq.gz... read 3904377 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_7A.fq.gz Loaded 5268813 RAD-Tags; inserted 1959360 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 9.4273; Std Dev: 39.3953; Max: 10066 Deleveraging trigger: 49; Removal trigger: 88 365813 initial stacks were populated; 1593547 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13415 stacks. 353422 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 8.08198; Std Dev: 69.2743; Max: 88 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 353422 stacks merged into 246290 stacks; deleveraged 6672 stacks; removed 11094 stacks. After merging, coverage depth Mean: 10.0513; Std Dev: 85.7209; Max: 152 Merging remainder radtags 1820185 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 929288 remainder reads; unable to match 890897 remainder reads. After remainders merged, coverage depth Mean: 14.0197; Std Dev: 85.8233; Max: 432 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4377916 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_7A.fq.gz... read 5268813 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_8A.fq.gz Loaded 4798534 RAD-Tags; inserted 2172020 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.5558; Std Dev: 47.8257; Max: 9814 Deleveraging trigger: 59; Removal trigger: 107 231956 initial stacks were populated; 1940064 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11193 stacks. 221472 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.94578; Std Dev: 106.803; Max: 107 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 221472 stacks merged into 160418 stacks; deleveraged 4591 stacks; removed 5061 stacks. After merging, coverage depth Mean: 11.8401; Std Dev: 129.286; Max: 192 Merging remainder radtags 2118106 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1258024 remainder reads; unable to match 860082 remainder reads. After remainders merged, coverage depth Mean: 19.9749; Std Dev: 129.96; Max: 600 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3938452 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_8A.fq.gz... read 4798534 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1HL_9A.fq.gz Loaded 5342354 RAD-Tags; inserted 2427408 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.7135; Std Dev: 49.3228; Max: 10441 Deleveraging trigger: 61; Removal trigger: 110 253629 initial stacks were populated; 2173779 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11789 stacks. 242593 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.1303; Std Dev: 97.9721; Max: 110 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 242593 stacks merged into 174599 stacks; deleveraged 5266 stacks; removed 5712 stacks. After merging, coverage depth Mean: 12.0296; Std Dev: 119.244; Max: 184 Merging remainder radtags 2371466 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1400867 remainder reads; unable to match 970599 remainder reads. After remainders merged, coverage depth Mean: 20.3615; Std Dev: 120.003; Max: 907 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4371755 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1HL_9A.fq.gz... read 5342354 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_10A.fq.gz Loaded 4052595 RAD-Tags; inserted 1908295 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.9502; Std Dev: 41.9322; Max: 9448 Deleveraging trigger: 53; Removal trigger: 95 200215 initial stacks were populated; 1708080 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 9608 stacks. 191231 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.49166; Std Dev: 88.115; Max: 95 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 191231 stacks merged into 142995 stacks; deleveraged 3731 stacks; removed 3675 stacks. After merging, coverage depth Mean: 11.111; Std Dev: 105.281; Max: 157 Merging remainder radtags 1860201 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1087907 remainder reads; unable to match 772294 remainder reads. After remainders merged, coverage depth Mean: 18.9548; Std Dev: 106.111; Max: 619 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3280301 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_10A.fq.gz... read 4052595 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_11A.fq.gz Loaded 4274972 RAD-Tags; inserted 1977055 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.1091; Std Dev: 42.5961; Max: 10875 Deleveraging trigger: 54; Removal trigger: 96 211499 initial stacks were populated; 1765556 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 10170 stacks. 202025 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.64909; Std Dev: 93.4423; Max: 96 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 202025 stacks merged into 148422 stacks; deleveraged 4187 stacks; removed 4220 stacks. After merging, coverage depth Mean: 11.4548; Std Dev: 112.017; Max: 143 Merging remainder radtags 1925399 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1153075 remainder reads; unable to match 772324 remainder reads. After remainders merged, coverage depth Mean: 19.4898; Std Dev: 112.844; Max: 638 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3502648 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_11A.fq.gz... read 4274972 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_12A.fq.gz Loaded 4111264 RAD-Tags; inserted 1892059 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.13; Std Dev: 42.6141; Max: 9420 Deleveraging trigger: 54; Removal trigger: 96 203984 initial stacks were populated; 1688075 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 9974 stacks. 194676 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.6397; Std Dev: 89.828; Max: 96 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 194676 stacks merged into 143929 stacks; deleveraged 3972 stacks; removed 4036 stacks. After merging, coverage depth Mean: 11.382; Std Dev: 107.945; Max: 175 Merging remainder radtags 1840924 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1108068 remainder reads; unable to match 732856 remainder reads. After remainders merged, coverage depth Mean: 19.3407; Std Dev: 108.751; Max: 474 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3378408 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_12A.fq.gz... read 4111264 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_13A.fq.gz Loaded 7336853 RAD-Tags; inserted 3196287 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.5275; Std Dev: 69.0963; Max: 15948 Deleveraging trigger: 82; Removal trigger: 151 335702 initial stacks were populated; 2860585 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 14250 stacks. 322165 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.7181; Std Dev: 130.167; Max: 151 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 322165 stacks merged into 221732 stacks; deleveraged 7364 stacks; removed 8830 stacks. After merging, coverage depth Mean: 12.7012; Std Dev: 162.293; Max: 246 Merging remainder radtags 3131361 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1878004 remainder reads; unable to match 1253357 remainder reads. After remainders merged, coverage depth Mean: 21.5518; Std Dev: 162.891; Max: 833 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 6083496 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_13A.fq.gz... read 7336853 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_14A.fq.gz Loaded 5128773 RAD-Tags; inserted 2356193 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.7834; Std Dev: 47.753; Max: 11370 Deleveraging trigger: 60; Removal trigger: 107 239602 initial stacks were populated; 2116591 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11674 stacks. 228688 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.1736; Std Dev: 101.67; Max: 107 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 228688 stacks merged into 167304 stacks; deleveraged 4757 stacks; removed 4920 stacks. After merging, coverage depth Mean: 12.0273; Std Dev: 122.676; Max: 211 Merging remainder radtags 2305455 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1396428 remainder reads; unable to match 909027 remainder reads. After remainders merged, coverage depth Mean: 20.6673; Std Dev: 123.516; Max: 495 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4219746 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_14A.fq.gz... read 5128773 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_15A.fq.gz Loaded 4817350 RAD-Tags; inserted 2200864 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.4261; Std Dev: 43.8164; Max: 11282 Deleveraging trigger: 55; Removal trigger: 99 233894 initial stacks were populated; 1966970 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11379 stacks. 223287 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.9225; Std Dev: 93.1662; Max: 99 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 223287 stacks merged into 163352 stacks; deleveraged 4673 stacks; removed 4913 stacks. After merging, coverage depth Mean: 11.762; Std Dev: 112.298; Max: 166 Merging remainder radtags 2144863 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1298009 remainder reads; unable to match 846854 remainder reads. After remainders merged, coverage depth Mean: 19.9946; Std Dev: 113.128; Max: 610 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3970496 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_15A.fq.gz... read 4817350 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_16A.fq.gz Loaded 5059173 RAD-Tags; inserted 2319794 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.4963; Std Dev: 53.7405; Max: 11547 Deleveraging trigger: 65; Removal trigger: 119 243389 initial stacks were populated; 2076405 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 10778 stacks. 233248 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.85763; Std Dev: 105.444; Max: 119 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 233248 stacks merged into 170682 stacks; deleveraged 4663 stacks; removed 4933 stacks. After merging, coverage depth Mean: 11.5876; Std Dev: 126.977; Max: 205 Merging remainder radtags 2261103 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1347406 remainder reads; unable to match 913697 remainder reads. After remainders merged, coverage depth Mean: 19.7482; Std Dev: 127.692; Max: 465 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4145476 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_16A.fq.gz... read 5059173 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_17A.fq.gz Loaded 5882258 RAD-Tags; inserted 2621936 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.9238; Std Dev: 46.8357; Max: 11480 Deleveraging trigger: 59; Removal trigger: 106 278407 initial stacks were populated; 2343529 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13954 stacks. 265344 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.3126; Std Dev: 105.587; Max: 106 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 265344 stacks merged into 188217 stacks; deleveraged 5983 stacks; removed 6757 stacks. After merging, coverage depth Mean: 12.3749; Std Dev: 129.36; Max: 180 Merging remainder radtags 2562587 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1535364 remainder reads; unable to match 1027223 remainder reads. After remainders merged, coverage depth Mean: 20.8779; Std Dev: 130.09; Max: 711 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4855035 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_17A.fq.gz... read 5882258 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_18A.fq.gz Loaded 3300384 RAD-Tags; inserted 1634244 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 9.80948; Std Dev: 34.7626; Max: 8552 Deleveraging trigger: 45; Removal trigger: 79 174537 initial stacks were populated; 1459707 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 8527 stacks. 166634 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 8.57339; Std Dev: 74.4968; Max: 79 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 166634 stacks merged into 129845 stacks; deleveraged 2949 stacks; removed 2676 stacks. After merging, coverage depth Mean: 9.91063; Std Dev: 86.4853; Max: 142 Merging remainder radtags 1588266 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 894065 remainder reads; unable to match 694201 remainder reads. After remainders merged, coverage depth Mean: 16.9758; Std Dev: 87.3143; Max: 973 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 2606183 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_18A.fq.gz... read 3300384 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_19A.fq.gz Loaded 3840879 RAD-Tags; inserted 1793714 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.1089; Std Dev: 42.2064; Max: 10447 Deleveraging trigger: 53; Removal trigger: 96 188448 initial stacks were populated; 1605266 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 9032 stacks. 180034 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.65757; Std Dev: 91.9147; Max: 96 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 180034 stacks merged into 134049 stacks; deleveraged 3592 stacks; removed 3553 stacks. After merging, coverage depth Mean: 11.413; Std Dev: 109.677; Max: 192 Merging remainder radtags 1747437 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1056298 remainder reads; unable to match 691139 remainder reads. After remainders merged, coverage depth Mean: 19.5461; Std Dev: 110.514; Max: 667 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3149740 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_19A.fq.gz... read 3840879 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_1A.fq.gz Loaded 2557282 RAD-Tags; inserted 1257058 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 9.74872; Std Dev: 33.6913; Max: 7011 Deleveraging trigger: 43; Removal trigger: 77 137537 initial stacks were populated; 1119521 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 6614 stacks. 131399 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 8.52011; Std Dev: 70.7827; Max: 77 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 131399 stacks merged into 102563 stacks; deleveraged 2165 stacks; removed 1943 stacks. After merging, coverage depth Mean: 9.83003; Std Dev: 82.5587; Max: 131 Merging remainder radtags 1216472 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 706376 remainder reads; unable to match 510096 remainder reads. After remainders merged, coverage depth Mean: 16.8836; Std Dev: 83.3248; Max: 430 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 2047186 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_1A.fq.gz... read 2557282 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_20A.fq.gz Loaded 4633581 RAD-Tags; inserted 2138621 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.1368; Std Dev: 42.507; Max: 10670 Deleveraging trigger: 54; Removal trigger: 96 229221 initial stacks were populated; 1909400 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11174 stacks. 218807 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.67249; Std Dev: 92.5246; Max: 96 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 218807 stacks merged into 161181 stacks; deleveraged 4530 stacks; removed 4576 stacks. After merging, coverage depth Mean: 11.4606; Std Dev: 111.039; Max: 163 Merging remainder radtags 2080803 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1255238 remainder reads; unable to match 825565 remainder reads. After remainders merged, coverage depth Mean: 19.515; Std Dev: 111.805; Max: 472 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3808016 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_20A.fq.gz... read 4633581 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_21A.fq.gz Loaded 5746289 RAD-Tags; inserted 2686326 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.1091; Std Dev: 56.4341; Max: 10086 Deleveraging trigger: 68; Removal trigger: 124 281182 initial stacks were populated; 2405144 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11963 stacks. 269864 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.56034; Std Dev: 104.733; Max: 124 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 269864 stacks merged into 199432 stacks; deleveraged 5311 stacks; removed 5388 stacks. After merging, coverage depth Mean: 11.1374; Std Dev: 125.305; Max: 172 Merging remainder radtags 2622601 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1496871 remainder reads; unable to match 1125730 remainder reads. After remainders merged, coverage depth Mean: 18.8772; Std Dev: 125.917; Max: 455 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4620559 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_21A.fq.gz... read 5746289 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_22A.fq.gz Loaded 5459531 RAD-Tags; inserted 2480981 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.7578; Std Dev: 48.2043; Max: 12360 Deleveraging trigger: 60; Removal trigger: 108 257971 initial stacks were populated; 2223010 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 12741 stacks. 246073 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.1519; Std Dev: 101.928; Max: 108 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 246073 stacks merged into 177194 stacks; deleveraged 5394 stacks; removed 5833 stacks. After merging, coverage depth Mean: 12.0491; Std Dev: 124.122; Max: 173 Merging remainder radtags 2426356 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1451769 remainder reads; unable to match 974587 remainder reads. After remainders merged, coverage depth Mean: 20.563; Std Dev: 124.914; Max: 804 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4484944 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_22A.fq.gz... read 5459531 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_23A.fq.gz Loaded 6046405 RAD-Tags; inserted 2754651 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.6202; Std Dev: 47.9332; Max: 12487 Deleveraging trigger: 60; Removal trigger: 107 288683 initial stacks were populated; 2465968 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 14034 stacks. 275558 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.017; Std Dev: 99.5893; Max: 107 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 275558 stacks merged into 198781 stacks; deleveraged 6141 stacks; removed 6350 stacks. After merging, coverage depth Mean: 11.9227; Std Dev: 120.965; Max: 180 Merging remainder radtags 2691843 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1617623 remainder reads; unable to match 1074220 remainder reads. After remainders merged, coverage depth Mean: 20.3689; Std Dev: 121.719; Max: 711 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4972185 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_23A.fq.gz... read 6046405 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_24A.fq.gz Loaded 5731313 RAD-Tags; inserted 2591162 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.7364; Std Dev: 48.2074; Max: 13121 Deleveraging trigger: 60; Removal trigger: 108 272367 initial stacks were populated; 2318795 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 12728 stacks. 260472 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.1859; Std Dev: 103.147; Max: 108 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 260472 stacks merged into 186428 stacks; deleveraged 5894 stacks; removed 6342 stacks. After merging, coverage depth Mean: 12.0915; Std Dev: 125.812; Max: 161 Merging remainder radtags 2534717 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1514803 remainder reads; unable to match 1019914 remainder reads. After remainders merged, coverage depth Mean: 20.5421; Std Dev: 126.604; Max: 648 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4711399 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_24A.fq.gz... read 5731313 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_25A.fq.gz Loaded 4154553 RAD-Tags; inserted 1926232 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.0256; Std Dev: 41.7633; Max: 10377 Deleveraging trigger: 53; Removal trigger: 95 206838 initial stacks were populated; 1719394 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 10331 stacks. 197225 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.58217; Std Dev: 91.85; Max: 95 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 197225 stacks merged into 147298 stacks; deleveraged 4036 stacks; removed 3834 stacks. After merging, coverage depth Mean: 11.3203; Std Dev: 109.157; Max: 164 Merging remainder radtags 1874036 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1132362 remainder reads; unable to match 741674 remainder reads. After remainders merged, coverage depth Mean: 19.253; Std Dev: 109.934; Max: 469 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3412879 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_25A.fq.gz... read 4154553 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_26A.fq.gz Loaded 5533796 RAD-Tags; inserted 2524143 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.2851; Std Dev: 41.3249; Max: 11083 Deleveraging trigger: 53; Removal trigger: 94 272524 initial stacks were populated; 2251619 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 14217 stacks. 259274 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.82609; Std Dev: 94.9013; Max: 94 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 259274 stacks merged into 188758 stacks; deleveraged 5677 stacks; removed 5753 stacks. After merging, coverage depth Mean: 11.7215; Std Dev: 114.144; Max: 152 Merging remainder radtags 2458323 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1492972 remainder reads; unable to match 965351 remainder reads. After remainders merged, coverage depth Mean: 19.9229; Std Dev: 114.888; Max: 489 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4568445 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_26A.fq.gz... read 5533796 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_27A.fq.gz Loaded 4285932 RAD-Tags; inserted 1967452 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.9909; Std Dev: 51.6351; Max: 10253 Deleveraging trigger: 63; Removal trigger: 114 216269 initial stacks were populated; 1751183 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 9734 stacks. 207083 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.42438; Std Dev: 100.067; Max: 114 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 207083 stacks merged into 153579 stacks; deleveraged 3895 stacks; removed 4127 stacks. After merging, coverage depth Mean: 10.9336; Std Dev: 119.816; Max: 148 Merging remainder radtags 1908943 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1132224 remainder reads; unable to match 776719 remainder reads. After remainders merged, coverage depth Mean: 18.5373; Std Dev: 120.44; Max: 502 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3509213 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_27A.fq.gz... read 4285932 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_28A.fq.gz Loaded 4422417 RAD-Tags; inserted 2055649 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.0409; Std Dev: 51.8233; Max: 8999 Deleveraging trigger: 63; Removal trigger: 115 219501 initial stacks were populated; 1836148 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 9332 stacks. 210695 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.4852; Std Dev: 97.3812; Max: 115 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 210695 stacks merged into 156574 stacks; deleveraged 4181 stacks; removed 4123 stacks. After merging, coverage depth Mean: 11.0433; Std Dev: 116.653; Max: 153 Merging remainder radtags 1998923 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1179405 remainder reads; unable to match 819518 remainder reads. After remainders merged, coverage depth Mean: 18.8064; Std Dev: 117.357; Max: 791 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3602899 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_28A.fq.gz... read 4422417 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_29A.fq.gz Loaded 7222750 RAD-Tags; inserted 3031205 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 13.2563; Std Dev: 60.0621; Max: 15059 Deleveraging trigger: 73; Removal trigger: 133 320613 initial stacks were populated; 2710592 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 15539 stacks. 305985 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 11.335; Std Dev: 127.915; Max: 133 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 305985 stacks merged into 201152 stacks; deleveraged 7914 stacks; removed 10001 stacks. After merging, coverage depth Mean: 13.797; Std Dev: 164.046; Max: 211 Merging remainder radtags 2972613 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1827661 remainder reads; unable to match 1144952 remainder reads. After remainders merged, coverage depth Mean: 23.4042; Std Dev: 164.67; Max: 786 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 6077798 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_29A.fq.gz... read 7222750 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_2A.fq.gz Loaded 6511850 RAD-Tags; inserted 2838749 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.5754; Std Dev: 53.3652; Max: 13945 Deleveraging trigger: 66; Removal trigger: 119 296862 initial stacks were populated; 2541887 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 14626 stacks. 283147 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.8143; Std Dev: 115.593; Max: 119 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 283147 stacks merged into 196188 stacks; deleveraged 6726 stacks; removed 7622 stacks. After merging, coverage depth Mean: 13.0253; Std Dev: 143.568; Max: 208 Merging remainder radtags 2778689 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1715422 remainder reads; unable to match 1063267 remainder reads. After remainders merged, coverage depth Mean: 22.1666; Std Dev: 144.268; Max: 843 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5448583 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_2A.fq.gz... read 6511850 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_30A.fq.gz Loaded 5093670 RAD-Tags; inserted 2288544 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.7504; Std Dev: 50.6071; Max: 11751 Deleveraging trigger: 62; Removal trigger: 113 243670 initial stacks were populated; 2044874 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11087 stacks. 233265 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.1239; Std Dev: 102.951; Max: 113 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 233265 stacks merged into 166587 stacks; deleveraged 4995 stacks; removed 5428 stacks. After merging, coverage depth Mean: 12.0494; Std Dev: 125.748; Max: 217 Merging remainder radtags 2230456 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1355841 remainder reads; unable to match 874615 remainder reads. After remainders merged, coverage depth Mean: 20.4983; Std Dev: 126.484; Max: 748 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4219055 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_30A.fq.gz... read 5093670 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_31A.fq.gz Loaded 6718376 RAD-Tags; inserted 2932321 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.3954; Std Dev: 55.4054; Max: 14535 Deleveraging trigger: 68; Removal trigger: 123 310613 initial stacks were populated; 2621708 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 14609 stacks. 296873 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.6746; Std Dev: 117.221; Max: 123 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 296873 stacks merged into 205019 stacks; deleveraged 7026 stacks; removed 8209 stacks. After merging, coverage depth Mean: 12.7942; Std Dev: 145.795; Max: 236 Merging remainder radtags 2868206 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1742620 remainder reads; unable to match 1125586 remainder reads. After remainders merged, coverage depth Mean: 21.6878; Std Dev: 146.443; Max: 678 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5592790 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_31A.fq.gz... read 6718376 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_32A.fq.gz Loaded 6560631 RAD-Tags; inserted 2891496 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.0881; Std Dev: 59.2028; Max: 12645 Deleveraging trigger: 71; Removal trigger: 130 309489 initial stacks were populated; 2582007 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13629 stacks. 296634 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.4144; Std Dev: 112.74; Max: 130 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 296634 stacks merged into 208515 stacks; deleveraged 6511 stacks; removed 7432 stacks. After merging, coverage depth Mean: 12.4063; Std Dev: 139.187; Max: 168 Merging remainder radtags 2819508 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1732074 remainder reads; unable to match 1087434 remainder reads. After remainders merged, coverage depth Mean: 21.0533; Std Dev: 139.795; Max: 604 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5473197 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_32A.fq.gz... read 6560631 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_33A.fq.gz Loaded 4908314 RAD-Tags; inserted 2227146 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.4246; Std Dev: 44.7506; Max: 10884 Deleveraging trigger: 56; Removal trigger: 101 239930 initial stacks were populated; 1987216 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11304 stacks. 229373 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.92291; Std Dev: 93.7765; Max: 101 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 229373 stacks merged into 166821 stacks; deleveraged 4836 stacks; removed 5112 stacks. After merging, coverage depth Mean: 11.7796; Std Dev: 113.514; Max: 180 Merging remainder radtags 2167204 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1325871 remainder reads; unable to match 841333 remainder reads. After remainders merged, coverage depth Mean: 20.0168; Std Dev: 114.29; Max: 405 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4066981 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_33A.fq.gz... read 4908314 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_4A.fq.gz Loaded 6757765 RAD-Tags; inserted 2967766 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.2989; Std Dev: 53.5787; Max: 14569 Deleveraging trigger: 66; Removal trigger: 119 313809 initial stacks were populated; 2653957 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 14985 stacks. 299717 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.6115; Std Dev: 109.557; Max: 119 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 299717 stacks merged into 209580 stacks; deleveraged 6709 stacks; removed 7782 stacks. After merging, coverage depth Mean: 12.7029; Std Dev: 135.561; Max: 187 Merging remainder radtags 2898256 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1782499 remainder reads; unable to match 1115757 remainder reads. After remainders merged, coverage depth Mean: 21.5752; Std Dev: 136.217; Max: 475 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5642008 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_4A.fq.gz... read 6757765 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_5A.fq.gz Loaded 5217491 RAD-Tags; inserted 2377977 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.3999; Std Dev: 42.2571; Max: 9963 Deleveraging trigger: 54; Removal trigger: 96 254610 initial stacks were populated; 2123367 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13212 stacks. 242277 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.90965; Std Dev: 92.4962; Max: 96 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 242277 stacks merged into 178211 stacks; deleveraged 5002 stacks; removed 5225 stacks. After merging, coverage depth Mean: 11.7562; Std Dev: 110.898; Max: 168 Merging remainder radtags 2314965 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1420296 remainder reads; unable to match 894669 remainder reads. After remainders merged, coverage depth Mean: 20.0086; Std Dev: 111.713; Max: 707 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4322822 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_5A.fq.gz... read 5217491 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_6A.fq.gz Loaded 4571490 RAD-Tags; inserted 2094212 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.2447; Std Dev: 49.3113; Max: 11361 Deleveraging trigger: 61; Removal trigger: 110 225309 initial stacks were populated; 1868903 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 10435 stacks. 215512 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.67253; Std Dev: 97.8616; Max: 110 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 215512 stacks merged into 157825 stacks; deleveraged 4258 stacks; removed 4619 stacks. After merging, coverage depth Mean: 11.3221; Std Dev: 118.201; Max: 176 Merging remainder radtags 2037949 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1213745 remainder reads; unable to match 824204 remainder reads. After remainders merged, coverage depth Mean: 19.2775; Std Dev: 118.924; Max: 500 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3747286 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_6A.fq.gz... read 4571490 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_7A.fq.gz Loaded 4884938 RAD-Tags; inserted 2197264 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.4924; Std Dev: 47.2667; Max: 11787 Deleveraging trigger: 59; Removal trigger: 106 238831 initial stacks were populated; 1958433 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11802 stacks. 227758 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.86152; Std Dev: 101.26; Max: 106 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 227758 stacks merged into 164291 stacks; deleveraged 4954 stacks; removed 5265 stacks. After merging, coverage depth Mean: 11.6745; Std Dev: 122.842; Max: 167 Merging remainder radtags 2140186 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1277608 remainder reads; unable to match 862578 remainder reads. After remainders merged, coverage depth Mean: 19.7455; Std Dev: 123.525; Max: 348 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4022360 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_7A.fq.gz... read 4884938 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_8A.fq.gz Loaded 5228938 RAD-Tags; inserted 2420852 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.8446; Std Dev: 47.5259; Max: 11944 Deleveraging trigger: 59; Removal trigger: 107 241068 initial stacks were populated; 2179784 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11498 stacks. 230332 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.2784; Std Dev: 100.662; Max: 107 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 230332 stacks merged into 170666 stacks; deleveraged 4852 stacks; removed 4591 stacks. After merging, coverage depth Mean: 12.1231; Std Dev: 120.347; Max: 177 Merging remainder radtags 2373584 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1451138 remainder reads; unable to match 922446 remainder reads. After remainders merged, coverage depth Mean: 20.9012; Std Dev: 121.262; Max: 649 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4306492 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_8A.fq.gz... read 5228938 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1NF_9A.fq.gz Loaded 6375340 RAD-Tags; inserted 2786097 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.3576; Std Dev: 50.794; Max: 13590 Deleveraging trigger: 63; Removal trigger: 114 295396 initial stacks were populated; 2490701 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 14276 stacks. 282010 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.6582; Std Dev: 111.764; Max: 114 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 282010 stacks merged into 195088 stacks; deleveraged 6699 stacks; removed 7806 stacks. After merging, coverage depth Mean: 12.801; Std Dev: 139.05; Max: 168 Merging remainder radtags 2724948 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1658761 remainder reads; unable to match 1066187 remainder reads. After remainders merged, coverage depth Mean: 21.7004; Std Dev: 139.761; Max: 619 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5309153 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1NF_9A.fq.gz... read 6375340 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_10A.fq.gz Loaded 4825522 RAD-Tags; inserted 2239896 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.097; Std Dev: 45.0771; Max: 10791 Deleveraging trigger: 56; Removal trigger: 101 237957 initial stacks were populated; 2001939 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11300 stacks. 227371 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.58566; Std Dev: 91.4723; Max: 101 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 227371 stacks merged into 167908 stacks; deleveraged 4549 stacks; removed 4821 stacks. After merging, coverage depth Mean: 11.2295; Std Dev: 109.701; Max: 165 Merging remainder radtags 2184915 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1267750 remainder reads; unable to match 917165 remainder reads. After remainders merged, coverage depth Mean: 19.0371; Std Dev: 110.479; Max: 562 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3908357 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_10A.fq.gz... read 4825522 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_11A.fq.gz Loaded 4872845 RAD-Tags; inserted 2257885 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.1386; Std Dev: 43.1736; Max: 10812 Deleveraging trigger: 54; Removal trigger: 97 239697 initial stacks were populated; 2018188 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11978 stacks. 228529 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.61455; Std Dev: 92.8319; Max: 97 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 228529 stacks merged into 168076 stacks; deleveraged 4603 stacks; removed 4868 stacks. After merging, coverage depth Mean: 11.3682; Std Dev: 111.347; Max: 170 Merging remainder radtags 2202964 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1297696 remainder reads; unable to match 905268 remainder reads. After remainders merged, coverage depth Mean: 19.3591; Std Dev: 112.131; Max: 401 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3967577 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_11A.fq.gz... read 4872845 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_12A.fq.gz Loaded 6457409 RAD-Tags; inserted 2879811 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.7756; Std Dev: 51.024; Max: 11705 Deleveraging trigger: 63; Removal trigger: 114 309976 initial stacks were populated; 2569835 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 15053 stacks. 295836 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.1287; Std Dev: 102.524; Max: 114 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 295836 stacks merged into 211098 stacks; deleveraged 6540 stacks; removed 7160 stacks. After merging, coverage depth Mean: 12.0574; Std Dev: 125.298; Max: 204 Merging remainder radtags 2807255 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1691135 remainder reads; unable to match 1116120 remainder reads. After remainders merged, coverage depth Mean: 20.3871; Std Dev: 125.998; Max: 722 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5341289 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_12A.fq.gz... read 6457409 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_13A.fq.gz Loaded 5577247 RAD-Tags; inserted 2528372 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.4931; Std Dev: 46.549; Max: 12748 Deleveraging trigger: 58; Removal trigger: 105 270798 initial stacks were populated; 2257574 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13397 stacks. 258246 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.92228; Std Dev: 100.138; Max: 105 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 258246 stacks merged into 186465 stacks; deleveraged 5528 stacks; removed 6059 stacks. After merging, coverage depth Mean: 11.7728; Std Dev: 121.368; Max: 200 Merging remainder radtags 2464938 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1487311 remainder reads; unable to match 977627 remainder reads. After remainders merged, coverage depth Mean: 20.0558; Std Dev: 122.125; Max: 821 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4599620 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_13A.fq.gz... read 5577247 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_14A.fq.gz Loaded 6684839 RAD-Tags; inserted 2917409 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.42; Std Dev: 55.1948; Max: 13539 Deleveraging trigger: 68; Removal trigger: 123 308355 initial stacks were populated; 2609054 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 14780 stacks. 294450 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.6668; Std Dev: 114.713; Max: 123 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 294450 stacks merged into 203364 stacks; deleveraged 6865 stacks; removed 8194 stacks. After merging, coverage depth Mean: 12.7493; Std Dev: 142.805; Max: 207 Merging remainder radtags 2855069 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1727287 remainder reads; unable to match 1127782 remainder reads. After remainders merged, coverage depth Mean: 21.6394; Std Dev: 143.498; Max: 738 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5557057 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_14A.fq.gz... read 6684839 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_15A.fq.gz Loaded 4726849 RAD-Tags; inserted 2182168 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.1336; Std Dev: 40.4599; Max: 10526 Deleveraging trigger: 52; Removal trigger: 92 233510 initial stacks were populated; 1948658 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 12099 stacks. 222251 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.71595; Std Dev: 89.6932; Max: 92 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 222251 stacks merged into 164080 stacks; deleveraged 4606 stacks; removed 4814 stacks. After merging, coverage depth Mean: 11.4988; Std Dev: 107.351; Max: 183 Merging remainder radtags 2127040 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1268375 remainder reads; unable to match 858665 remainder reads. After remainders merged, coverage depth Mean: 19.5049; Std Dev: 108.166; Max: 622 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3868184 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_15A.fq.gz... read 4726849 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_16A.fq.gz Loaded 4935559 RAD-Tags; inserted 2318863 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.5139; Std Dev: 44.7033; Max: 10565 Deleveraging trigger: 56; Removal trigger: 101 231190 initial stacks were populated; 2087673 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11078 stacks. 220882 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.94853; Std Dev: 97.085; Max: 101 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 220882 stacks merged into 164708 stacks; deleveraged 4530 stacks; removed 4270 stacks. After merging, coverage depth Mean: 11.7437; Std Dev: 115.433; Max: 176 Merging remainder radtags 2273658 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1380609 remainder reads; unable to match 893049 remainder reads. After remainders merged, coverage depth Mean: 20.3905; Std Dev: 116.306; Max: 505 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4042510 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_16A.fq.gz... read 4935559 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_17A.fq.gz Loaded 5627081 RAD-Tags; inserted 2552545 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.4613; Std Dev: 46.2004; Max: 11679 Deleveraging trigger: 58; Removal trigger: 104 273989 initial stacks were populated; 2278556 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13216 stacks. 261615 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.92291; Std Dev: 98.5602; Max: 104 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 261615 stacks merged into 189699 stacks; deleveraged 5745 stacks; removed 5935 stacks. After merging, coverage depth Mean: 11.7916; Std Dev: 119.272; Max: 149 Merging remainder radtags 2486824 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1497917 remainder reads; unable to match 988907 remainder reads. After remainders merged, coverage depth Mean: 19.9805; Std Dev: 120.016; Max: 629 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4638174 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_17A.fq.gz... read 5627081 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_18A.fq.gz Loaded 6125904 RAD-Tags; inserted 2801452 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.0345; Std Dev: 51.7742; Max: 13648 Deleveraging trigger: 64; Removal trigger: 116 280533 initial stacks were populated; 2520919 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 12550 stacks. 268796 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.3718; Std Dev: 105.519; Max: 116 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 268796 stacks merged into 192179 stacks; deleveraged 6072 stacks; removed 6233 stacks. After merging, coverage depth Mean: 12.335; Std Dev: 129.04; Max: 194 Merging remainder radtags 2749839 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1656164 remainder reads; unable to match 1093675 remainder reads. After remainders merged, coverage depth Mean: 21.2808; Std Dev: 129.867; Max: 617 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5032229 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_18A.fq.gz... read 6125904 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_19A.fq.gz Loaded 5728294 RAD-Tags; inserted 2600964 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.5599; Std Dev: 45.9235; Max: 11382 Deleveraging trigger: 57; Removal trigger: 103 275794 initial stacks were populated; 2325170 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13613 stacks. 263073 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.99596; Std Dev: 97.5123; Max: 103 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 263073 stacks merged into 189636 stacks; deleveraged 5600 stacks; removed 6204 stacks. After merging, coverage depth Mean: 11.8623; Std Dev: 118.559; Max: 158 Merging remainder radtags 2540138 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1506307 remainder reads; unable to match 1033831 remainder reads. After remainders merged, coverage depth Mean: 20.1143; Std Dev: 119.32; Max: 581 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4694463 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_19A.fq.gz... read 5728294 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_1A.fq.gz Loaded 5736434 RAD-Tags; inserted 2523359 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.1915; Std Dev: 49.4423; Max: 13672 Deleveraging trigger: 62; Removal trigger: 111 268287 initial stacks were populated; 2255072 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13618 stacks. 255527 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.5092; Std Dev: 112.192; Max: 111 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 255527 stacks merged into 179533 stacks; deleveraged 5798 stacks; removed 6744 stacks. After merging, coverage depth Mean: 12.5962; Std Dev: 138.209; Max: 175 Merging remainder radtags 2465615 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1513048 remainder reads; unable to match 952567 remainder reads. After remainders merged, coverage depth Mean: 21.3965; Std Dev: 138.939; Max: 736 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4783867 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_1A.fq.gz... read 5736434 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_20A.fq.gz Loaded 4063112 RAD-Tags; inserted 1966895 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.6775; Std Dev: 41.4654; Max: 9244 Deleveraging trigger: 52; Removal trigger: 94 200249 initial stacks were populated; 1766646 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 9126 stacks. 191739 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.24512; Std Dev: 85.587; Max: 94 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 191739 stacks merged into 144629 stacks; deleveraged 3683 stacks; removed 3558 stacks. After merging, coverage depth Mean: 10.7737; Std Dev: 101.662; Max: 143 Merging remainder radtags 1924947 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1073596 remainder reads; unable to match 851351 remainder reads. After remainders merged, coverage depth Mean: 18.4174; Std Dev: 102.528; Max: 807 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3211761 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_20A.fq.gz... read 4063112 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_21A.fq.gz Loaded 6678890 RAD-Tags; inserted 2986432 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.9986; Std Dev: 47.7656; Max: 13549 Deleveraging trigger: 60; Removal trigger: 108 312727 initial stacks were populated; 2673705 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 15338 stacks. 298398 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.3826; Std Dev: 105.408; Max: 108 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 298398 stacks merged into 209348 stacks; deleveraged 6915 stacks; removed 7849 stacks. After merging, coverage depth Mean: 12.4707; Std Dev: 130.159; Max: 176 Merging remainder radtags 2926602 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1725526 remainder reads; unable to match 1201076 remainder reads. After remainders merged, coverage depth Mean: 21.0772; Std Dev: 130.901; Max: 652 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5477814 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_21A.fq.gz... read 6678890 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_22A.fq.gz Loaded 5773384 RAD-Tags; inserted 2596247 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.6594; Std Dev: 46.5544; Max: 11756 Deleveraging trigger: 58; Removal trigger: 105 277838 initial stacks were populated; 2318409 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13925 stacks. 264811 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.0475; Std Dev: 100.887; Max: 105 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 264811 stacks merged into 189174 stacks; deleveraged 5783 stacks; removed 6394 stacks. After merging, coverage depth Mean: 11.9979; Std Dev: 123.174; Max: 163 Merging remainder radtags 2533958 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1521006 remainder reads; unable to match 1012952 remainder reads. After remainders merged, coverage depth Mean: 20.3605; Std Dev: 123.952; Max: 1112 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4760432 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_22A.fq.gz... read 5773384 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_23A.fq.gz Loaded 6970736 RAD-Tags; inserted 3089705 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.126; Std Dev: 46.0158; Max: 12245 Deleveraging trigger: 58; Removal trigger: 104 325783 initial stacks were populated; 2763922 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 17281 stacks. 309656 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.4988; Std Dev: 102.296; Max: 104 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 309656 stacks merged into 218079 stacks; deleveraged 7106 stacks; removed 8038 stacks. After merging, coverage depth Mean: 12.6801; Std Dev: 125.748; Max: 169 Merging remainder radtags 3020295 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1854975 remainder reads; unable to match 1165320 remainder reads. After remainders merged, coverage depth Mean: 21.5604; Std Dev: 126.47; Max: 595 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5805416 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_23A.fq.gz... read 6970736 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_24A.fq.gz Loaded 3556611 RAD-Tags; inserted 1713606 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.3718; Std Dev: 38.9823; Max: 9162 Deleveraging trigger: 49; Removal trigger: 88 182119 initial stacks were populated; 1531487 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 8695 stacks. 174016 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.01782; Std Dev: 87.4051; Max: 88 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 174016 stacks merged into 132927 stacks; deleveraged 3152 stacks; removed 2973 stacks. After merging, coverage depth Mean: 10.5215; Std Dev: 102.669; Max: 132 Merging remainder radtags 1667710 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 959796 remainder reads; unable to match 707914 remainder reads. After remainders merged, coverage depth Mean: 17.941; Std Dev: 103.404; Max: 456 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 2848697 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_24A.fq.gz... read 3556611 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_25A.fq.gz Loaded 5727614 RAD-Tags; inserted 2617890 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.8343; Std Dev: 47.7108; Max: 11700 Deleveraging trigger: 60; Removal trigger: 107 267176 initial stacks were populated; 2350714 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13209 stacks. 254808 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.2064; Std Dev: 102.422; Max: 107 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 254808 stacks merged into 182871 stacks; deleveraged 5525 stacks; removed 6159 stacks. After merging, coverage depth Mean: 12.1351; Std Dev: 124.803; Max: 187 Merging remainder radtags 2565772 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1499169 remainder reads; unable to match 1066603 remainder reads. After remainders merged, coverage depth Mean: 20.6594; Std Dev: 125.601; Max: 615 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4661011 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_25A.fq.gz... read 5727614 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_26A.fq.gz Loaded 5203440 RAD-Tags; inserted 2361191 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.3852; Std Dev: 43.9032; Max: 11475 Deleveraging trigger: 55; Removal trigger: 99 254931 initial stacks were populated; 2106260 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 12819 stacks. 242963 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.83341; Std Dev: 97.63; Max: 99 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 242963 stacks merged into 176092 stacks; deleveraged 5202 stacks; removed 5531 stacks. After merging, coverage depth Mean: 11.6902; Std Dev: 118.059; Max: 176 Merging remainder radtags 2301009 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1370094 remainder reads; unable to match 930915 remainder reads. After remainders merged, coverage depth Mean: 19.7633; Std Dev: 118.852; Max: 865 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4272525 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_26A.fq.gz... read 5203440 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_27A.fq.gz Loaded 4917653 RAD-Tags; inserted 2238561 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.458; Std Dev: 48.2728; Max: 11987 Deleveraging trigger: 60; Removal trigger: 108 238604 initial stacks were populated; 1999957 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11404 stacks. 227910 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.87219; Std Dev: 103.603; Max: 108 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 227910 stacks merged into 165752 stacks; deleveraged 4768 stacks; removed 5220 stacks. After merging, coverage depth Mean: 11.6941; Std Dev: 125.101; Max: 191 Merging remainder radtags 2183728 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1285187 remainder reads; unable to match 898541 remainder reads. After remainders merged, coverage depth Mean: 19.7355; Std Dev: 125.823; Max: 1131 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4019112 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_27A.fq.gz... read 4917653 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_28A.fq.gz Loaded 5359774 RAD-Tags; inserted 2420149 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.6008; Std Dev: 46.7735; Max: 10720 Deleveraging trigger: 58; Removal trigger: 105 258496 initial stacks were populated; 2161653 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 12427 stacks. 246883 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.0213; Std Dev: 103.86; Max: 105 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 246883 stacks merged into 176467 stacks; deleveraged 5447 stacks; removed 6025 stacks. After merging, coverage depth Mean: 11.9742; Std Dev: 126.796; Max: 186 Merging remainder radtags 2361012 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1416316 remainder reads; unable to match 944696 remainder reads. After remainders merged, coverage depth Mean: 20.3238; Std Dev: 127.515; Max: 634 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4415078 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_28A.fq.gz... read 5359774 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_29A.fq.gz Loaded 4258401 RAD-Tags; inserted 2016527 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.7727; Std Dev: 44.6953; Max: 10109 Deleveraging trigger: 56; Removal trigger: 101 193200 initial stacks were populated; 1823327 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 8524 stacks. 185308 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.1805; Std Dev: 94.3167; Max: 101 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 185308 stacks merged into 135381 stacks; deleveraged 3889 stacks; removed 3802 stacks. After merging, coverage depth Mean: 12.1193; Std Dev: 114.278; Max: 160 Merging remainder radtags 1983923 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1173783 remainder reads; unable to match 810140 remainder reads. After remainders merged, coverage depth Mean: 21.0831; Std Dev: 115.246; Max: 907 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3448261 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_29A.fq.gz... read 4258401 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_2A.fq.gz Loaded 5809192 RAD-Tags; inserted 2604340 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.8813; Std Dev: 49.3821; Max: 12581 Deleveraging trigger: 61; Removal trigger: 111 274647 initial stacks were populated; 2329693 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13277 stacks. 262204 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.2069; Std Dev: 104.724; Max: 111 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 262204 stacks merged into 185928 stacks; deleveraged 6030 stacks; removed 6656 stacks. After merging, coverage depth Mean: 12.1348; Std Dev: 128.27; Max: 183 Merging remainder radtags 2546025 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1515530 remainder reads; unable to match 1030495 remainder reads. After remainders merged, coverage depth Mean: 20.6281; Std Dev: 129.011; Max: 450 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4778697 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_2A.fq.gz... read 5809192 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_30A.fq.gz Loaded 7242620 RAD-Tags; inserted 3206464 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.3327; Std Dev: 46.7428; Max: 12929 Deleveraging trigger: 59; Removal trigger: 106 332498 initial stacks were populated; 2873966 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 17014 stacks. 316631 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.6882; Std Dev: 102.808; Max: 106 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 316631 stacks merged into 220870 stacks; deleveraged 7297 stacks; removed 8271 stacks. After merging, coverage depth Mean: 13.0086; Std Dev: 127.045; Max: 170 Merging remainder radtags 3142015 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1916581 remainder reads; unable to match 1225434 remainder reads. After remainders merged, coverage depth Mean: 22.0725; Std Dev: 127.804; Max: 726 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 6017186 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_30A.fq.gz... read 7242620 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_31A.fq.gz Loaded 6325270 RAD-Tags; inserted 2760748 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.2753; Std Dev: 49.6793; Max: 12994 Deleveraging trigger: 62; Removal trigger: 112 295448 initial stacks were populated; 2465300 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 15189 stacks. 281222 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.5698; Std Dev: 109.985; Max: 112 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 281222 stacks merged into 195050 stacks; deleveraged 6611 stacks; removed 7922 stacks. After merging, coverage depth Mean: 12.6845; Std Dev: 136.474; Max: 203 Merging remainder radtags 2698559 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1634611 remainder reads; unable to match 1063948 remainder reads. After remainders merged, coverage depth Mean: 21.465; Std Dev: 137.166; Max: 515 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5261322 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_31A.fq.gz... read 6325270 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_32A.fq.gz Loaded 4814454 RAD-Tags; inserted 2245065 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.2639; Std Dev: 42.6249; Max: 10931 Deleveraging trigger: 54; Removal trigger: 97 232472 initial stacks were populated; 2012593 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 11445 stacks. 221788 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.76822; Std Dev: 91.9829; Max: 97 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 221788 stacks merged into 162897 stacks; deleveraged 4613 stacks; removed 4857 stacks. After merging, coverage depth Mean: 11.5525; Std Dev: 110.61; Max: 210 Merging remainder radtags 2195924 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1269668 remainder reads; unable to match 926256 remainder reads. After remainders merged, coverage depth Mean: 19.6252; Std Dev: 111.434; Max: 655 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3888198 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_32A.fq.gz... read 4814454 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_3A.fq.gz Loaded 4606266 RAD-Tags; inserted 2247556 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 10.6474; Std Dev: 41.5619; Max: 9766 Deleveraging trigger: 52; Removal trigger: 94 226104 initial stacks were populated; 2021452 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 10565 stacks. 216283 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.23525; Std Dev: 84.6284; Max: 94 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 216283 stacks merged into 164946 stacks; deleveraged 4051 stacks; removed 3838 stacks. After merging, coverage depth Mean: 10.7165; Std Dev: 99.9303; Max: 179 Merging remainder radtags 2198857 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1236215 remainder reads; unable to match 962642 remainder reads. After remainders merged, coverage depth Mean: 18.4253; Std Dev: 100.836; Max: 641 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 3643624 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_3A.fq.gz... read 4606266 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_4A.fq.gz Loaded 6213963 RAD-Tags; inserted 2780646 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.7088; Std Dev: 42.7017; Max: 12230 Deleveraging trigger: 54; Removal trigger: 97 298965 initial stacks were populated; 2481681 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 15632 stacks. 284431 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.1756; Std Dev: 97.0306; Max: 97 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 284431 stacks merged into 203153 stacks; deleveraged 6393 stacks; removed 7093 stacks. After merging, coverage depth Mean: 12.2288; Std Dev: 118.195; Max: 186 Merging remainder radtags 2713429 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1658267 remainder reads; unable to match 1055162 remainder reads. After remainders merged, coverage depth Mean: 20.7344; Std Dev: 118.937; Max: 389 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5158801 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_4A.fq.gz... read 6213963 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_5A.fq.gz Loaded 5659349 RAD-Tags; inserted 2615931 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.168; Std Dev: 41.524; Max: 10652 Deleveraging trigger: 53; Removal trigger: 94 278285 initial stacks were populated; 2337646 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13915 stacks. 265321 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.69323; Std Dev: 91.4491; Max: 94 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 265321 stacks merged into 194634 stacks; deleveraged 5490 stacks; removed 5700 stacks. After merging, coverage depth Mean: 11.4886; Std Dev: 109.935; Max: 151 Merging remainder radtags 2551464 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1497787 remainder reads; unable to match 1053677 remainder reads. After remainders merged, coverage depth Mean: 19.4563; Std Dev: 110.713; Max: 558 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4605672 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_5A.fq.gz... read 5659349 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_6A.fq.gz Loaded 6325274 RAD-Tags; inserted 2803806 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.0925; Std Dev: 53.055; Max: 12703 Deleveraging trigger: 65; Removal trigger: 118 296504 initial stacks were populated; 2507302 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13730 stacks. 283592 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.408; Std Dev: 107.714; Max: 118 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 283592 stacks merged into 199159 stacks; deleveraged 6325 stacks; removed 7307 stacks. After merging, coverage depth Mean: 12.4236; Std Dev: 132.979; Max: 192 Merging remainder radtags 2739803 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1662623 remainder reads; unable to match 1077180 remainder reads. After remainders merged, coverage depth Mean: 21.1269; Std Dev: 133.681; Max: 501 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5248094 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_6A.fq.gz... read 6325274 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_7A.fq.gz Loaded 5589887 RAD-Tags; inserted 2530343 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.5723; Std Dev: 44.1971; Max: 10009 Deleveraging trigger: 56; Removal trigger: 100 269907 initial stacks were populated; 2260436 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 13728 stacks. 257070 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.99103; Std Dev: 95.6874; Max: 100 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 257070 stacks merged into 186477 stacks; deleveraged 5445 stacks; removed 5770 stacks. After merging, coverage depth Mean: 11.9242; Std Dev: 115.599; Max: 177 Merging remainder radtags 2466450 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1485718 remainder reads; unable to match 980732 remainder reads. After remainders merged, coverage depth Mean: 20.1867; Std Dev: 116.37; Max: 948 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4609155 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_7A.fq.gz... read 5589887 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_8A.fq.gz Loaded 6167038 RAD-Tags; inserted 2710506 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 12.0421; Std Dev: 60.5668; Max: 14610 Deleveraging trigger: 73; Removal trigger: 133 292843 initial stacks were populated; 2417663 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 12664 stacks. 280855 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 10.3774; Std Dev: 119.584; Max: 133 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 280855 stacks merged into 198058 stacks; deleveraged 6235 stacks; removed 7127 stacks. After merging, coverage depth Mean: 12.344; Std Dev: 146.874; Max: 219 Merging remainder radtags 2640601 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1633448 remainder reads; unable to match 1007153 remainder reads. After remainders merged, coverage depth Mean: 20.9296; Std Dev: 147.491; Max: 956 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 5159885 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_8A.fq.gz... read 6167038 sequence IDs. done. ustacks paramters selected: Min depth of coverage to create a stack: 3 Max distance allowed between stacks: 2 Max distance allowed to align secondary reads: 4 Max number of stacks allowed per de novo locus: 3 Deleveraging algorithm: enabled Removal algorithm: enabled Model type: SNP Alpha significance level for model: 0.05 Gapped alignments: disabled Parsing 1SN_9A.fq.gz Loaded 5992443 RAD-Tags; inserted 2719633 elements into the RAD-Tags hash map. 0 reads contained uncalled nucleotides that were modified. Initial coverage mean: 11.4554; Std Dev: 43.8638; Max: 11798 Deleveraging trigger: 55; Removal trigger: 99 291522 initial stacks were populated; 2428111 stacks were set aside as secondary reads. Calculating distance for removing repetitive stacks. Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. Removing repetitive stacks. Removed 14699 stacks. 277787 stacks remain for merging. Post-Repeat Removal, coverage depth Mean: 9.91986; Std Dev: 95.3963; Max: 99 Calculating distance between stacks... Distance allowed between stacks: 2; searching with a k-mer length of 29 (62 k-mers per read); 4 k-mer hits required. Merging stacks, maximum allowed distance: 2 nucleotide(s) 277787 stacks merged into 199962 stacks; deleveraged 6025 stacks; removed 6522 stacks. After merging, coverage depth Mean: 11.8253; Std Dev: 115.756; Max: 165 Merging remainder radtags 2652946 remainder sequences left to merge. Distance allowed between stacks: 4; searching with a k-mer length of 17 (74 k-mers per read); 6 k-mer hits required. Matched 1570596 remainder reads; unable to match 1082350 remainder reads. After remainders merged, coverage depth Mean: 19.9852; Std Dev: 116.475; Max: 473 Calling final consensus sequences, invoking SNP-calling model... Number of utilized reads: 4910093 Writing loci, SNPs, and alleles to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/'... Refetching sequencing IDs from 1SN_9A.fq.gz... read 5992443 sequence IDs. done. real 5687m16.066s user 5627m5.287s sys 55m54.666s
%%bash
#Uses printf statement to print just the first part of each filename, without the extension, and ads a "-s" and a " \"
#to each line for use in the subsequent cstacks command.
for fname in /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/*; do printf " %s\n" "-s ${fname%%.*} \\" >> tmp.txt; done
cat tmp.txt | uniq
rm tmp.txt
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A \ -s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A \
cd /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/
/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks
%%bash
#cstacks command.
time /usr/local/bioinformatics/stacks-1.40/cstacks \
-b 1 \
-o /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/ \
-p 16 \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A
Number of mismatches allowed between stacks: 1 Loci matched based on sequence identity. Constructing catalog from 96 samples. Initializing new catalog... Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A.alleles.tsv.gz 183160 loci were newly added to the catalog. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A [2 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 183160 loci in the catalog, 8110358 kmers in the catalog hash. Merging matches into catalog... 104767 loci were matched to a catalog locus. 1920 loci were matched to a catalog locus using gapped alignments. 92963 loci were newly added to the catalog. 1165 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A [3 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 276123 loci in the catalog, 12198042 kmers in the catalog hash. Merging matches into catalog... 105732 loci were matched to a catalog locus. 1670 loci were matched to a catalog locus using gapped alignments. 60766 loci were newly added to the catalog. 1940 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A [4 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 336889 loci in the catalog, 14971112 kmers in the catalog hash. Merging matches into catalog... 114432 loci were matched to a catalog locus. 2030 loci were matched to a catalog locus using gapped alignments. 42467 loci were newly added to the catalog. 2544 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A [5 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 379356 loci in the catalog, 16860233 kmers in the catalog hash. Merging matches into catalog... 104564 loci were matched to a catalog locus. 1601 loci were matched to a catalog locus using gapped alignments. 27581 loci were newly added to the catalog. 2523 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A [6 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 406937 loci in the catalog, 18086563 kmers in the catalog hash. Merging matches into catalog... 112519 loci were matched to a catalog locus. 1974 loci were matched to a catalog locus using gapped alignments. 28316 loci were newly added to the catalog. 2996 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A [7 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 435253 loci in the catalog, 19362608 kmers in the catalog hash. Merging matches into catalog... 122195 loci were matched to a catalog locus. 2135 loci were matched to a catalog locus using gapped alignments. 22975 loci were newly added to the catalog. 3062 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A [8 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 458228 loci in the catalog, 20360343 kmers in the catalog hash. Merging matches into catalog... 150003 loci were matched to a catalog locus. 3558 loci were matched to a catalog locus using gapped alignments. 34680 loci were newly added to the catalog. 3864 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A [9 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 492908 loci in the catalog, 21801899 kmers in the catalog hash. Merging matches into catalog... 157042 loci were matched to a catalog locus. 3886 loci were matched to a catalog locus using gapped alignments. 29567 loci were newly added to the catalog. 4087 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A [10 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 522475 loci in the catalog, 23014660 kmers in the catalog hash. Merging matches into catalog... 130965 loci were matched to a catalog locus. 2334 loci were matched to a catalog locus using gapped alignments. 12093 loci were newly added to the catalog. 3762 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A [11 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 534568 loci in the catalog, 23550938 kmers in the catalog hash. Merging matches into catalog... 133591 loci were matched to a catalog locus. 3001 loci were matched to a catalog locus using gapped alignments. 25537 loci were newly added to the catalog. 3818 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A [12 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 560105 loci in the catalog, 24630028 kmers in the catalog hash. Merging matches into catalog... 139118 loci were matched to a catalog locus. 2306 loci were matched to a catalog locus using gapped alignments. 14665 loci were newly added to the catalog. 3650 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A [13 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 574770 loci in the catalog, 25286839 kmers in the catalog hash. Merging matches into catalog... 119357 loci were matched to a catalog locus. 1986 loci were matched to a catalog locus using gapped alignments. 18370 loci were newly added to the catalog. 3384 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A [14 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 593140 loci in the catalog, 26119335 kmers in the catalog hash. Merging matches into catalog... 166710 loci were matched to a catalog locus. 4128 loci were matched to a catalog locus using gapped alignments. 20605 loci were newly added to the catalog. 4709 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A [15 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 613745 loci in the catalog, 26949235 kmers in the catalog hash. Merging matches into catalog... 134109 loci were matched to a catalog locus. 2872 loci were matched to a catalog locus using gapped alignments. 19874 loci were newly added to the catalog. 3992 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A [16 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 633619 loci in the catalog, 27790155 kmers in the catalog hash. Merging matches into catalog... 153315 loci were matched to a catalog locus. 3495 loci were matched to a catalog locus using gapped alignments. 13258 loci were newly added to the catalog. 4526 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A [17 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 646877 loci in the catalog, 28313360 kmers in the catalog hash. Merging matches into catalog... 159952 loci were matched to a catalog locus. 3537 loci were matched to a catalog locus using gapped alignments. 13982 loci were newly added to the catalog. 4425 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A [18 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 660859 loci in the catalog, 28867400 kmers in the catalog hash. Merging matches into catalog... 168249 loci were matched to a catalog locus. 3997 loci were matched to a catalog locus using gapped alignments. 13093 loci were newly added to the catalog. 5130 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A [19 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 673952 loci in the catalog, 29398942 kmers in the catalog hash. Merging matches into catalog... 172176 loci were matched to a catalog locus. 3040 loci were matched to a catalog locus using gapped alignments. 69769 loci were newly added to the catalog. 3599 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A [20 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 743721 loci in the catalog, 30454647 kmers in the catalog hash. Merging matches into catalog... 148578 loci were matched to a catalog locus. 3514 loci were matched to a catalog locus using gapped alignments. 20680 loci were newly added to the catalog. 4649 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A [21 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 764401 loci in the catalog, 31346732 kmers in the catalog hash. Merging matches into catalog... 141105 loci were matched to a catalog locus. 3014 loci were matched to a catalog locus using gapped alignments. 16598 loci were newly added to the catalog. 4427 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A [22 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 780999 loci in the catalog, 32061535 kmers in the catalog hash. Merging matches into catalog... 143352 loci were matched to a catalog locus. 2868 loci were matched to a catalog locus using gapped alignments. 7799 loci were newly added to the catalog. 4320 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A [23 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 788798 loci in the catalog, 32382361 kmers in the catalog hash. Merging matches into catalog... 146883 loci were matched to a catalog locus. 2809 loci were matched to a catalog locus using gapped alignments. 9380 loci were newly added to the catalog. 4296 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A [24 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 798178 loci in the catalog, 32759738 kmers in the catalog hash. Merging matches into catalog... 155078 loci were matched to a catalog locus. 3415 loci were matched to a catalog locus using gapped alignments. 10175 loci were newly added to the catalog. 4932 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A [25 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 808353 loci in the catalog, 33175470 kmers in the catalog hash. Merging matches into catalog... 153536 loci were matched to a catalog locus. 3254 loci were matched to a catalog locus using gapped alignments. 7917 loci were newly added to the catalog. 4674 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A [26 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 816270 loci in the catalog, 33510090 kmers in the catalog hash. Merging matches into catalog... 137936 loci were matched to a catalog locus. 2407 loci were matched to a catalog locus using gapped alignments. 7537 loci were newly added to the catalog. 3907 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A [27 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 823807 loci in the catalog, 33828932 kmers in the catalog hash. Merging matches into catalog... 140764 loci were matched to a catalog locus. 2985 loci were matched to a catalog locus using gapped alignments. 14130 loci were newly added to the catalog. 4356 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A [28 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 837937 loci in the catalog, 34457967 kmers in the catalog hash. Merging matches into catalog... 122087 loci were matched to a catalog locus. 2133 loci were matched to a catalog locus using gapped alignments. 10821 loci were newly added to the catalog. 3657 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A [29 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 848758 loci in the catalog, 34961553 kmers in the catalog hash. Merging matches into catalog... 129697 loci were matched to a catalog locus. 2382 loci were matched to a catalog locus using gapped alignments. 5572 loci were newly added to the catalog. 4095 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A [30 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 854330 loci in the catalog, 35183852 kmers in the catalog hash. Merging matches into catalog... 170299 loci were matched to a catalog locus. 4061 loci were matched to a catalog locus using gapped alignments. 55287 loci were newly added to the catalog. 4525 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A [31 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 909617 loci in the catalog, 36191260 kmers in the catalog hash. Merging matches into catalog... 136484 loci were matched to a catalog locus. 2909 loci were matched to a catalog locus using gapped alignments. 10740 loci were newly added to the catalog. 4515 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A [32 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 920357 loci in the catalog, 36653013 kmers in the catalog hash. Merging matches into catalog... 151544 loci were matched to a catalog locus. 3363 loci were matched to a catalog locus using gapped alignments. 8733 loci were newly added to the catalog. 4494 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A [33 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 929090 loci in the catalog, 37001558 kmers in the catalog hash. Merging matches into catalog... 122531 loci were matched to a catalog locus. 2279 loci were matched to a catalog locus using gapped alignments. 9993 loci were newly added to the catalog. 3893 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A [34 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 939083 loci in the catalog, 37471326 kmers in the catalog hash. Merging matches into catalog... 126920 loci were matched to a catalog locus. 2531 loci were matched to a catalog locus using gapped alignments. 9983 loci were newly added to the catalog. 4072 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A [35 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 949066 loci in the catalog, 37933610 kmers in the catalog hash. Merging matches into catalog... 124403 loci were matched to a catalog locus. 2594 loci were matched to a catalog locus using gapped alignments. 8261 loci were newly added to the catalog. 3969 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A [36 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 957327 loci in the catalog, 38312906 kmers in the catalog hash. Merging matches into catalog... 180145 loci were matched to a catalog locus. 4955 loci were matched to a catalog locus using gapped alignments. 21140 loci were newly added to the catalog. 5949 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A [37 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 978467 loci in the catalog, 39266559 kmers in the catalog hash. Merging matches into catalog... 142499 loci were matched to a catalog locus. 3086 loci were matched to a catalog locus using gapped alignments. 11472 loci were newly added to the catalog. 4567 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A [38 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 989939 loci in the catalog, 39781739 kmers in the catalog hash. Merging matches into catalog... 140418 loci were matched to a catalog locus. 3066 loci were matched to a catalog locus using gapped alignments. 9934 loci were newly added to the catalog. 4249 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A [39 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 999873 loci in the catalog, 40227318 kmers in the catalog hash. Merging matches into catalog... 145386 loci were matched to a catalog locus. 3178 loci were matched to a catalog locus using gapped alignments. 11836 loci were newly added to the catalog. 4712 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A [40 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1011709 loci in the catalog, 40768532 kmers in the catalog hash. Merging matches into catalog... 157801 loci were matched to a catalog locus. 4018 loci were matched to a catalog locus using gapped alignments. 13522 loci were newly added to the catalog. 5228 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A [41 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1025231 loci in the catalog, 41369702 kmers in the catalog hash. Merging matches into catalog... 113649 loci were matched to a catalog locus. 1942 loci were matched to a catalog locus using gapped alignments. 7197 loci were newly added to the catalog. 3757 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A [42 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1032428 loci in the catalog, 41703211 kmers in the catalog hash. Merging matches into catalog... 117852 loci were matched to a catalog locus. 2256 loci were matched to a catalog locus using gapped alignments. 5995 loci were newly added to the catalog. 3775 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A [43 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1038423 loci in the catalog, 41974645 kmers in the catalog hash. Merging matches into catalog... 93290 loci were matched to a catalog locus. 1397 loci were matched to a catalog locus using gapped alignments. 2381 loci were newly added to the catalog. 3076 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A [44 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1040804 loci in the catalog, 42097979 kmers in the catalog hash. Merging matches into catalog... 139929 loci were matched to a catalog locus. 3082 loci were matched to a catalog locus using gapped alignments. 8321 loci were newly added to the catalog. 4513 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A [45 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1049125 loci in the catalog, 42480411 kmers in the catalog hash. Merging matches into catalog... 161973 loci were matched to a catalog locus. 4213 loci were matched to a catalog locus using gapped alignments. 21986 loci were newly added to the catalog. 5227 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A [46 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1071111 loci in the catalog, 43514289 kmers in the catalog hash. Merging matches into catalog... 150967 loci were matched to a catalog locus. 3714 loci were matched to a catalog locus using gapped alignments. 10885 loci were newly added to the catalog. 4952 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A [47 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1081996 loci in the catalog, 44005193 kmers in the catalog hash. Merging matches into catalog... 168044 loci were matched to a catalog locus. 4230 loci were matched to a catalog locus using gapped alignments. 13881 loci were newly added to the catalog. 5367 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A [48 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1095877 loci in the catalog, 44619247 kmers in the catalog hash. Merging matches into catalog... 158547 loci were matched to a catalog locus. 3891 loci were matched to a catalog locus using gapped alignments. 11713 loci were newly added to the catalog. 5102 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A [49 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1107590 loci in the catalog, 45148968 kmers in the catalog hash. Merging matches into catalog... 130501 loci were matched to a catalog locus. 2764 loci were matched to a catalog locus using gapped alignments. 5144 loci were newly added to the catalog. 4337 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A [50 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1112734 loci in the catalog, 45388350 kmers in the catalog hash. Merging matches into catalog... 162717 loci were matched to a catalog locus. 4143 loci were matched to a catalog locus using gapped alignments. 9781 loci were newly added to the catalog. 5397 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A [51 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1122515 loci in the catalog, 45838173 kmers in the catalog hash. Merging matches into catalog... 135980 loci were matched to a catalog locus. 2514 loci were matched to a catalog locus using gapped alignments. 6135 loci were newly added to the catalog. 4275 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A [52 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1128650 loci in the catalog, 46131694 kmers in the catalog hash. Merging matches into catalog... 138293 loci were matched to a catalog locus. 2816 loci were matched to a catalog locus using gapped alignments. 6326 loci were newly added to the catalog. 4490 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A [53 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1134976 loci in the catalog, 46427547 kmers in the catalog hash. Merging matches into catalog... 168267 loci were matched to a catalog locus. 5120 loci were matched to a catalog locus using gapped alignments. 10695 loci were newly added to the catalog. 6158 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A [54 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1145671 loci in the catalog, 46882780 kmers in the catalog hash. Merging matches into catalog... 166885 loci were matched to a catalog locus. 4425 loci were matched to a catalog locus using gapped alignments. 10863 loci were newly added to the catalog. 5482 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A [55 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1156534 loci in the catalog, 47367943 kmers in the catalog hash. Merging matches into catalog... 146605 loci were matched to a catalog locus. 3450 loci were matched to a catalog locus using gapped alignments. 5613 loci were newly added to the catalog. 4809 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A [56 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1162147 loci in the catalog, 47612108 kmers in the catalog hash. Merging matches into catalog... 174655 loci were matched to a catalog locus. 4962 loci were matched to a catalog locus using gapped alignments. 10345 loci were newly added to the catalog. 5979 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A [57 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1172492 loci in the catalog, 48049440 kmers in the catalog hash. Merging matches into catalog... 179396 loci were matched to a catalog locus. 4922 loci were matched to a catalog locus using gapped alignments. 10120 loci were newly added to the catalog. 5871 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A [58 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1182612 loci in the catalog, 48495086 kmers in the catalog hash. Merging matches into catalog... 147076 loci were matched to a catalog locus. 3288 loci were matched to a catalog locus using gapped alignments. 5840 loci were newly added to the catalog. 4758 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A [59 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1188452 loci in the catalog, 48761950 kmers in the catalog hash. Merging matches into catalog... 180719 loci were matched to a catalog locus. 5206 loci were matched to a catalog locus using gapped alignments. 9030 loci were newly added to the catalog. 5950 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A [60 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1197482 loci in the catalog, 49163909 kmers in the catalog hash. Merging matches into catalog... 156394 loci were matched to a catalog locus. 3502 loci were matched to a catalog locus using gapped alignments. 7189 loci were newly added to the catalog. 5022 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A [61 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1204671 loci in the catalog, 49501494 kmers in the catalog hash. Merging matches into catalog... 141262 loci were matched to a catalog locus. 2738 loci were matched to a catalog locus using gapped alignments. 4166 loci were newly added to the catalog. 4402 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A [62 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1208837 loci in the catalog, 49691904 kmers in the catalog hash. Merging matches into catalog... 143824 loci were matched to a catalog locus. 3366 loci were matched to a catalog locus using gapped alignments. 6312 loci were newly added to the catalog. 4795 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A [63 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1215149 loci in the catalog, 49987240 kmers in the catalog hash. Merging matches into catalog... 149431 loci were matched to a catalog locus. 3481 loci were matched to a catalog locus using gapped alignments. 7529 loci were newly added to the catalog. 4872 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A [64 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1222678 loci in the catalog, 50322455 kmers in the catalog hash. Merging matches into catalog... 167112 loci were matched to a catalog locus. 4449 loci were matched to a catalog locus using gapped alignments. 9174 loci were newly added to the catalog. 5657 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A [65 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1231852 loci in the catalog, 50732054 kmers in the catalog hash. Merging matches into catalog... 145884 loci were matched to a catalog locus. 3164 loci were matched to a catalog locus using gapped alignments. 8718 loci were newly added to the catalog. 4607 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A [66 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1240570 loci in the catalog, 51124069 kmers in the catalog hash. Merging matches into catalog... 147279 loci were matched to a catalog locus. 3160 loci were matched to a catalog locus using gapped alignments. 6894 loci were newly added to the catalog. 5065 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A [67 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1247464 loci in the catalog, 51442197 kmers in the catalog hash. Merging matches into catalog... 180500 loci were matched to a catalog locus. 4985 loci were matched to a catalog locus using gapped alignments. 11519 loci were newly added to the catalog. 6021 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A [68 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1258983 loci in the catalog, 51944010 kmers in the catalog hash. Merging matches into catalog... 161533 loci were matched to a catalog locus. 3745 loci were matched to a catalog locus using gapped alignments. 9067 loci were newly added to the catalog. 5216 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A [69 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1268050 loci in the catalog, 52364892 kmers in the catalog hash. Merging matches into catalog... 173631 loci were matched to a catalog locus. 4829 loci were matched to a catalog locus using gapped alignments. 9779 loci were newly added to the catalog. 6056 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A [70 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1277829 loci in the catalog, 52782712 kmers in the catalog hash. Merging matches into catalog... 144860 loci were matched to a catalog locus. 3201 loci were matched to a catalog locus using gapped alignments. 5758 loci were newly added to the catalog. 4607 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A [71 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1283587 loci in the catalog, 53032378 kmers in the catalog hash. Merging matches into catalog... 144771 loci were matched to a catalog locus. 3234 loci were matched to a catalog locus using gapped alignments. 6509 loci were newly added to the catalog. 5154 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A [72 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1290096 loci in the catalog, 53312634 kmers in the catalog hash. Merging matches into catalog... 165406 loci were matched to a catalog locus. 4129 loci were matched to a catalog locus using gapped alignments. 8041 loci were newly added to the catalog. 5346 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A [73 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1298137 loci in the catalog, 53662757 kmers in the catalog hash. Merging matches into catalog... 166197 loci were matched to a catalog locus. 4242 loci were matched to a catalog locus using gapped alignments. 9113 loci were newly added to the catalog. 5581 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A [74 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1307250 loci in the catalog, 54036847 kmers in the catalog hash. Merging matches into catalog... 165152 loci were matched to a catalog locus. 4052 loci were matched to a catalog locus using gapped alignments. 7876 loci were newly added to the catalog. 5460 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A [75 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1315126 loci in the catalog, 54384733 kmers in the catalog hash. Merging matches into catalog... 156453 loci were matched to a catalog locus. 3968 loci were matched to a catalog locus using gapped alignments. 6171 loci were newly added to the catalog. 5339 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A [76 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1321297 loci in the catalog, 54658761 kmers in the catalog hash. Merging matches into catalog... 127265 loci were matched to a catalog locus. 2518 loci were matched to a catalog locus using gapped alignments. 6419 loci were newly added to the catalog. 4253 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A [77 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1327716 loci in the catalog, 54953438 kmers in the catalog hash. Merging matches into catalog... 178663 loci were matched to a catalog locus. 5150 loci were matched to a catalog locus using gapped alignments. 10472 loci were newly added to the catalog. 6205 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A [78 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1338188 loci in the catalog, 55401038 kmers in the catalog hash. Merging matches into catalog... 164476 loci were matched to a catalog locus. 4039 loci were matched to a catalog locus using gapped alignments. 7603 loci were newly added to the catalog. 5764 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A [79 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1345791 loci in the catalog, 55735476 kmers in the catalog hash. Merging matches into catalog... 185852 loci were matched to a catalog locus. 5689 loci were matched to a catalog locus using gapped alignments. 10971 loci were newly added to the catalog. 6375 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A [80 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1356762 loci in the catalog, 56203922 kmers in the catalog hash. Merging matches into catalog... 119609 loci were matched to a catalog locus. 2098 loci were matched to a catalog locus using gapped alignments. 3898 loci were newly added to the catalog. 3757 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A [81 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1360660 loci in the catalog, 56368517 kmers in the catalog hash. Merging matches into catalog... 159202 loci were matched to a catalog locus. 3940 loci were matched to a catalog locus using gapped alignments. 7393 loci were newly added to the catalog. 5336 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A [82 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1368053 loci in the catalog, 56678447 kmers in the catalog hash. Merging matches into catalog... 155327 loci were matched to a catalog locus. 3757 loci were matched to a catalog locus using gapped alignments. 5498 loci were newly added to the catalog. 5128 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A [83 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1373551 loci in the catalog, 56889919 kmers in the catalog hash. Merging matches into catalog... 146202 loci were matched to a catalog locus. 3132 loci were matched to a catalog locus using gapped alignments. 5530 loci were newly added to the catalog. 4958 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A [84 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1379081 loci in the catalog, 57114237 kmers in the catalog hash. Merging matches into catalog... 154046 loci were matched to a catalog locus. 3586 loci were matched to a catalog locus using gapped alignments. 6935 loci were newly added to the catalog. 5061 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A [85 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1386016 loci in the catalog, 57398744 kmers in the catalog hash. Merging matches into catalog... 116402 loci were matched to a catalog locus. 2724 loci were matched to a catalog locus using gapped alignments. 7654 loci were newly added to the catalog. 4167 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A [86 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1393670 loci in the catalog, 57712433 kmers in the catalog hash. Merging matches into catalog... 162404 loci were matched to a catalog locus. 4017 loci were matched to a catalog locus using gapped alignments. 6502 loci were newly added to the catalog. 5515 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A [87 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1400172 loci in the catalog, 57990740 kmers in the catalog hash. Merging matches into catalog... 189111 loci were matched to a catalog locus. 5784 loci were matched to a catalog locus using gapped alignments. 10147 loci were newly added to the catalog. 6410 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A [88 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1410319 loci in the catalog, 58394530 kmers in the catalog hash. Merging matches into catalog... 168640 loci were matched to a catalog locus. 4395 loci were matched to a catalog locus using gapped alignments. 7295 loci were newly added to the catalog. 5835 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A [89 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1417614 loci in the catalog, 58679011 kmers in the catalog hash. Merging matches into catalog... 142712 loci were matched to a catalog locus. 3169 loci were matched to a catalog locus using gapped alignments. 6733 loci were newly added to the catalog. 4665 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A [90 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1424347 loci in the catalog, 58966864 kmers in the catalog hash. Merging matches into catalog... 143387 loci were matched to a catalog locus. 2875 loci were matched to a catalog locus using gapped alignments. 9673 loci were newly added to the catalog. 4429 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A [91 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1434020 loci in the catalog, 59413308 kmers in the catalog hash. Merging matches into catalog... 177652 loci were matched to a catalog locus. 4934 loci were matched to a catalog locus using gapped alignments. 6430 loci were newly added to the catalog. 5946 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A [92 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1440450 loci in the catalog, 59676746 kmers in the catalog hash. Merging matches into catalog... 171208 loci were matched to a catalog locus. 4199 loci were matched to a catalog locus using gapped alignments. 6895 loci were newly added to the catalog. 5681 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A [93 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1447345 loci in the catalog, 59976029 kmers in the catalog hash. Merging matches into catalog... 172530 loci were matched to a catalog locus. 4752 loci were matched to a catalog locus using gapped alignments. 7801 loci were newly added to the catalog. 5951 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A [94 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1455146 loci in the catalog, 60300566 kmers in the catalog hash. Merging matches into catalog... 163373 loci were matched to a catalog locus. 4111 loci were matched to a catalog locus using gapped alignments. 6957 loci were newly added to the catalog. 5375 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A [95 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1462103 loci in the catalog, 60600774 kmers in the catalog hash. Merging matches into catalog... 173497 loci were matched to a catalog locus. 4564 loci were matched to a catalog locus using gapped alignments. 6564 loci were newly added to the catalog. 5630 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A [96 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1468667 loci in the catalog, 60878194 kmers in the catalog hash. Merging matches into catalog... 174474 loci were matched to a catalog locus. 4913 loci were matched to a catalog locus using gapped alignments. 7226 loci were newly added to the catalog. 5863 loci matched more than one catalog locus and were excluded. Writing catalog to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/... done. real 1509m6.170s user 1485m47.201s sys 22m22.721s
ls /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/
1HL_10A.alleles.tsv.gz 1HL_26A.models.tsv.gz 1NF_10A.snps.tsv.gz 1NF_25A.tags.tsv.gz 1SN_11A.alleles.tsv.gz 1SN_26A.models.tsv.gz 1HL_10A.models.tsv.gz 1HL_26A.snps.tsv.gz 1NF_10A.tags.tsv.gz 1NF_26A.alleles.tsv.gz 1SN_11A.models.tsv.gz 1SN_26A.snps.tsv.gz 1HL_10A.snps.tsv.gz 1HL_26A.tags.tsv.gz 1NF_11A.alleles.tsv.gz 1NF_26A.models.tsv.gz 1SN_11A.snps.tsv.gz 1SN_26A.tags.tsv.gz 1HL_10A.tags.tsv.gz 1HL_27A.alleles.tsv.gz 1NF_11A.models.tsv.gz 1NF_26A.snps.tsv.gz 1SN_11A.tags.tsv.gz 1SN_27A.alleles.tsv.gz 1HL_11A.alleles.tsv.gz 1HL_27A.models.tsv.gz 1NF_11A.snps.tsv.gz 1NF_26A.tags.tsv.gz 1SN_12A.alleles.tsv.gz 1SN_27A.models.tsv.gz 1HL_11A.models.tsv.gz 1HL_27A.snps.tsv.gz 1NF_11A.tags.tsv.gz 1NF_27A.alleles.tsv.gz 1SN_12A.models.tsv.gz 1SN_27A.snps.tsv.gz 1HL_11A.snps.tsv.gz 1HL_27A.tags.tsv.gz 1NF_12A.alleles.tsv.gz 1NF_27A.models.tsv.gz 1SN_12A.snps.tsv.gz 1SN_27A.tags.tsv.gz 1HL_11A.tags.tsv.gz 1HL_28A.alleles.tsv.gz 1NF_12A.models.tsv.gz 1NF_27A.snps.tsv.gz 1SN_12A.tags.tsv.gz 1SN_28A.alleles.tsv.gz 1HL_12A.alleles.tsv.gz 1HL_28A.models.tsv.gz 1NF_12A.snps.tsv.gz 1NF_27A.tags.tsv.gz 1SN_13A.alleles.tsv.gz 1SN_28A.models.tsv.gz 1HL_12A.models.tsv.gz 1HL_28A.snps.tsv.gz 1NF_12A.tags.tsv.gz 1NF_28A.alleles.tsv.gz 1SN_13A.models.tsv.gz 1SN_28A.snps.tsv.gz 1HL_12A.snps.tsv.gz 1HL_28A.tags.tsv.gz 1NF_13A.alleles.tsv.gz 1NF_28A.models.tsv.gz 1SN_13A.snps.tsv.gz 1SN_28A.tags.tsv.gz 1HL_12A.tags.tsv.gz 1HL_29A.alleles.tsv.gz 1NF_13A.models.tsv.gz 1NF_28A.snps.tsv.gz 1SN_13A.tags.tsv.gz 1SN_29A.alleles.tsv.gz 1HL_13A.alleles.tsv.gz 1HL_29A.models.tsv.gz 1NF_13A.snps.tsv.gz 1NF_28A.tags.tsv.gz 1SN_14A.alleles.tsv.gz 1SN_29A.models.tsv.gz 1HL_13A.models.tsv.gz 1HL_29A.snps.tsv.gz 1NF_13A.tags.tsv.gz 1NF_29A.alleles.tsv.gz 1SN_14A.models.tsv.gz 1SN_29A.snps.tsv.gz 1HL_13A.snps.tsv.gz 1HL_29A.tags.tsv.gz 1NF_14A.alleles.tsv.gz 1NF_29A.models.tsv.gz 1SN_14A.snps.tsv.gz 1SN_29A.tags.tsv.gz 1HL_13A.tags.tsv.gz 1HL_2A.alleles.tsv.gz 1NF_14A.models.tsv.gz 1NF_29A.snps.tsv.gz 1SN_14A.tags.tsv.gz 1SN_2A.alleles.tsv.gz 1HL_14A.alleles.tsv.gz 1HL_2A.models.tsv.gz 1NF_14A.snps.tsv.gz 1NF_29A.tags.tsv.gz 1SN_15A.alleles.tsv.gz 1SN_2A.models.tsv.gz 1HL_14A.models.tsv.gz 1HL_2A.snps.tsv.gz 1NF_14A.tags.tsv.gz 1NF_2A.alleles.tsv.gz 1SN_15A.models.tsv.gz 1SN_2A.snps.tsv.gz 1HL_14A.snps.tsv.gz 1HL_2A.tags.tsv.gz 1NF_15A.alleles.tsv.gz 1NF_2A.models.tsv.gz 1SN_15A.snps.tsv.gz 1SN_2A.tags.tsv.gz 1HL_14A.tags.tsv.gz 1HL_31A.alleles.tsv.gz 1NF_15A.models.tsv.gz 1NF_2A.snps.tsv.gz 1SN_15A.tags.tsv.gz 1SN_30A.alleles.tsv.gz 1HL_15A.alleles.tsv.gz 1HL_31A.models.tsv.gz 1NF_15A.snps.tsv.gz 1NF_2A.tags.tsv.gz 1SN_16A.alleles.tsv.gz 1SN_30A.models.tsv.gz 1HL_15A.models.tsv.gz 1HL_31A.snps.tsv.gz 1NF_15A.tags.tsv.gz 1NF_30A.alleles.tsv.gz 1SN_16A.models.tsv.gz 1SN_30A.snps.tsv.gz 1HL_15A.snps.tsv.gz 1HL_31A.tags.tsv.gz 1NF_16A.alleles.tsv.gz 1NF_30A.models.tsv.gz 1SN_16A.snps.tsv.gz 1SN_30A.tags.tsv.gz 1HL_15A.tags.tsv.gz 1HL_33A.alleles.tsv.gz 1NF_16A.models.tsv.gz 1NF_30A.snps.tsv.gz 1SN_16A.tags.tsv.gz 1SN_31A.alleles.tsv.gz 1HL_16A.alleles.tsv.gz 1HL_33A.models.tsv.gz 1NF_16A.snps.tsv.gz 1NF_30A.tags.tsv.gz 1SN_17A.alleles.tsv.gz 1SN_31A.models.tsv.gz 1HL_16A.models.tsv.gz 1HL_33A.snps.tsv.gz 1NF_16A.tags.tsv.gz 1NF_31A.alleles.tsv.gz 1SN_17A.models.tsv.gz 1SN_31A.snps.tsv.gz 1HL_16A.snps.tsv.gz 1HL_33A.tags.tsv.gz 1NF_17A.alleles.tsv.gz 1NF_31A.models.tsv.gz 1SN_17A.snps.tsv.gz 1SN_31A.tags.tsv.gz 1HL_16A.tags.tsv.gz 1HL_34A.alleles.tsv.gz 1NF_17A.models.tsv.gz 1NF_31A.snps.tsv.gz 1SN_17A.tags.tsv.gz 1SN_32A.alleles.tsv.gz 1HL_17A.alleles.tsv.gz 1HL_34A.models.tsv.gz 1NF_17A.snps.tsv.gz 1NF_31A.tags.tsv.gz 1SN_18A.alleles.tsv.gz 1SN_32A.models.tsv.gz 1HL_17A.models.tsv.gz 1HL_34A.snps.tsv.gz 1NF_17A.tags.tsv.gz 1NF_32A.alleles.tsv.gz 1SN_18A.models.tsv.gz 1SN_32A.snps.tsv.gz 1HL_17A.snps.tsv.gz 1HL_34A.tags.tsv.gz 1NF_18A.alleles.tsv.gz 1NF_32A.models.tsv.gz 1SN_18A.snps.tsv.gz 1SN_32A.tags.tsv.gz 1HL_17A.tags.tsv.gz 1HL_35A.alleles.tsv.gz 1NF_18A.models.tsv.gz 1NF_32A.snps.tsv.gz 1SN_18A.tags.tsv.gz 1SN_3A.alleles.tsv.gz 1HL_19A.alleles.tsv.gz 1HL_35A.models.tsv.gz 1NF_18A.snps.tsv.gz 1NF_32A.tags.tsv.gz 1SN_19A.alleles.tsv.gz 1SN_3A.models.tsv.gz 1HL_19A.models.tsv.gz 1HL_35A.snps.tsv.gz 1NF_18A.tags.tsv.gz 1NF_33A.alleles.tsv.gz 1SN_19A.models.tsv.gz 1SN_3A.snps.tsv.gz 1HL_19A.snps.tsv.gz 1HL_35A.tags.tsv.gz 1NF_19A.alleles.tsv.gz 1NF_33A.models.tsv.gz 1SN_19A.snps.tsv.gz 1SN_3A.tags.tsv.gz 1HL_19A.tags.tsv.gz 1HL_3A.alleles.tsv.gz 1NF_19A.models.tsv.gz 1NF_33A.snps.tsv.gz 1SN_19A.tags.tsv.gz 1SN_4A.alleles.tsv.gz 1HL_1A.alleles.tsv.gz 1HL_3A.models.tsv.gz 1NF_19A.snps.tsv.gz 1NF_33A.tags.tsv.gz 1SN_1A.alleles.tsv.gz 1SN_4A.models.tsv.gz 1HL_1A.models.tsv.gz 1HL_3A.snps.tsv.gz 1NF_19A.tags.tsv.gz 1NF_4A.alleles.tsv.gz 1SN_1A.models.tsv.gz 1SN_4A.snps.tsv.gz 1HL_1A.snps.tsv.gz 1HL_3A.tags.tsv.gz 1NF_1A.alleles.tsv.gz 1NF_4A.models.tsv.gz 1SN_1A.snps.tsv.gz 1SN_4A.tags.tsv.gz 1HL_1A.tags.tsv.gz 1HL_4A.alleles.tsv.gz 1NF_1A.models.tsv.gz 1NF_4A.snps.tsv.gz 1SN_1A.tags.tsv.gz 1SN_5A.alleles.tsv.gz 1HL_20A.alleles.tsv.gz 1HL_4A.models.tsv.gz 1NF_1A.snps.tsv.gz 1NF_4A.tags.tsv.gz 1SN_20A.alleles.tsv.gz 1SN_5A.models.tsv.gz 1HL_20A.models.tsv.gz 1HL_4A.snps.tsv.gz 1NF_1A.tags.tsv.gz 1NF_5A.alleles.tsv.gz 1SN_20A.models.tsv.gz 1SN_5A.snps.tsv.gz 1HL_20A.snps.tsv.gz 1HL_4A.tags.tsv.gz 1NF_20A.alleles.tsv.gz 1NF_5A.models.tsv.gz 1SN_20A.snps.tsv.gz 1SN_5A.tags.tsv.gz 1HL_20A.tags.tsv.gz 1HL_5A.alleles.tsv.gz 1NF_20A.models.tsv.gz 1NF_5A.snps.tsv.gz 1SN_20A.tags.tsv.gz 1SN_6A.alleles.tsv.gz 1HL_21A.alleles.tsv.gz 1HL_5A.models.tsv.gz 1NF_20A.snps.tsv.gz 1NF_5A.tags.tsv.gz 1SN_21A.alleles.tsv.gz 1SN_6A.models.tsv.gz 1HL_21A.models.tsv.gz 1HL_5A.snps.tsv.gz 1NF_20A.tags.tsv.gz 1NF_6A.alleles.tsv.gz 1SN_21A.models.tsv.gz 1SN_6A.snps.tsv.gz 1HL_21A.snps.tsv.gz 1HL_5A.tags.tsv.gz 1NF_21A.alleles.tsv.gz 1NF_6A.models.tsv.gz 1SN_21A.snps.tsv.gz 1SN_6A.tags.tsv.gz 1HL_21A.tags.tsv.gz 1HL_6A.alleles.tsv.gz 1NF_21A.models.tsv.gz 1NF_6A.snps.tsv.gz 1SN_21A.tags.tsv.gz 1SN_7A.alleles.tsv.gz 1HL_22A.alleles.tsv.gz 1HL_6A.models.tsv.gz 1NF_21A.snps.tsv.gz 1NF_6A.tags.tsv.gz 1SN_22A.alleles.tsv.gz 1SN_7A.models.tsv.gz 1HL_22A.models.tsv.gz 1HL_6A.snps.tsv.gz 1NF_21A.tags.tsv.gz 1NF_7A.alleles.tsv.gz 1SN_22A.models.tsv.gz 1SN_7A.snps.tsv.gz 1HL_22A.snps.tsv.gz 1HL_6A.tags.tsv.gz 1NF_22A.alleles.tsv.gz 1NF_7A.models.tsv.gz 1SN_22A.snps.tsv.gz 1SN_7A.tags.tsv.gz 1HL_22A.tags.tsv.gz 1HL_7A.alleles.tsv.gz 1NF_22A.models.tsv.gz 1NF_7A.snps.tsv.gz 1SN_22A.tags.tsv.gz 1SN_8A.alleles.tsv.gz 1HL_23A.alleles.tsv.gz 1HL_7A.models.tsv.gz 1NF_22A.snps.tsv.gz 1NF_7A.tags.tsv.gz 1SN_23A.alleles.tsv.gz 1SN_8A.models.tsv.gz 1HL_23A.models.tsv.gz 1HL_7A.snps.tsv.gz 1NF_22A.tags.tsv.gz 1NF_8A.alleles.tsv.gz 1SN_23A.models.tsv.gz 1SN_8A.snps.tsv.gz 1HL_23A.snps.tsv.gz 1HL_7A.tags.tsv.gz 1NF_23A.alleles.tsv.gz 1NF_8A.models.tsv.gz 1SN_23A.snps.tsv.gz 1SN_8A.tags.tsv.gz 1HL_23A.tags.tsv.gz 1HL_8A.alleles.tsv.gz 1NF_23A.models.tsv.gz 1NF_8A.snps.tsv.gz 1SN_23A.tags.tsv.gz 1SN_9A.alleles.tsv.gz 1HL_24A.alleles.tsv.gz 1HL_8A.models.tsv.gz 1NF_23A.snps.tsv.gz 1NF_8A.tags.tsv.gz 1SN_24A.alleles.tsv.gz 1SN_9A.models.tsv.gz 1HL_24A.models.tsv.gz 1HL_8A.snps.tsv.gz 1NF_23A.tags.tsv.gz 1NF_9A.alleles.tsv.gz 1SN_24A.models.tsv.gz 1SN_9A.snps.tsv.gz 1HL_24A.snps.tsv.gz 1HL_8A.tags.tsv.gz 1NF_24A.alleles.tsv.gz 1NF_9A.models.tsv.gz 1SN_24A.snps.tsv.gz 1SN_9A.tags.tsv.gz 1HL_24A.tags.tsv.gz 1HL_9A.alleles.tsv.gz 1NF_24A.models.tsv.gz 1NF_9A.snps.tsv.gz 1SN_24A.tags.tsv.gz batch_1.catalog.alleles.tsv.gz 1HL_25A.alleles.tsv.gz 1HL_9A.models.tsv.gz 1NF_24A.snps.tsv.gz 1NF_9A.tags.tsv.gz 1SN_25A.alleles.tsv.gz batch_1.catalog.snps.tsv.gz 1HL_25A.models.tsv.gz 1HL_9A.snps.tsv.gz 1NF_24A.tags.tsv.gz 1SN_10A.alleles.tsv.gz 1SN_25A.models.tsv.gz batch_1.catalog.tags.tsv.gz 1HL_25A.snps.tsv.gz 1HL_9A.tags.tsv.gz 1NF_25A.alleles.tsv.gz 1SN_10A.models.tsv.gz 1SN_25A.snps.tsv.gz 1HL_25A.tags.tsv.gz 1NF_10A.alleles.tsv.gz 1NF_25A.models.tsv.gz 1SN_10A.snps.tsv.gz 1SN_25A.tags.tsv.gz 1HL_26A.alleles.tsv.gz 1NF_10A.models.tsv.gz 1NF_25A.snps.tsv.gz 1SN_10A.tags.tsv.gz 1SN_26A.alleles.tsv.gz
ls /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/batch*
/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/batch_1.catalog.alleles.tsv.gz /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/batch_1.catalog.tags.tsv.gz /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/batch_1.catalog.snps.tsv.gz
cd /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/
/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks
%%bash
#sstacks command.
time /usr/local/bioinformatics/stacks-1.40/sstacks \
-b 1 \
-c /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/batch_1 \
-o /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/ \
-p 16 \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A
Searching for matches by sequence identity... Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/batch_1.catalog.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/batch_1.catalog.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/batch_1.catalog.alleles.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A' [1 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A.alleles.tsv.gz Searching for sequence matches... 183160 stacks compared against the catalog containing 1475893 loci. 183037 matching loci, 534 contained no verified haplotypes. 421 loci matched more than one catalog locus and were excluded. 92 loci contained SNPs unaccounted for in the catalog and were excluded. 237338 total haplotypes examined from matching loci, 236055 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A' [2 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A.alleles.tsv.gz Searching for sequence matches... 200815 stacks compared against the catalog containing 1475893 loci. 200602 matching loci, 1181 contained no verified haplotypes. 1003 loci matched more than one catalog locus and were excluded. 156 loci contained SNPs unaccounted for in the catalog and were excluded. 258442 total haplotypes examined from matching loci, 255589 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A' [3 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A.alleles.tsv.gz Searching for sequence matches... 170108 stacks compared against the catalog containing 1475893 loci. 169901 matching loci, 1573 contained no verified haplotypes. 1393 loci matched more than one catalog locus and were excluded. 161 loci contained SNPs unaccounted for in the catalog and were excluded. 219194 total haplotypes examined from matching loci, 215400 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A' [4 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A.alleles.tsv.gz Searching for sequence matches... 161473 stacks compared against the catalog containing 1475893 loci. 161197 matching loci, 1966 contained no verified haplotypes. 1750 loci matched more than one catalog locus and were excluded. 184 loci contained SNPs unaccounted for in the catalog and were excluded. 209242 total haplotypes examined from matching loci, 204474 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A' [5 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A.alleles.tsv.gz Searching for sequence matches... 136269 stacks compared against the catalog containing 1475893 loci. 136044 matching loci, 1941 contained no verified haplotypes. 1760 loci matched more than one catalog locus and were excluded. 165 loci contained SNPs unaccounted for in the catalog and were excluded. 173744 total haplotypes examined from matching loci, 169165 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A' [6 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A.alleles.tsv.gz Searching for sequence matches... 145805 stacks compared against the catalog containing 1475893 loci. 145497 matching loci, 2169 contained no verified haplotypes. 1975 loci matched more than one catalog locus and were excluded. 178 loci contained SNPs unaccounted for in the catalog and were excluded. 186290 total haplotypes examined from matching loci, 181113 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A' [7 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A.alleles.tsv.gz Searching for sequence matches... 150367 stacks compared against the catalog containing 1475893 loci. 150046 matching loci, 2329 contained no verified haplotypes. 2152 loci matched more than one catalog locus and were excluded. 164 loci contained SNPs unaccounted for in the catalog and were excluded. 191513 total haplotypes examined from matching loci, 185964 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A' [8 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A.alleles.tsv.gz Searching for sequence matches... 192105 stacks compared against the catalog containing 1475893 loci. 191450 matching loci, 2842 contained no verified haplotypes. 2529 loci matched more than one catalog locus and were excluded. 287 loci contained SNPs unaccounted for in the catalog and were excluded. 249162 total haplotypes examined from matching loci, 242471 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A' [9 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A.alleles.tsv.gz Searching for sequence matches... 194582 stacks compared against the catalog containing 1475893 loci. 193967 matching loci, 2970 contained no verified haplotypes. 2688 loci matched more than one catalog locus and were excluded. 261 loci contained SNPs unaccounted for in the catalog and were excluded. 252631 total haplotypes examined from matching loci, 245588 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A' [10 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A.alleles.tsv.gz Searching for sequence matches... 149154 stacks compared against the catalog containing 1475893 loci. 148662 matching loci, 2907 contained no verified haplotypes. 2705 loci matched more than one catalog locus and were excluded. 187 loci contained SNPs unaccounted for in the catalog and were excluded. 192299 total haplotypes examined from matching loci, 185570 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A' [11 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A.alleles.tsv.gz Searching for sequence matches... 165947 stacks compared against the catalog containing 1475893 loci. 165409 matching loci, 2715 contained no verified haplotypes. 2449 loci matched more than one catalog locus and were excluded. 242 loci contained SNPs unaccounted for in the catalog and were excluded. 212400 total haplotypes examined from matching loci, 206070 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A' [12 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A.alleles.tsv.gz Searching for sequence matches... 159739 stacks compared against the catalog containing 1475893 loci. 159254 matching loci, 2793 contained no verified haplotypes. 2603 loci matched more than one catalog locus and were excluded. 187 loci contained SNPs unaccounted for in the catalog and were excluded. 205909 total haplotypes examined from matching loci, 199304 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A' [13 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A.alleles.tsv.gz Searching for sequence matches... 143097 stacks compared against the catalog containing 1475893 loci. 142661 matching loci, 2674 contained no verified haplotypes. 2425 loci matched more than one catalog locus and were excluded. 244 loci contained SNPs unaccounted for in the catalog and were excluded. 188858 total haplotypes examined from matching loci, 182664 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A' [14 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A.alleles.tsv.gz Searching for sequence matches... 196152 stacks compared against the catalog containing 1475893 loci. 195334 matching loci, 3407 contained no verified haplotypes. 3121 loci matched more than one catalog locus and were excluded. 255 loci contained SNPs unaccounted for in the catalog and were excluded. 250661 total haplotypes examined from matching loci, 242748 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A' [15 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A.alleles.tsv.gz Searching for sequence matches... 160847 stacks compared against the catalog containing 1475893 loci. 160223 matching loci, 2902 contained no verified haplotypes. 2639 loci matched more than one catalog locus and were excluded. 226 loci contained SNPs unaccounted for in the catalog and were excluded. 205989 total haplotypes examined from matching loci, 199215 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A' [16 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A.alleles.tsv.gz Searching for sequence matches... 174594 stacks compared against the catalog containing 1475893 loci. 173858 matching loci, 3320 contained no verified haplotypes. 3058 loci matched more than one catalog locus and were excluded. 210 loci contained SNPs unaccounted for in the catalog and were excluded. 223486 total haplotypes examined from matching loci, 215579 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A' [17 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A.alleles.tsv.gz Searching for sequence matches... 181896 stacks compared against the catalog containing 1475893 loci. 181138 matching loci, 3280 contained no verified haplotypes. 3015 loci matched more than one catalog locus and were excluded. 241 loci contained SNPs unaccounted for in the catalog and were excluded. 232722 total haplotypes examined from matching loci, 225130 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A' [18 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A.alleles.tsv.gz Searching for sequence matches... 190469 stacks compared against the catalog containing 1475893 loci. 189375 matching loci, 3624 contained no verified haplotypes. 3376 loci matched more than one catalog locus and were excluded. 220 loci contained SNPs unaccounted for in the catalog and were excluded. 245201 total haplotypes examined from matching loci, 236785 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A' [19 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A.alleles.tsv.gz Searching for sequence matches... 248584 stacks compared against the catalog containing 1475893 loci. 247912 matching loci, 3199 contained no verified haplotypes. 2822 loci matched more than one catalog locus and were excluded. 348 loci contained SNPs unaccounted for in the catalog and were excluded. 396895 total haplotypes examined from matching loci, 390070 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A' [20 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A.alleles.tsv.gz Searching for sequence matches... 177421 stacks compared against the catalog containing 1475893 loci. 176499 matching loci, 3261 contained no verified haplotypes. 2986 loci matched more than one catalog locus and were excluded. 254 loci contained SNPs unaccounted for in the catalog and were excluded. 227818 total haplotypes examined from matching loci, 219980 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A' [21 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A.alleles.tsv.gz Searching for sequence matches... 165144 stacks compared against the catalog containing 1475893 loci. 164386 matching loci, 3159 contained no verified haplotypes. 2922 loci matched more than one catalog locus and were excluded. 215 loci contained SNPs unaccounted for in the catalog and were excluded. 210616 total haplotypes examined from matching loci, 203190 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A' [22 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A.alleles.tsv.gz Searching for sequence matches... 158339 stacks compared against the catalog containing 1475893 loci. 157603 matching loci, 3262 contained no verified haplotypes. 3067 loci matched more than one catalog locus and were excluded. 175 loci contained SNPs unaccounted for in the catalog and were excluded. 202937 total haplotypes examined from matching loci, 195113 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A' [23 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A.alleles.tsv.gz Searching for sequence matches... 163368 stacks compared against the catalog containing 1475893 loci. 162543 matching loci, 3191 contained no verified haplotypes. 2989 loci matched more than one catalog locus and were excluded. 183 loci contained SNPs unaccounted for in the catalog and were excluded. 209716 total haplotypes examined from matching loci, 202094 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A' [24 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A.alleles.tsv.gz Searching for sequence matches... 173600 stacks compared against the catalog containing 1475893 loci. 172481 matching loci, 3492 contained no verified haplotypes. 3226 loci matched more than one catalog locus and were excluded. 239 loci contained SNPs unaccounted for in the catalog and were excluded. 221578 total haplotypes examined from matching loci, 213441 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A' [25 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A.alleles.tsv.gz Searching for sequence matches... 169381 stacks compared against the catalog containing 1475893 loci. 168596 matching loci, 3600 contained no verified haplotypes. 3410 loci matched more than one catalog locus and were excluded. 160 loci contained SNPs unaccounted for in the catalog and were excluded. 215887 total haplotypes examined from matching loci, 207380 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A' [26 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A.alleles.tsv.gz Searching for sequence matches... 151787 stacks compared against the catalog containing 1475893 loci. 151262 matching loci, 3158 contained no verified haplotypes. 3001 loci matched more than one catalog locus and were excluded. 137 loci contained SNPs unaccounted for in the catalog and were excluded. 193335 total haplotypes examined from matching loci, 185810 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A' [27 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A.alleles.tsv.gz Searching for sequence matches... 162235 stacks compared against the catalog containing 1475893 loci. 161442 matching loci, 3141 contained no verified haplotypes. 2918 loci matched more than one catalog locus and were excluded. 195 loci contained SNPs unaccounted for in the catalog and were excluded. 206637 total haplotypes examined from matching loci, 199241 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A' [28 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A.alleles.tsv.gz Searching for sequence matches... 138698 stacks compared against the catalog containing 1475893 loci. 138047 matching loci, 2750 contained no verified haplotypes. 2577 loci matched more than one catalog locus and were excluded. 152 loci contained SNPs unaccounted for in the catalog and were excluded. 174575 total haplotypes examined from matching loci, 168174 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A' [29 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A.alleles.tsv.gz Searching for sequence matches... 141746 stacks compared against the catalog containing 1475893 loci. 140789 matching loci, 3082 contained no verified haplotypes. 2877 loci matched more than one catalog locus and were excluded. 187 loci contained SNPs unaccounted for in the catalog and were excluded. 195328 total haplotypes examined from matching loci, 188004 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A' [30 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A.alleles.tsv.gz Searching for sequence matches... 234172 stacks compared against the catalog containing 1475893 loci. 232398 matching loci, 3075 contained no verified haplotypes. 2864 loci matched more than one catalog locus and were excluded. 185 loci contained SNPs unaccounted for in the catalog and were excluded. 328180 total haplotypes examined from matching loci, 321552 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A' [31 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A.alleles.tsv.gz Searching for sequence matches... 154648 stacks compared against the catalog containing 1475893 loci. 153728 matching loci, 3246 contained no verified haplotypes. 3054 loci matched more than one catalog locus and were excluded. 174 loci contained SNPs unaccounted for in the catalog and were excluded. 196541 total haplotypes examined from matching loci, 188903 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A' [32 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A.alleles.tsv.gz Searching for sequence matches... 168134 stacks compared against the catalog containing 1475893 loci. 167230 matching loci, 3363 contained no verified haplotypes. 3154 loci matched more than one catalog locus and were excluded. 184 loci contained SNPs unaccounted for in the catalog and were excluded. 214440 total haplotypes examined from matching loci, 206439 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A' [33 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A.alleles.tsv.gz Searching for sequence matches... 138696 stacks compared against the catalog containing 1475893 loci. 137935 matching loci, 2799 contained no verified haplotypes. 2632 loci matched more than one catalog locus and were excluded. 147 loci contained SNPs unaccounted for in the catalog and were excluded. 175819 total haplotypes examined from matching loci, 169168 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A' [34 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A.alleles.tsv.gz Searching for sequence matches... 143506 stacks compared against the catalog containing 1475893 loci. 142758 matching loci, 3011 contained no verified haplotypes. 2855 loci matched more than one catalog locus and were excluded. 135 loci contained SNPs unaccounted for in the catalog and were excluded. 183159 total haplotypes examined from matching loci, 175902 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A' [35 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A.alleles.tsv.gz Searching for sequence matches... 139227 stacks compared against the catalog containing 1475893 loci. 138490 matching loci, 2961 contained no verified haplotypes. 2800 loci matched more than one catalog locus and were excluded. 141 loci contained SNPs unaccounted for in the catalog and were excluded. 176036 total haplotypes examined from matching loci, 169001 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A' [36 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A.alleles.tsv.gz Searching for sequence matches... 212189 stacks compared against the catalog containing 1475893 loci. 210806 matching loci, 4040 contained no verified haplotypes. 3769 loci matched more than one catalog locus and were excluded. 248 loci contained SNPs unaccounted for in the catalog and were excluded. 270526 total haplotypes examined from matching loci, 260986 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A' [37 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A.alleles.tsv.gz Searching for sequence matches... 161624 stacks compared against the catalog containing 1475893 loci. 160635 matching loci, 3249 contained no verified haplotypes. 3029 loci matched more than one catalog locus and were excluded. 201 loci contained SNPs unaccounted for in the catalog and were excluded. 208841 total haplotypes examined from matching loci, 201088 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A' [38 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A.alleles.tsv.gz Searching for sequence matches... 157667 stacks compared against the catalog containing 1475893 loci. 156850 matching loci, 3167 contained no verified haplotypes. 2992 loci matched more than one catalog locus and were excluded. 164 loci contained SNPs unaccounted for in the catalog and were excluded. 200295 total haplotypes examined from matching loci, 192803 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A' [39 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A.alleles.tsv.gz Searching for sequence matches... 165112 stacks compared against the catalog containing 1475893 loci. 164044 matching loci, 3377 contained no verified haplotypes. 3188 loci matched more than one catalog locus and were excluded. 167 loci contained SNPs unaccounted for in the catalog and were excluded. 210162 total haplotypes examined from matching loci, 202101 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A' [40 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A.alleles.tsv.gz Searching for sequence matches... 180569 stacks compared against the catalog containing 1475893 loci. 179320 matching loci, 3628 contained no verified haplotypes. 3395 loci matched more than one catalog locus and were excluded. 193 loci contained SNPs unaccounted for in the catalog and were excluded. 229587 total haplotypes examined from matching loci, 220873 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A' [41 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A.alleles.tsv.gz Searching for sequence matches... 126545 stacks compared against the catalog containing 1475893 loci. 125898 matching loci, 2990 contained no verified haplotypes. 2860 loci matched more than one catalog locus and were excluded. 107 loci contained SNPs unaccounted for in the catalog and were excluded. 161011 total haplotypes examined from matching loci, 153958 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A' [42 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A.alleles.tsv.gz Searching for sequence matches... 129878 stacks compared against the catalog containing 1475893 loci. 129175 matching loci, 2916 contained no verified haplotypes. 2732 loci matched more than one catalog locus and were excluded. 165 loci contained SNPs unaccounted for in the catalog and were excluded. 165450 total haplotypes examined from matching loci, 158553 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A' [43 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A.alleles.tsv.gz Searching for sequence matches... 100144 stacks compared against the catalog containing 1475893 loci. 99762 matching loci, 2619 contained no verified haplotypes. 2519 loci matched more than one catalog locus and were excluded. 94 loci contained SNPs unaccounted for in the catalog and were excluded. 127284 total haplotypes examined from matching loci, 121126 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A' [44 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A.alleles.tsv.gz Searching for sequence matches... 155845 stacks compared against the catalog containing 1475893 loci. 154924 matching loci, 3322 contained no verified haplotypes. 3161 loci matched more than one catalog locus and were excluded. 137 loci contained SNPs unaccounted for in the catalog and were excluded. 198620 total haplotypes examined from matching loci, 190729 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A' [45 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A.alleles.tsv.gz Searching for sequence matches... 193399 stacks compared against the catalog containing 1475893 loci. 192233 matching loci, 3770 contained no verified haplotypes. 3544 loci matched more than one catalog locus and were excluded. 163 loci contained SNPs unaccounted for in the catalog and were excluded. 245047 total haplotypes examined from matching loci, 236232 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A' [46 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A.alleles.tsv.gz Searching for sequence matches... 170518 stacks compared against the catalog containing 1475893 loci. 169387 matching loci, 3514 contained no verified haplotypes. 3319 loci matched more than one catalog locus and were excluded. 176 loci contained SNPs unaccounted for in the catalog and were excluded. 217448 total haplotypes examined from matching loci, 209052 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A' [47 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A.alleles.tsv.gz Searching for sequence matches... 191522 stacks compared against the catalog containing 1475893 loci. 190341 matching loci, 3881 contained no verified haplotypes. 3688 loci matched more than one catalog locus and were excluded. 160 loci contained SNPs unaccounted for in the catalog and were excluded. 245608 total haplotypes examined from matching loci, 236360 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A' [48 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A.alleles.tsv.gz Searching for sequence matches... 179253 stacks compared against the catalog containing 1475893 loci. 177983 matching loci, 3640 contained no verified haplotypes. 3453 loci matched more than one catalog locus and were excluded. 176 loci contained SNPs unaccounted for in the catalog and were excluded. 229156 total haplotypes examined from matching loci, 220525 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A' [49 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A.alleles.tsv.gz Searching for sequence matches... 142746 stacks compared against the catalog containing 1475893 loci. 141790 matching loci, 3249 contained no verified haplotypes. 3101 loci matched more than one catalog locus and were excluded. 125 loci contained SNPs unaccounted for in the catalog and were excluded. 181162 total haplotypes examined from matching loci, 173451 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A' [50 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A.alleles.tsv.gz Searching for sequence matches... 182038 stacks compared against the catalog containing 1475893 loci. 180685 matching loci, 3859 contained no verified haplotypes. 3671 loci matched more than one catalog locus and were excluded. 166 loci contained SNPs unaccounted for in the catalog and were excluded. 232156 total haplotypes examined from matching loci, 223012 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A' [51 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A.alleles.tsv.gz Searching for sequence matches... 148904 stacks compared against the catalog containing 1475893 loci. 148158 matching loci, 3400 contained no verified haplotypes. 3265 loci matched more than one catalog locus and were excluded. 113 loci contained SNPs unaccounted for in the catalog and were excluded. 187616 total haplotypes examined from matching loci, 179510 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A' [52 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A.alleles.tsv.gz Searching for sequence matches... 151925 stacks compared against the catalog containing 1475893 loci. 151023 matching loci, 3484 contained no verified haplotypes. 3350 loci matched more than one catalog locus and were excluded. 117 loci contained SNPs unaccounted for in the catalog and were excluded. 193776 total haplotypes examined from matching loci, 185478 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A' [53 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A.alleles.tsv.gz Searching for sequence matches... 190240 stacks compared against the catalog containing 1475893 loci. 188409 matching loci, 4106 contained no verified haplotypes. 3855 loci matched more than one catalog locus and were excluded. 226 loci contained SNPs unaccounted for in the catalog and were excluded. 245009 total haplotypes examined from matching loci, 235075 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A' [54 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A.alleles.tsv.gz Searching for sequence matches... 187655 stacks compared against the catalog containing 1475893 loci. 186217 matching loci, 3792 contained no verified haplotypes. 3614 loci matched more than one catalog locus and were excluded. 161 loci contained SNPs unaccounted for in the catalog and were excluded. 239710 total haplotypes examined from matching loci, 230546 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A' [55 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A.alleles.tsv.gz Searching for sequence matches... 160477 stacks compared against the catalog containing 1475893 loci. 159293 matching loci, 3532 contained no verified haplotypes. 3363 loci matched more than one catalog locus and were excluded. 143 loci contained SNPs unaccounted for in the catalog and were excluded. 205277 total haplotypes examined from matching loci, 196754 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A' [56 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A.alleles.tsv.gz Searching for sequence matches... 195941 stacks compared against the catalog containing 1475893 loci. 194321 matching loci, 4129 contained no verified haplotypes. 3915 loci matched more than one catalog locus and were excluded. 171 loci contained SNPs unaccounted for in the catalog and were excluded. 250787 total haplotypes examined from matching loci, 240913 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A' [57 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A.alleles.tsv.gz Searching for sequence matches... 200309 stacks compared against the catalog containing 1475893 loci. 198759 matching loci, 4146 contained no verified haplotypes. 3922 loci matched more than one catalog locus and were excluded. 151 loci contained SNPs unaccounted for in the catalog and were excluded. 254951 total haplotypes examined from matching loci, 245274 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A' [58 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A.alleles.tsv.gz Searching for sequence matches... 160962 stacks compared against the catalog containing 1475893 loci. 159822 matching loci, 3522 contained no verified haplotypes. 3387 loci matched more than one catalog locus and were excluded. 122 loci contained SNPs unaccounted for in the catalog and were excluded. 204570 total haplotypes examined from matching loci, 196131 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A' [59 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A.alleles.tsv.gz Searching for sequence matches... 200905 stacks compared against the catalog containing 1475893 loci. 199340 matching loci, 4223 contained no verified haplotypes. 3998 loci matched more than one catalog locus and were excluded. 159 loci contained SNPs unaccounted for in the catalog and were excluded. 256119 total haplotypes examined from matching loci, 246156 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A' [60 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A.alleles.tsv.gz Searching for sequence matches... 172107 stacks compared against the catalog containing 1475893 loci. 170970 matching loci, 3742 contained no verified haplotypes. 3605 loci matched more than one catalog locus and were excluded. 117 loci contained SNPs unaccounted for in the catalog and were excluded. 218714 total haplotypes examined from matching loci, 209683 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A' [61 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A.alleles.tsv.gz Searching for sequence matches... 152568 stacks compared against the catalog containing 1475893 loci. 151719 matching loci, 3472 contained no verified haplotypes. 3368 loci matched more than one catalog locus and were excluded. 96 loci contained SNPs unaccounted for in the catalog and were excluded. 193542 total haplotypes examined from matching loci, 185333 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A' [62 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A.alleles.tsv.gz Searching for sequence matches... 158297 stacks compared against the catalog containing 1475893 loci. 157214 matching loci, 3580 contained no verified haplotypes. 3453 loci matched more than one catalog locus and were excluded. 105 loci contained SNPs unaccounted for in the catalog and were excluded. 201180 total haplotypes examined from matching loci, 192631 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A' [63 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A.alleles.tsv.gz Searching for sequence matches... 165313 stacks compared against the catalog containing 1475893 loci. 163963 matching loci, 3460 contained no verified haplotypes. 3321 loci matched more than one catalog locus and were excluded. 122 loci contained SNPs unaccounted for in the catalog and were excluded. 218025 total haplotypes examined from matching loci, 209849 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A' [64 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A.alleles.tsv.gz Searching for sequence matches... 186392 stacks compared against the catalog containing 1475893 loci. 184813 matching loci, 3889 contained no verified haplotypes. 3691 loci matched more than one catalog locus and were excluded. 166 loci contained SNPs unaccounted for in the catalog and were excluded. 238391 total haplotypes examined from matching loci, 229082 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A' [65 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A.alleles.tsv.gz Searching for sequence matches... 162373 stacks compared against the catalog containing 1475893 loci. 161397 matching loci, 3501 contained no verified haplotypes. 3366 loci matched more than one catalog locus and were excluded. 125 loci contained SNPs unaccounted for in the catalog and were excluded. 204965 total haplotypes examined from matching loci, 196610 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A' [66 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A.alleles.tsv.gz Searching for sequence matches... 162398 stacks compared against the catalog containing 1475893 loci. 161203 matching loci, 3767 contained no verified haplotypes. 3647 loci matched more than one catalog locus and were excluded. 96 loci contained SNPs unaccounted for in the catalog and were excluded. 206525 total haplotypes examined from matching loci, 197365 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A' [67 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A.alleles.tsv.gz Searching for sequence matches... 203025 stacks compared against the catalog containing 1475893 loci. 201347 matching loci, 4266 contained no verified haplotypes. 4104 loci matched more than one catalog locus and were excluded. 119 loci contained SNPs unaccounted for in the catalog and were excluded. 258008 total haplotypes examined from matching loci, 247808 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A' [68 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A.alleles.tsv.gz Searching for sequence matches... 179561 stacks compared against the catalog containing 1475893 loci. 178240 matching loci, 3767 contained no verified haplotypes. 3620 loci matched more than one catalog locus and were excluded. 137 loci contained SNPs unaccounted for in the catalog and were excluded. 228856 total haplotypes examined from matching loci, 219858 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A' [69 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A.alleles.tsv.gz Searching for sequence matches... 194295 stacks compared against the catalog containing 1475893 loci. 192404 matching loci, 4107 contained no verified haplotypes. 3927 loci matched more than one catalog locus and were excluded. 105 loci contained SNPs unaccounted for in the catalog and were excluded. 246310 total haplotypes examined from matching loci, 236596 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A' [70 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A.alleles.tsv.gz Searching for sequence matches... 158426 stacks compared against the catalog containing 1475893 loci. 157368 matching loci, 3515 contained no verified haplotypes. 3399 loci matched more than one catalog locus and were excluded. 79 loci contained SNPs unaccounted for in the catalog and were excluded. 201215 total haplotypes examined from matching loci, 192675 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A' [71 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A.alleles.tsv.gz Searching for sequence matches... 159668 stacks compared against the catalog containing 1475893 loci. 158130 matching loci, 3571 contained no verified haplotypes. 3446 loci matched more than one catalog locus and were excluded. 100 loci contained SNPs unaccounted for in the catalog and were excluded. 209544 total haplotypes examined from matching loci, 200978 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A' [72 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A.alleles.tsv.gz Searching for sequence matches... 182922 stacks compared against the catalog containing 1475893 loci. 181615 matching loci, 3977 contained no verified haplotypes. 3854 loci matched more than one catalog locus and were excluded. 86 loci contained SNPs unaccounted for in the catalog and were excluded. 233378 total haplotypes examined from matching loci, 223868 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A' [73 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A.alleles.tsv.gz Searching for sequence matches... 185133 stacks compared against the catalog containing 1475893 loci. 183406 matching loci, 3762 contained no verified haplotypes. 3632 loci matched more than one catalog locus and were excluded. 104 loci contained SNPs unaccounted for in the catalog and were excluded. 239434 total haplotypes examined from matching loci, 230393 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A' [74 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A.alleles.tsv.gz Searching for sequence matches... 182540 stacks compared against the catalog containing 1475893 loci. 181134 matching loci, 4012 contained no verified haplotypes. 3893 loci matched more than one catalog locus and were excluded. 94 loci contained SNPs unaccounted for in the catalog and were excluded. 232640 total haplotypes examined from matching loci, 222967 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A' [75 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A.alleles.tsv.gz Searching for sequence matches... 171931 stacks compared against the catalog containing 1475893 loci. 170382 matching loci, 3736 contained no verified haplotypes. 3610 loci matched more than one catalog locus and were excluded. 101 loci contained SNPs unaccounted for in the catalog and were excluded. 218685 total haplotypes examined from matching loci, 209635 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A' [76 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A.alleles.tsv.gz Searching for sequence matches... 140455 stacks compared against the catalog containing 1475893 loci. 139429 matching loci, 3233 contained no verified haplotypes. 3131 loci matched more than one catalog locus and were excluded. 77 loci contained SNPs unaccounted for in the catalog and were excluded. 178534 total haplotypes examined from matching loci, 170762 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A' [77 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A.alleles.tsv.gz Searching for sequence matches... 200490 stacks compared against the catalog containing 1475893 loci. 198601 matching loci, 4279 contained no verified haplotypes. 4106 loci matched more than one catalog locus and were excluded. 119 loci contained SNPs unaccounted for in the catalog and were excluded. 256048 total haplotypes examined from matching loci, 245848 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A' [78 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A.alleles.tsv.gz Searching for sequence matches... 181882 stacks compared against the catalog containing 1475893 loci. 180109 matching loci, 3973 contained no verified haplotypes. 3862 loci matched more than one catalog locus and were excluded. 88 loci contained SNPs unaccounted for in the catalog and were excluded. 231096 total haplotypes examined from matching loci, 221588 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A' [79 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A.alleles.tsv.gz Searching for sequence matches... 208887 stacks compared against the catalog containing 1475893 loci. 206841 matching loci, 4390 contained no verified haplotypes. 4206 loci matched more than one catalog locus and were excluded. 104 loci contained SNPs unaccounted for in the catalog and were excluded. 265712 total haplotypes examined from matching loci, 255289 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A' [80 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A.alleles.tsv.gz Searching for sequence matches... 129362 stacks compared against the catalog containing 1475893 loci. 128601 matching loci, 3021 contained no verified haplotypes. 2965 loci matched more than one catalog locus and were excluded. 45 loci contained SNPs unaccounted for in the catalog and were excluded. 163493 total haplotypes examined from matching loci, 156240 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A' [81 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A.alleles.tsv.gz Searching for sequence matches... 175871 stacks compared against the catalog containing 1475893 loci. 174336 matching loci, 3829 contained no verified haplotypes. 3727 loci matched more than one catalog locus and were excluded. 78 loci contained SNPs unaccounted for in the catalog and were excluded. 223598 total haplotypes examined from matching loci, 214468 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A' [82 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A.alleles.tsv.gz Searching for sequence matches... 169710 stacks compared against the catalog containing 1475893 loci. 168335 matching loci, 3755 contained no verified haplotypes. 3670 loci matched more than one catalog locus and were excluded. 60 loci contained SNPs unaccounted for in the catalog and were excluded. 215290 total haplotypes examined from matching loci, 206265 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A' [83 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A.alleles.tsv.gz Searching for sequence matches... 159822 stacks compared against the catalog containing 1475893 loci. 158522 matching loci, 3681 contained no verified haplotypes. 3592 loci matched more than one catalog locus and were excluded. 64 loci contained SNPs unaccounted for in the catalog and were excluded. 203090 total haplotypes examined from matching loci, 194144 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A' [84 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A.alleles.tsv.gz Searching for sequence matches... 169628 stacks compared against the catalog containing 1475893 loci. 168305 matching loci, 3723 contained no verified haplotypes. 3662 loci matched more than one catalog locus and were excluded. 53 loci contained SNPs unaccounted for in the catalog and were excluded. 218405 total haplotypes examined from matching loci, 209335 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A' [85 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A.alleles.tsv.gz Searching for sequence matches... 130947 stacks compared against the catalog containing 1475893 loci. 129697 matching loci, 2917 contained no verified haplotypes. 2849 loci matched more than one catalog locus and were excluded. 47 loci contained SNPs unaccounted for in the catalog and were excluded. 170485 total haplotypes examined from matching loci, 163309 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A' [86 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A.alleles.tsv.gz Searching for sequence matches... 178438 stacks compared against the catalog containing 1475893 loci. 176861 matching loci, 4002 contained no verified haplotypes. 3915 loci matched more than one catalog locus and were excluded. 73 loci contained SNPs unaccounted for in the catalog and were excluded. 229333 total haplotypes examined from matching loci, 219595 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A' [87 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A.alleles.tsv.gz Searching for sequence matches... 211452 stacks compared against the catalog containing 1475893 loci. 209434 matching loci, 4454 contained no verified haplotypes. 4322 loci matched more than one catalog locus and were excluded. 63 loci contained SNPs unaccounted for in the catalog and were excluded. 271358 total haplotypes examined from matching loci, 260673 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A' [88 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A.alleles.tsv.gz Searching for sequence matches... 186165 stacks compared against the catalog containing 1475893 loci. 184235 matching loci, 4016 contained no verified haplotypes. 3930 loci matched more than one catalog locus and were excluded. 59 loci contained SNPs unaccounted for in the catalog and were excluded. 237343 total haplotypes examined from matching loci, 227494 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A' [89 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A.alleles.tsv.gz Searching for sequence matches... 157279 stacks compared against the catalog containing 1475893 loci. 156119 matching loci, 3563 contained no verified haplotypes. 3511 loci matched more than one catalog locus and were excluded. 38 loci contained SNPs unaccounted for in the catalog and were excluded. 199052 total haplotypes examined from matching loci, 190447 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A' [90 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A.alleles.tsv.gz Searching for sequence matches... 160364 stacks compared against the catalog containing 1475893 loci. 159325 matching loci, 3420 contained no verified haplotypes. 3388 loci matched more than one catalog locus and were excluded. 25 loci contained SNPs unaccounted for in the catalog and were excluded. 203868 total haplotypes examined from matching loci, 195638 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A' [91 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A.alleles.tsv.gz Searching for sequence matches... 194962 stacks compared against the catalog containing 1475893 loci. 193164 matching loci, 4205 contained no verified haplotypes. 4152 loci matched more than one catalog locus and were excluded. 27 loci contained SNPs unaccounted for in the catalog and were excluded. 247426 total haplotypes examined from matching loci, 237239 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A' [92 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A.alleles.tsv.gz Searching for sequence matches... 187983 stacks compared against the catalog containing 1475893 loci. 186471 matching loci, 4262 contained no verified haplotypes. 4177 loci matched more than one catalog locus and were excluded. 21 loci contained SNPs unaccounted for in the catalog and were excluded. 237868 total haplotypes examined from matching loci, 227656 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A' [93 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A.alleles.tsv.gz Searching for sequence matches... 191034 stacks compared against the catalog containing 1475893 loci. 189128 matching loci, 4183 contained no verified haplotypes. 4105 loci matched more than one catalog locus and were excluded. 17 loci contained SNPs unaccounted for in the catalog and were excluded. 244428 total haplotypes examined from matching loci, 234217 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A' [94 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A.alleles.tsv.gz Searching for sequence matches... 179816 stacks compared against the catalog containing 1475893 loci. 178160 matching loci, 3798 contained no verified haplotypes. 3745 loci matched more than one catalog locus and were excluded. 12 loci contained SNPs unaccounted for in the catalog and were excluded. 227890 total haplotypes examined from matching loci, 218690 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A' [95 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A.alleles.tsv.gz Searching for sequence matches... 190255 stacks compared against the catalog containing 1475893 loci. 188637 matching loci, 4093 contained no verified haplotypes. 4049 loci matched more than one catalog locus and were excluded. 6 loci contained SNPs unaccounted for in the catalog and were excluded. 241782 total haplotypes examined from matching loci, 231904 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A.matches.tsv.gz Processing sample '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A' [96 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A.alleles.tsv.gz Searching for sequence matches... 192476 stacks compared against the catalog containing 1475893 loci. 190724 matching loci, 4245 contained no verified haplotypes. 4183 loci matched more than one catalog locus and were excluded. 0 loci contained SNPs unaccounted for in the catalog and were excluded. 244965 total haplotypes examined from matching loci, 234595 verified. Outputing to file /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A.matches.tsv.gz real 149m51.435s user 147m13.092s sys 2m17.031s
%%bash
#Formats a population map file (popmap) with each individual and associates each individual with the correct population.
#Uses paramter substitution to extract the just the filename from the full path (${fname##*/}).
#Uses printf statement and parameter substitution to print just the first part of each filename without the extension (${fname%%.*}),
#separated by a TAB and then just the corresponding population, derived from the filename by
#removing the underscore and any text following the underscore (${fname%%_*}).
for fname in /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1[HNS][FLN]*; do fname="${fname##*/}"; printf "%s\t%s\n" "${fname%%.*}" "${fname%%_*}" >> tmp.txt; done
cat tmp.txt | uniq > popmap
rm tmp.txt
%%bash
cat /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/popmap
1HL_10A 1HL 1HL_11A 1HL 1HL_12A 1HL 1HL_13A 1HL 1HL_14A 1HL 1HL_15A 1HL 1HL_16A 1HL 1HL_17A 1HL 1HL_19A 1HL 1HL_1A 1HL 1HL_20A 1HL 1HL_21A 1HL 1HL_22A 1HL 1HL_23A 1HL 1HL_24A 1HL 1HL_25A 1HL 1HL_26A 1HL 1HL_27A 1HL 1HL_28A 1HL 1HL_29A 1HL 1HL_2A 1HL 1HL_31A 1HL 1HL_33A 1HL 1HL_34A 1HL 1HL_35A 1HL 1HL_3A 1HL 1HL_4A 1HL 1HL_5A 1HL 1HL_6A 1HL 1HL_7A 1HL 1HL_8A 1HL 1HL_9A 1HL 1NF_10A 1NF 1NF_11A 1NF 1NF_12A 1NF 1NF_13A 1NF 1NF_14A 1NF 1NF_15A 1NF 1NF_16A 1NF 1NF_17A 1NF 1NF_18A 1NF 1NF_19A 1NF 1NF_1A 1NF 1NF_20A 1NF 1NF_21A 1NF 1NF_22A 1NF 1NF_23A 1NF 1NF_24A 1NF 1NF_25A 1NF 1NF_26A 1NF 1NF_27A 1NF 1NF_28A 1NF 1NF_29A 1NF 1NF_2A 1NF 1NF_30A 1NF 1NF_31A 1NF 1NF_32A 1NF 1NF_33A 1NF 1NF_4A 1NF 1NF_5A 1NF 1NF_6A 1NF 1NF_7A 1NF 1NF_8A 1NF 1NF_9A 1NF 1SN_10A 1SN 1SN_11A 1SN 1SN_12A 1SN 1SN_13A 1SN 1SN_14A 1SN 1SN_15A 1SN 1SN_16A 1SN 1SN_17A 1SN 1SN_18A 1SN 1SN_19A 1SN 1SN_1A 1SN 1SN_20A 1SN 1SN_21A 1SN 1SN_22A 1SN 1SN_23A 1SN 1SN_24A 1SN 1SN_25A 1SN 1SN_26A 1SN 1SN_27A 1SN 1SN_28A 1SN 1SN_29A 1SN 1SN_2A 1SN 1SN_30A 1SN 1SN_31A 1SN 1SN_32A 1SN 1SN_3A 1SN 1SN_4A 1SN 1SN_5A 1SN 1SN_6A 1SN 1SN_7A 1SN 1SN_8A 1SN 1SN_9A 1SN
mv popmap ../populations/popmap
%%bash
cat /Volumes/toaster/sam/stacks/oly_BGI_GBS/populations/popmap
1HL_10A 1HL 1HL_11A 1HL 1HL_12A 1HL 1HL_13A 1HL 1HL_14A 1HL 1HL_15A 1HL 1HL_16A 1HL 1HL_17A 1HL 1HL_19A 1HL 1HL_1A 1HL 1HL_20A 1HL 1HL_21A 1HL 1HL_22A 1HL 1HL_23A 1HL 1HL_24A 1HL 1HL_25A 1HL 1HL_26A 1HL 1HL_27A 1HL 1HL_28A 1HL 1HL_29A 1HL 1HL_2A 1HL 1HL_31A 1HL 1HL_33A 1HL 1HL_34A 1HL 1HL_35A 1HL 1HL_3A 1HL 1HL_4A 1HL 1HL_5A 1HL 1HL_6A 1HL 1HL_7A 1HL 1HL_8A 1HL 1HL_9A 1HL 1NF_10A 1NF 1NF_11A 1NF 1NF_12A 1NF 1NF_13A 1NF 1NF_14A 1NF 1NF_15A 1NF 1NF_16A 1NF 1NF_17A 1NF 1NF_18A 1NF 1NF_19A 1NF 1NF_1A 1NF 1NF_20A 1NF 1NF_21A 1NF 1NF_22A 1NF 1NF_23A 1NF 1NF_24A 1NF 1NF_25A 1NF 1NF_26A 1NF 1NF_27A 1NF 1NF_28A 1NF 1NF_29A 1NF 1NF_2A 1NF 1NF_30A 1NF 1NF_31A 1NF 1NF_32A 1NF 1NF_33A 1NF 1NF_4A 1NF 1NF_5A 1NF 1NF_6A 1NF 1NF_7A 1NF 1NF_8A 1NF 1NF_9A 1NF 1SN_10A 1SN 1SN_11A 1SN 1SN_12A 1SN 1SN_13A 1SN 1SN_14A 1SN 1SN_15A 1SN 1SN_16A 1SN 1SN_17A 1SN 1SN_18A 1SN 1SN_19A 1SN 1SN_1A 1SN 1SN_20A 1SN 1SN_21A 1SN 1SN_22A 1SN 1SN_23A 1SN 1SN_24A 1SN 1SN_25A 1SN 1SN_26A 1SN 1SN_27A 1SN 1SN_28A 1SN 1SN_29A 1SN 1SN_2A 1SN 1SN_30A 1SN 1SN_31A 1SN 1SN_32A 1SN 1SN_3A 1SN 1SN_4A 1SN 1SN_5A 1SN 1SN_6A 1SN 1SN_7A 1SN 1SN_8A 1SN 1SN_9A 1SN
%%bash
time /usr/local/bioinformatics/stacks-1.40/populations \
-P /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks \
-M /Volumes/toaster/sam/stacks/oly_BGI_GBS/populations/popmap \
-b 1 \
-k \
-s \
-e apeKI \
--genomic \
--fasta \
--vcf \
-t 16
%%bash
time /usr/local/bioinformatics/stacks-1.40/populations \
-P /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks \
-M /Volumes/toaster/sam/stacks/oly_BGI_GBS/populations/popmap \
-b 1 \
-k \
-s \
-e apeKI \
--genomic \
--fasta \
--vcf \
-t 16
%%bash
time /usr/local/bioinformatics/stacks-1.40/populations \
-P /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks \
-M /Volumes/toaster/sam/stacks/oly_BGI_GBS/populations/popmap \
-b 1 \
-k \
-s \
-e apeKI \
--genomic \
--fasta \
--vcf \
-t 16
%%bash
date
Thu Jun 16 12:51:18 PDT 2016
cd /Volumes/toaster/sam/stacks/oly_BGI_GBS/populations/
/Volumes/toaster/sam/stacks/oly_BGI_GBS/populations
%%bash
time /usr/local/bioinformatics/stacks-1.40/populations \
-P /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks \
-M /Volumes/toaster/sam/stacks/oly_BGI_GBS/populations/popmap \
-b 1 \
-k \
-s \
-e apeKI \
--genomic \
--fasta \
--vcf \
-t 16
cd /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/
/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks
%%bash
ls -l
total 23393232 -rw-r--r-- 1 Sam staff 594594 May 24 08:03 1HL_10A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2178852 Jun 9 10:17 1HL_10A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7864239 May 24 08:03 1HL_10A.models.tsv.gz -rw-r--r-- 1 Sam staff 53860003 May 24 08:03 1HL_10A.snps.tsv.gz -rw-r--r-- 1 Sam staff 69294722 May 24 08:03 1HL_10A.tags.tsv.gz -rw-r--r-- 1 Sam staff 648123 May 24 09:27 1HL_11A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2449188 Jun 9 10:18 1HL_11A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8637981 May 24 09:27 1HL_11A.models.tsv.gz -rw-r--r-- 1 Sam staff 59243547 May 24 09:27 1HL_11A.snps.tsv.gz -rw-r--r-- 1 Sam staff 77250525 May 24 09:27 1HL_11A.tags.tsv.gz -rw-r--r-- 1 Sam staff 524233 May 24 10:14 1HL_12A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2075243 Jun 9 10:20 1HL_12A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7237980 May 24 10:14 1HL_12A.models.tsv.gz -rw-r--r-- 1 Sam staff 49605928 May 24 10:14 1HL_12A.snps.tsv.gz -rw-r--r-- 1 Sam staff 55383785 May 24 10:14 1HL_12A.tags.tsv.gz -rw-r--r-- 1 Sam staff 523892 May 24 11:04 1HL_13A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1997768 Jun 9 10:21 1HL_13A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6899818 May 24 11:04 1HL_13A.models.tsv.gz -rw-r--r-- 1 Sam staff 47261726 May 24 11:04 1HL_13A.snps.tsv.gz -rw-r--r-- 1 Sam staff 58591767 May 24 11:04 1HL_13A.tags.tsv.gz -rw-r--r-- 1 Sam staff 407311 May 24 11:38 1HL_14A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1663989 Jun 9 10:23 1HL_14A.matches.tsv.gz -rw-r--r-- 1 Sam staff 5801906 May 24 11:38 1HL_14A.models.tsv.gz -rw-r--r-- 1 Sam staff 39660678 May 24 11:38 1HL_14A.snps.tsv.gz -rw-r--r-- 1 Sam staff 44828788 May 24 11:38 1HL_14A.tags.tsv.gz -rw-r--r-- 1 Sam staff 443582 May 24 12:16 1HL_15A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1782756 Jun 9 10:24 1HL_15A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6214828 May 24 12:16 1HL_15A.models.tsv.gz -rw-r--r-- 1 Sam staff 42444968 May 24 12:16 1HL_15A.snps.tsv.gz -rw-r--r-- 1 Sam staff 48869204 May 24 12:16 1HL_15A.tags.tsv.gz -rw-r--r-- 1 Sam staff 453138 May 24 12:59 1HL_16A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1837758 Jun 9 10:26 1HL_16A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6410272 May 24 12:59 1HL_16A.models.tsv.gz -rw-r--r-- 1 Sam staff 43841412 May 24 12:59 1HL_16A.snps.tsv.gz -rw-r--r-- 1 Sam staff 51558547 May 24 12:59 1HL_16A.tags.tsv.gz -rw-r--r-- 1 Sam staff 658140 May 24 14:22 1HL_17A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2386862 Jun 9 10:28 1HL_17A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8268485 May 24 14:22 1HL_17A.models.tsv.gz -rw-r--r-- 1 Sam staff 56748995 May 24 14:22 1HL_17A.snps.tsv.gz -rw-r--r-- 1 Sam staff 78710494 May 24 14:22 1HL_17A.tags.tsv.gz -rw-r--r-- 1 Sam staff 663644 May 24 15:45 1HL_19A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2424212 Jun 9 10:29 1HL_19A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8355170 May 24 15:45 1HL_19A.models.tsv.gz -rw-r--r-- 1 Sam staff 57425032 May 24 15:45 1HL_19A.snps.tsv.gz -rw-r--r-- 1 Sam staff 77898849 May 24 15:45 1HL_19A.tags.tsv.gz -rw-r--r-- 1 Sam staff 474661 May 24 16:24 1HL_1A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1844105 Jun 9 10:31 1HL_1A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6374330 May 24 16:24 1HL_1A.models.tsv.gz -rw-r--r-- 1 Sam staff 43828410 May 24 16:24 1HL_1A.snps.tsv.gz -rw-r--r-- 1 Sam staff 50168345 May 24 16:24 1HL_1A.tags.tsv.gz -rw-r--r-- 1 Sam staff 532995 May 24 17:21 1HL_20A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2055940 Jun 9 10:32 1HL_20A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7128324 May 24 17:21 1HL_20A.models.tsv.gz -rw-r--r-- 1 Sam staff 49068347 May 24 17:21 1HL_20A.snps.tsv.gz -rw-r--r-- 1 Sam staff 63155351 May 24 17:21 1HL_20A.tags.tsv.gz -rw-r--r-- 1 Sam staff 517726 May 24 18:08 1HL_21A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1961580 Jun 9 10:34 1HL_21A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6842101 May 24 18:08 1HL_21A.models.tsv.gz -rw-r--r-- 1 Sam staff 47060911 May 24 18:08 1HL_21A.snps.tsv.gz -rw-r--r-- 1 Sam staff 56843017 May 24 18:08 1HL_21A.tags.tsv.gz -rw-r--r-- 1 Sam staff 487541 May 24 18:41 1HL_22A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1790238 Jun 9 10:35 1HL_22A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6113590 May 24 18:41 1HL_22A.models.tsv.gz -rw-r--r-- 1 Sam staff 41988327 May 24 18:41 1HL_22A.snps.tsv.gz -rw-r--r-- 1 Sam staff 45755417 May 24 18:41 1HL_22A.tags.tsv.gz -rw-r--r-- 1 Sam staff 643684 May 24 20:04 1HL_23A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2426704 Jun 9 10:37 1HL_23A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8453597 May 24 20:04 1HL_23A.models.tsv.gz -rw-r--r-- 1 Sam staff 57888254 May 24 20:04 1HL_23A.snps.tsv.gz -rw-r--r-- 1 Sam staff 78713437 May 24 20:04 1HL_23A.tags.tsv.gz -rw-r--r-- 1 Sam staff 510173 May 24 20:57 1HL_24A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1991447 Jun 9 10:38 1HL_24A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6892015 May 24 20:57 1HL_24A.models.tsv.gz -rw-r--r-- 1 Sam staff 47443333 May 24 20:57 1HL_24A.snps.tsv.gz -rw-r--r-- 1 Sam staff 59652180 May 24 20:57 1HL_24A.tags.tsv.gz -rw-r--r-- 1 Sam staff 560279 May 24 22:02 1HL_25A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2159631 Jun 9 10:40 1HL_25A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7499245 May 24 22:02 1HL_25A.models.tsv.gz -rw-r--r-- 1 Sam staff 51552879 May 24 22:02 1HL_25A.snps.tsv.gz -rw-r--r-- 1 Sam staff 65147772 May 24 22:02 1HL_25A.tags.tsv.gz -rw-r--r-- 1 Sam staff 586448 May 24 23:06 1HL_26A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2250992 Jun 9 10:42 1HL_26A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7803971 May 24 23:06 1HL_26A.models.tsv.gz -rw-r--r-- 1 Sam staff 53588943 May 24 23:06 1HL_26A.snps.tsv.gz -rw-r--r-- 1 Sam staff 68569855 May 24 23:06 1HL_26A.tags.tsv.gz -rw-r--r-- 1 Sam staff 627436 May 25 00:15 1HL_27A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2367217 Jun 9 10:43 1HL_27A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8156584 May 25 00:15 1HL_27A.models.tsv.gz -rw-r--r-- 1 Sam staff 55866110 May 25 00:15 1HL_27A.snps.tsv.gz -rw-r--r-- 1 Sam staff 70590845 May 25 00:15 1HL_27A.tags.tsv.gz -rw-r--r-- 1 Sam staff 1596768 May 25 02:50 1HL_28A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 3419812 Jun 9 10:45 1HL_28A.matches.tsv.gz -rw-r--r-- 1 Sam staff 11145999 May 25 02:50 1HL_28A.models.tsv.gz -rw-r--r-- 1 Sam staff 75785906 May 25 02:50 1HL_28A.snps.tsv.gz -rw-r--r-- 1 Sam staff 84426164 May 25 02:50 1HL_28A.tags.tsv.gz -rw-r--r-- 1 Sam staff 583209 May 25 03:52 1HL_29A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2202366 Jun 9 10:47 1HL_29A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7616999 May 25 03:52 1HL_29A.models.tsv.gz -rw-r--r-- 1 Sam staff 52359690 May 25 03:52 1HL_29A.snps.tsv.gz -rw-r--r-- 1 Sam staff 67056665 May 25 03:52 1HL_29A.tags.tsv.gz -rw-r--r-- 1 Sam staff 525542 May 25 04:46 1HL_2A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2043117 Jun 9 10:48 1HL_2A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7095716 May 25 04:46 1HL_2A.models.tsv.gz -rw-r--r-- 1 Sam staff 48797561 May 25 04:46 1HL_2A.snps.tsv.gz -rw-r--r-- 1 Sam staff 60676405 May 25 04:46 1HL_2A.tags.tsv.gz -rw-r--r-- 1 Sam staff 500299 May 25 05:35 1HL_31A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1948018 Jun 9 10:50 1HL_31A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6770048 May 25 05:35 1HL_31A.models.tsv.gz -rw-r--r-- 1 Sam staff 46630408 May 25 05:35 1HL_31A.snps.tsv.gz -rw-r--r-- 1 Sam staff 54149983 May 25 05:35 1HL_31A.tags.tsv.gz -rw-r--r-- 1 Sam staff 528232 May 25 06:28 1HL_33A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1999363 Jun 9 10:51 1HL_33A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7011213 May 25 06:28 1HL_33A.models.tsv.gz -rw-r--r-- 1 Sam staff 48255783 May 25 06:28 1HL_33A.snps.tsv.gz -rw-r--r-- 1 Sam staff 59634114 May 25 06:28 1HL_33A.tags.tsv.gz -rw-r--r-- 1 Sam staff 558663 May 25 07:29 1HL_34A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2131662 Jun 9 10:53 1HL_34A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7455857 May 25 07:29 1HL_34A.models.tsv.gz -rw-r--r-- 1 Sam staff 51211004 May 25 07:29 1HL_34A.snps.tsv.gz -rw-r--r-- 1 Sam staff 63836332 May 25 07:29 1HL_34A.tags.tsv.gz -rw-r--r-- 1 Sam staff 526098 May 25 08:23 1HL_35A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2076088 Jun 9 10:54 1HL_35A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7252433 May 25 08:23 1HL_35A.models.tsv.gz -rw-r--r-- 1 Sam staff 49880341 May 25 08:23 1HL_35A.snps.tsv.gz -rw-r--r-- 1 Sam staff 58238477 May 25 08:23 1HL_35A.tags.tsv.gz -rw-r--r-- 1 Sam staff 455066 May 25 09:05 1HL_3A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1854448 Jun 9 10:56 1HL_3A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6478355 May 25 09:05 1HL_3A.models.tsv.gz -rw-r--r-- 1 Sam staff 44597799 May 25 09:05 1HL_3A.snps.tsv.gz -rw-r--r-- 1 Sam staff 48717954 May 25 09:05 1HL_3A.tags.tsv.gz -rw-r--r-- 1 Sam staff 505438 May 25 09:54 1HL_4A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1999959 Jun 9 10:57 1HL_4A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6939032 May 25 09:54 1HL_4A.models.tsv.gz -rw-r--r-- 1 Sam staff 47710495 May 25 09:54 1HL_4A.snps.tsv.gz -rw-r--r-- 1 Sam staff 56912314 May 25 09:54 1HL_4A.tags.tsv.gz -rw-r--r-- 1 Sam staff 398888 May 25 10:26 1HL_5A.alleles.tsv.gz 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-rw-r--r-- 1 Sam staff 41345975 May 27 08:16 1SN_20A.snps.tsv.gz -rw-r--r-- 1 Sam staff 46521847 May 27 08:16 1SN_20A.tags.tsv.gz -rw-r--r-- 1 Sam staff 659702 May 27 09:41 1SN_21A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2479447 Jun 9 12:15 1SN_21A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8612735 May 27 09:41 1SN_21A.models.tsv.gz -rw-r--r-- 1 Sam staff 59277414 May 27 09:41 1SN_21A.snps.tsv.gz -rw-r--r-- 1 Sam staff 76303974 May 27 09:41 1SN_21A.tags.tsv.gz -rw-r--r-- 1 Sam staff 582456 May 27 10:48 1SN_22A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2242240 Jun 9 12:16 1SN_22A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7804993 May 27 10:48 1SN_22A.models.tsv.gz -rw-r--r-- 1 Sam staff 53735857 May 27 10:48 1SN_22A.snps.tsv.gz -rw-r--r-- 1 Sam staff 66961535 May 27 10:48 1SN_22A.tags.tsv.gz -rw-r--r-- 1 Sam staff 681358 May 27 12:17 1SN_23A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2590459 Jun 9 12:18 1SN_23A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8985705 May 27 12:17 1SN_23A.models.tsv.gz -rw-r--r-- 1 Sam staff 61626467 May 27 12:17 1SN_23A.snps.tsv.gz -rw-r--r-- 1 Sam staff 80702952 May 27 12:17 1SN_23A.tags.tsv.gz -rw-r--r-- 1 Sam staff 379493 May 27 12:48 1SN_24A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1577328 Jun 9 12:19 1SN_24A.matches.tsv.gz -rw-r--r-- 1 Sam staff 5505968 May 27 12:48 1SN_24A.models.tsv.gz -rw-r--r-- 1 Sam staff 38024712 May 27 12:48 1SN_24A.snps.tsv.gz -rw-r--r-- 1 Sam staff 41663880 May 27 12:48 1SN_24A.tags.tsv.gz -rw-r--r-- 1 Sam staff 555929 May 27 13:50 1SN_25A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2168833 Jun 9 12:21 1SN_25A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7535347 May 27 13:50 1SN_25A.models.tsv.gz -rw-r--r-- 1 Sam staff 51928619 May 27 13:50 1SN_25A.snps.tsv.gz -rw-r--r-- 1 Sam staff 65362113 May 27 13:50 1SN_25A.tags.tsv.gz -rw-r--r-- 1 Sam staff 527271 May 27 14:47 1SN_26A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2088610 Jun 9 12:23 1SN_26A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7276410 May 27 14:47 1SN_26A.models.tsv.gz -rw-r--r-- 1 Sam staff 50119759 May 27 14:47 1SN_26A.snps.tsv.gz -rw-r--r-- 1 Sam staff 60543089 May 27 14:47 1SN_26A.tags.tsv.gz -rw-r--r-- 1 Sam staff 500268 May 27 15:37 1SN_27A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1962524 Jun 9 12:24 1SN_27A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6836172 May 27 15:37 1SN_27A.models.tsv.gz -rw-r--r-- 1 Sam staff 47183230 May 27 15:37 1SN_27A.snps.tsv.gz -rw-r--r-- 1 Sam staff 56936191 May 27 15:37 1SN_27A.tags.tsv.gz -rw-r--r-- 1 Sam staff 564930 May 27 16:36 1SN_28A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2108722 Jun 9 12:26 1SN_28A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7287531 May 27 16:36 1SN_28A.models.tsv.gz -rw-r--r-- 1 Sam staff 50136498 May 27 16:36 1SN_28A.snps.tsv.gz -rw-r--r-- 1 Sam staff 62174777 May 27 16:36 1SN_28A.tags.tsv.gz -rw-r--r-- 1 Sam staff 452396 May 27 17:11 1SN_29A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1637909 Jun 9 12:27 1SN_29A.matches.tsv.gz -rw-r--r-- 1 Sam staff 5593749 May 27 17:11 1SN_29A.models.tsv.gz -rw-r--r-- 1 Sam staff 38511862 May 27 17:11 1SN_29A.snps.tsv.gz -rw-r--r-- 1 Sam staff 48595430 May 27 17:11 1SN_29A.tags.tsv.gz -rw-r--r-- 1 Sam staff 591046 May 27 18:17 1SN_2A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2217135 Jun 9 12:29 1SN_2A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7653368 May 27 18:17 1SN_2A.models.tsv.gz -rw-r--r-- 1 Sam staff 52819864 May 27 18:17 1SN_2A.snps.tsv.gz -rw-r--r-- 1 Sam staff 66817903 May 27 18:17 1SN_2A.tags.tsv.gz -rw-r--r-- 1 Sam staff 713410 May 27 19:48 1SN_30A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2637709 Jun 9 12:30 1SN_30A.matches.tsv.gz -rw-r--r-- 1 Sam staff 9094468 May 27 19:48 1SN_30A.models.tsv.gz -rw-r--r-- 1 Sam staff 62298469 May 27 19:48 1SN_30A.snps.tsv.gz -rw-r--r-- 1 Sam staff 83206146 May 27 19:48 1SN_30A.tags.tsv.gz -rw-r--r-- 1 Sam staff 613594 May 27 21:03 1SN_31A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2308763 Jun 9 12:32 1SN_31A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8021777 May 27 21:03 1SN_31A.models.tsv.gz -rw-r--r-- 1 Sam staff 55233750 May 27 21:03 1SN_31A.snps.tsv.gz -rw-r--r-- 1 Sam staff 72757806 May 27 21:03 1SN_31A.tags.tsv.gz -rw-r--r-- 1 Sam staff 480077 May 27 21:51 1SN_32A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1925978 Jun 9 12:34 1SN_32A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6721042 May 27 21:51 1SN_32A.models.tsv.gz -rw-r--r-- 1 Sam staff 46414804 May 27 21:51 1SN_32A.snps.tsv.gz -rw-r--r-- 1 Sam staff 55360903 May 27 21:51 1SN_32A.tags.tsv.gz -rw-r--r-- 1 Sam staff 481813 May 27 22:34 1SN_3A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1961350 Jun 9 12:35 1SN_3A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6836633 May 27 22:34 1SN_3A.models.tsv.gz -rw-r--r-- 1 Sam staff 47207507 May 27 22:34 1SN_3A.snps.tsv.gz -rw-r--r-- 1 Sam staff 52903748 May 27 22:34 1SN_3A.tags.tsv.gz -rw-r--r-- 1 Sam staff 619969 May 27 23:50 1SN_4A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2409121 Jun 9 12:37 1SN_4A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8376813 May 27 23:50 1SN_4A.models.tsv.gz -rw-r--r-- 1 Sam staff 57524706 May 27 23:50 1SN_4A.snps.tsv.gz -rw-r--r-- 1 Sam staff 72446768 May 27 23:50 1SN_4A.tags.tsv.gz -rw-r--r-- 1 Sam staff 576711 May 28 00:56 1SN_5A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2300146 Jun 9 12:38 1SN_5A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8050023 May 28 00:56 1SN_5A.models.tsv.gz -rw-r--r-- 1 Sam staff 55335171 May 28 00:56 1SN_5A.snps.tsv.gz -rw-r--r-- 1 Sam staff 65656318 May 28 00:56 1SN_5A.tags.tsv.gz -rw-r--r-- 1 Sam staff 628449 May 28 02:12 1SN_6A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2371514 Jun 9 12:40 1SN_6A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8207053 May 28 02:12 1SN_6A.models.tsv.gz -rw-r--r-- 1 Sam staff 56467531 May 28 02:12 1SN_6A.snps.tsv.gz -rw-r--r-- 1 Sam staff 72995159 May 28 02:12 1SN_6A.tags.tsv.gz -rw-r--r-- 1 Sam staff 560702 May 28 03:15 1SN_7A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2215832 Jun 9 12:42 1SN_7A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7702428 May 28 03:15 1SN_7A.models.tsv.gz -rw-r--r-- 1 Sam staff 52959593 May 28 03:15 1SN_7A.snps.tsv.gz -rw-r--r-- 1 Sam staff 65080027 May 28 03:15 1SN_7A.tags.tsv.gz -rw-r--r-- 1 Sam staff 610591 May 28 04:26 1SN_8A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2357559 Jun 9 12:43 1SN_8A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8160485 May 28 04:26 1SN_8A.models.tsv.gz -rw-r--r-- 1 Sam staff 56132050 May 28 04:26 1SN_8A.snps.tsv.gz -rw-r--r-- 1 Sam staff 71909892 May 28 04:26 1SN_8A.tags.tsv.gz -rw-r--r-- 1 Sam staff 611305 May 28 05:41 1SN_9A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2371371 Jun 9 12:45 1SN_9A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8252751 May 28 05:41 1SN_9A.models.tsv.gz -rw-r--r-- 1 Sam staff 56754889 May 28 05:41 1SN_9A.snps.tsv.gz -rw-r--r-- 1 Sam staff 69383399 May 28 05:41 1SN_9A.tags.tsv.gz -rw-r--r-- 1 Sam staff 9675995 Jun 2 08:38 batch_1.catalog.alleles.tsv.gz -rw-r--r-- 1 Sam staff 7233456 Jun 2 08:38 batch_1.catalog.snps.tsv.gz -rw-r--r-- 1 Sam staff 106542220 Jun 2 08:38 batch_1.catalog.tags.tsv.gz -rw-r--r-- 1 Sam staff 110000181 Jun 16 13:03 batch_1.markers.tsv -rw-r--r-- 1 Sam staff 4096 Jun 16 13:03 batch_1.populations.log
rm batch_1.catalog*
ls -l
total 23152104 -rw-r--r-- 1 Sam staff 594594 May 24 08:03 1HL_10A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2178852 Jun 9 10:17 1HL_10A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7864239 May 24 08:03 1HL_10A.models.tsv.gz -rw-r--r-- 1 Sam staff 53860003 May 24 08:03 1HL_10A.snps.tsv.gz -rw-r--r-- 1 Sam staff 69294722 May 24 08:03 1HL_10A.tags.tsv.gz -rw-r--r-- 1 Sam staff 648123 May 24 09:27 1HL_11A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2449188 Jun 9 10:18 1HL_11A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8637981 May 24 09:27 1HL_11A.models.tsv.gz -rw-r--r-- 1 Sam staff 59243547 May 24 09:27 1HL_11A.snps.tsv.gz -rw-r--r-- 1 Sam staff 77250525 May 24 09:27 1HL_11A.tags.tsv.gz -rw-r--r-- 1 Sam staff 524233 May 24 10:14 1HL_12A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2075243 Jun 9 10:20 1HL_12A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7237980 May 24 10:14 1HL_12A.models.tsv.gz -rw-r--r-- 1 Sam staff 49605928 May 24 10:14 1HL_12A.snps.tsv.gz -rw-r--r-- 1 Sam staff 55383785 May 24 10:14 1HL_12A.tags.tsv.gz -rw-r--r-- 1 Sam staff 523892 May 24 11:04 1HL_13A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1997768 Jun 9 10:21 1HL_13A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6899818 May 24 11:04 1HL_13A.models.tsv.gz -rw-r--r-- 1 Sam staff 47261726 May 24 11:04 1HL_13A.snps.tsv.gz -rw-r--r-- 1 Sam staff 58591767 May 24 11:04 1HL_13A.tags.tsv.gz -rw-r--r-- 1 Sam staff 407311 May 24 11:38 1HL_14A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1663989 Jun 9 10:23 1HL_14A.matches.tsv.gz -rw-r--r-- 1 Sam staff 5801906 May 24 11:38 1HL_14A.models.tsv.gz -rw-r--r-- 1 Sam staff 39660678 May 24 11:38 1HL_14A.snps.tsv.gz -rw-r--r-- 1 Sam staff 44828788 May 24 11:38 1HL_14A.tags.tsv.gz -rw-r--r-- 1 Sam staff 443582 May 24 12:16 1HL_15A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1782756 Jun 9 10:24 1HL_15A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6214828 May 24 12:16 1HL_15A.models.tsv.gz -rw-r--r-- 1 Sam staff 42444968 May 24 12:16 1HL_15A.snps.tsv.gz -rw-r--r-- 1 Sam staff 48869204 May 24 12:16 1HL_15A.tags.tsv.gz -rw-r--r-- 1 Sam staff 453138 May 24 12:59 1HL_16A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1837758 Jun 9 10:26 1HL_16A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6410272 May 24 12:59 1HL_16A.models.tsv.gz -rw-r--r-- 1 Sam staff 43841412 May 24 12:59 1HL_16A.snps.tsv.gz -rw-r--r-- 1 Sam staff 51558547 May 24 12:59 1HL_16A.tags.tsv.gz -rw-r--r-- 1 Sam staff 658140 May 24 14:22 1HL_17A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2386862 Jun 9 10:28 1HL_17A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8268485 May 24 14:22 1HL_17A.models.tsv.gz -rw-r--r-- 1 Sam staff 56748995 May 24 14:22 1HL_17A.snps.tsv.gz -rw-r--r-- 1 Sam staff 78710494 May 24 14:22 1HL_17A.tags.tsv.gz -rw-r--r-- 1 Sam staff 663644 May 24 15:45 1HL_19A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2424212 Jun 9 10:29 1HL_19A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8355170 May 24 15:45 1HL_19A.models.tsv.gz -rw-r--r-- 1 Sam staff 57425032 May 24 15:45 1HL_19A.snps.tsv.gz -rw-r--r-- 1 Sam staff 77898849 May 24 15:45 1HL_19A.tags.tsv.gz -rw-r--r-- 1 Sam staff 474661 May 24 16:24 1HL_1A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1844105 Jun 9 10:31 1HL_1A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6374330 May 24 16:24 1HL_1A.models.tsv.gz -rw-r--r-- 1 Sam staff 43828410 May 24 16:24 1HL_1A.snps.tsv.gz -rw-r--r-- 1 Sam staff 50168345 May 24 16:24 1HL_1A.tags.tsv.gz -rw-r--r-- 1 Sam staff 532995 May 24 17:21 1HL_20A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2055940 Jun 9 10:32 1HL_20A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7128324 May 24 17:21 1HL_20A.models.tsv.gz -rw-r--r-- 1 Sam staff 49068347 May 24 17:21 1HL_20A.snps.tsv.gz -rw-r--r-- 1 Sam staff 63155351 May 24 17:21 1HL_20A.tags.tsv.gz -rw-r--r-- 1 Sam staff 517726 May 24 18:08 1HL_21A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1961580 Jun 9 10:34 1HL_21A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6842101 May 24 18:08 1HL_21A.models.tsv.gz -rw-r--r-- 1 Sam staff 47060911 May 24 18:08 1HL_21A.snps.tsv.gz -rw-r--r-- 1 Sam staff 56843017 May 24 18:08 1HL_21A.tags.tsv.gz -rw-r--r-- 1 Sam staff 487541 May 24 18:41 1HL_22A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1790238 Jun 9 10:35 1HL_22A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6113590 May 24 18:41 1HL_22A.models.tsv.gz -rw-r--r-- 1 Sam staff 41988327 May 24 18:41 1HL_22A.snps.tsv.gz -rw-r--r-- 1 Sam staff 45755417 May 24 18:41 1HL_22A.tags.tsv.gz -rw-r--r-- 1 Sam staff 643684 May 24 20:04 1HL_23A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2426704 Jun 9 10:37 1HL_23A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8453597 May 24 20:04 1HL_23A.models.tsv.gz -rw-r--r-- 1 Sam staff 57888254 May 24 20:04 1HL_23A.snps.tsv.gz -rw-r--r-- 1 Sam staff 78713437 May 24 20:04 1HL_23A.tags.tsv.gz -rw-r--r-- 1 Sam staff 510173 May 24 20:57 1HL_24A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1991447 Jun 9 10:38 1HL_24A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6892015 May 24 20:57 1HL_24A.models.tsv.gz -rw-r--r-- 1 Sam staff 47443333 May 24 20:57 1HL_24A.snps.tsv.gz -rw-r--r-- 1 Sam staff 59652180 May 24 20:57 1HL_24A.tags.tsv.gz -rw-r--r-- 1 Sam staff 560279 May 24 22:02 1HL_25A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2159631 Jun 9 10:40 1HL_25A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7499245 May 24 22:02 1HL_25A.models.tsv.gz -rw-r--r-- 1 Sam staff 51552879 May 24 22:02 1HL_25A.snps.tsv.gz -rw-r--r-- 1 Sam staff 65147772 May 24 22:02 1HL_25A.tags.tsv.gz -rw-r--r-- 1 Sam staff 586448 May 24 23:06 1HL_26A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2250992 Jun 9 10:42 1HL_26A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7803971 May 24 23:06 1HL_26A.models.tsv.gz -rw-r--r-- 1 Sam staff 53588943 May 24 23:06 1HL_26A.snps.tsv.gz -rw-r--r-- 1 Sam staff 68569855 May 24 23:06 1HL_26A.tags.tsv.gz -rw-r--r-- 1 Sam staff 627436 May 25 00:15 1HL_27A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2367217 Jun 9 10:43 1HL_27A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8156584 May 25 00:15 1HL_27A.models.tsv.gz -rw-r--r-- 1 Sam staff 55866110 May 25 00:15 1HL_27A.snps.tsv.gz -rw-r--r-- 1 Sam staff 70590845 May 25 00:15 1HL_27A.tags.tsv.gz -rw-r--r-- 1 Sam staff 1596768 May 25 02:50 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1SN_15A.models.tsv.gz -rw-r--r-- 1 Sam staff 46726420 May 27 02:44 1SN_15A.snps.tsv.gz -rw-r--r-- 1 Sam staff 55278383 May 27 02:44 1SN_15A.tags.tsv.gz -rw-r--r-- 1 Sam staff 559527 May 27 03:31 1SN_16A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2009882 Jun 9 12:05 1SN_16A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6830275 May 27 03:31 1SN_16A.models.tsv.gz -rw-r--r-- 1 Sam staff 46921119 May 27 03:31 1SN_16A.snps.tsv.gz -rw-r--r-- 1 Sam staff 57440924 May 27 03:31 1SN_16A.tags.tsv.gz -rw-r--r-- 1 Sam staff 579418 May 27 04:32 1SN_17A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2260691 Jun 9 12:07 1SN_17A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7836056 May 27 04:32 1SN_17A.models.tsv.gz -rw-r--r-- 1 Sam staff 53897864 May 27 04:32 1SN_17A.snps.tsv.gz -rw-r--r-- 1 Sam staff 65645647 May 27 04:32 1SN_17A.tags.tsv.gz -rw-r--r-- 1 Sam staff 629986 May 27 05:38 1SN_18A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2318124 Jun 9 12:09 1SN_18A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7931231 May 27 05:38 1SN_18A.models.tsv.gz -rw-r--r-- 1 Sam staff 54540628 May 27 05:38 1SN_18A.snps.tsv.gz -rw-r--r-- 1 Sam staff 70244534 May 27 05:38 1SN_18A.tags.tsv.gz -rw-r--r-- 1 Sam staff 581506 May 27 06:40 1SN_19A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2250182 Jun 9 12:10 1SN_19A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7836640 May 27 06:40 1SN_19A.models.tsv.gz -rw-r--r-- 1 Sam staff 53843581 May 27 06:40 1SN_19A.snps.tsv.gz -rw-r--r-- 1 Sam staff 66249309 May 27 06:40 1SN_19A.tags.tsv.gz -rw-r--r-- 1 Sam staff 554422 May 27 07:42 1SN_1A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2131170 Jun 9 12:12 1SN_1A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7389275 May 27 07:42 1SN_1A.models.tsv.gz -rw-r--r-- 1 Sam staff 50912478 May 27 07:42 1SN_1A.snps.tsv.gz -rw-r--r-- 1 Sam staff 66427038 May 27 07:42 1SN_1A.tags.tsv.gz -rw-r--r-- 1 Sam staff 428373 May 27 08:16 1SN_20A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1713882 Jun 9 12:13 1SN_20A.matches.tsv.gz -rw-r--r-- 1 Sam staff 5975239 May 27 08:16 1SN_20A.models.tsv.gz -rw-r--r-- 1 Sam staff 41345975 May 27 08:16 1SN_20A.snps.tsv.gz -rw-r--r-- 1 Sam staff 46521847 May 27 08:16 1SN_20A.tags.tsv.gz -rw-r--r-- 1 Sam staff 659702 May 27 09:41 1SN_21A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2479447 Jun 9 12:15 1SN_21A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8612735 May 27 09:41 1SN_21A.models.tsv.gz -rw-r--r-- 1 Sam staff 59277414 May 27 09:41 1SN_21A.snps.tsv.gz -rw-r--r-- 1 Sam staff 76303974 May 27 09:41 1SN_21A.tags.tsv.gz -rw-r--r-- 1 Sam staff 582456 May 27 10:48 1SN_22A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2242240 Jun 9 12:16 1SN_22A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7804993 May 27 10:48 1SN_22A.models.tsv.gz -rw-r--r-- 1 Sam staff 53735857 May 27 10:48 1SN_22A.snps.tsv.gz -rw-r--r-- 1 Sam staff 66961535 May 27 10:48 1SN_22A.tags.tsv.gz -rw-r--r-- 1 Sam staff 681358 May 27 12:17 1SN_23A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2590459 Jun 9 12:18 1SN_23A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8985705 May 27 12:17 1SN_23A.models.tsv.gz -rw-r--r-- 1 Sam staff 61626467 May 27 12:17 1SN_23A.snps.tsv.gz -rw-r--r-- 1 Sam staff 80702952 May 27 12:17 1SN_23A.tags.tsv.gz -rw-r--r-- 1 Sam staff 379493 May 27 12:48 1SN_24A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1577328 Jun 9 12:19 1SN_24A.matches.tsv.gz -rw-r--r-- 1 Sam staff 5505968 May 27 12:48 1SN_24A.models.tsv.gz -rw-r--r-- 1 Sam staff 38024712 May 27 12:48 1SN_24A.snps.tsv.gz -rw-r--r-- 1 Sam staff 41663880 May 27 12:48 1SN_24A.tags.tsv.gz -rw-r--r-- 1 Sam staff 555929 May 27 13:50 1SN_25A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2168833 Jun 9 12:21 1SN_25A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7535347 May 27 13:50 1SN_25A.models.tsv.gz -rw-r--r-- 1 Sam staff 51928619 May 27 13:50 1SN_25A.snps.tsv.gz -rw-r--r-- 1 Sam staff 65362113 May 27 13:50 1SN_25A.tags.tsv.gz -rw-r--r-- 1 Sam staff 527271 May 27 14:47 1SN_26A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2088610 Jun 9 12:23 1SN_26A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7276410 May 27 14:47 1SN_26A.models.tsv.gz -rw-r--r-- 1 Sam staff 50119759 May 27 14:47 1SN_26A.snps.tsv.gz -rw-r--r-- 1 Sam staff 60543089 May 27 14:47 1SN_26A.tags.tsv.gz -rw-r--r-- 1 Sam staff 500268 May 27 15:37 1SN_27A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1962524 Jun 9 12:24 1SN_27A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6836172 May 27 15:37 1SN_27A.models.tsv.gz -rw-r--r-- 1 Sam staff 47183230 May 27 15:37 1SN_27A.snps.tsv.gz -rw-r--r-- 1 Sam staff 56936191 May 27 15:37 1SN_27A.tags.tsv.gz -rw-r--r-- 1 Sam staff 564930 May 27 16:36 1SN_28A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2108722 Jun 9 12:26 1SN_28A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7287531 May 27 16:36 1SN_28A.models.tsv.gz -rw-r--r-- 1 Sam staff 50136498 May 27 16:36 1SN_28A.snps.tsv.gz -rw-r--r-- 1 Sam staff 62174777 May 27 16:36 1SN_28A.tags.tsv.gz -rw-r--r-- 1 Sam staff 452396 May 27 17:11 1SN_29A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1637909 Jun 9 12:27 1SN_29A.matches.tsv.gz -rw-r--r-- 1 Sam staff 5593749 May 27 17:11 1SN_29A.models.tsv.gz -rw-r--r-- 1 Sam staff 38511862 May 27 17:11 1SN_29A.snps.tsv.gz -rw-r--r-- 1 Sam staff 48595430 May 27 17:11 1SN_29A.tags.tsv.gz -rw-r--r-- 1 Sam staff 591046 May 27 18:17 1SN_2A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2217135 Jun 9 12:29 1SN_2A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7653368 May 27 18:17 1SN_2A.models.tsv.gz -rw-r--r-- 1 Sam staff 52819864 May 27 18:17 1SN_2A.snps.tsv.gz -rw-r--r-- 1 Sam staff 66817903 May 27 18:17 1SN_2A.tags.tsv.gz -rw-r--r-- 1 Sam staff 713410 May 27 19:48 1SN_30A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2637709 Jun 9 12:30 1SN_30A.matches.tsv.gz -rw-r--r-- 1 Sam staff 9094468 May 27 19:48 1SN_30A.models.tsv.gz -rw-r--r-- 1 Sam staff 62298469 May 27 19:48 1SN_30A.snps.tsv.gz -rw-r--r-- 1 Sam staff 83206146 May 27 19:48 1SN_30A.tags.tsv.gz -rw-r--r-- 1 Sam staff 613594 May 27 21:03 1SN_31A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2308763 Jun 9 12:32 1SN_31A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8021777 May 27 21:03 1SN_31A.models.tsv.gz -rw-r--r-- 1 Sam staff 55233750 May 27 21:03 1SN_31A.snps.tsv.gz -rw-r--r-- 1 Sam staff 72757806 May 27 21:03 1SN_31A.tags.tsv.gz -rw-r--r-- 1 Sam staff 480077 May 27 21:51 1SN_32A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1925978 Jun 9 12:34 1SN_32A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6721042 May 27 21:51 1SN_32A.models.tsv.gz -rw-r--r-- 1 Sam staff 46414804 May 27 21:51 1SN_32A.snps.tsv.gz -rw-r--r-- 1 Sam staff 55360903 May 27 21:51 1SN_32A.tags.tsv.gz -rw-r--r-- 1 Sam staff 481813 May 27 22:34 1SN_3A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 1961350 Jun 9 12:35 1SN_3A.matches.tsv.gz -rw-r--r-- 1 Sam staff 6836633 May 27 22:34 1SN_3A.models.tsv.gz -rw-r--r-- 1 Sam staff 47207507 May 27 22:34 1SN_3A.snps.tsv.gz -rw-r--r-- 1 Sam staff 52903748 May 27 22:34 1SN_3A.tags.tsv.gz -rw-r--r-- 1 Sam staff 619969 May 27 23:50 1SN_4A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2409121 Jun 9 12:37 1SN_4A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8376813 May 27 23:50 1SN_4A.models.tsv.gz -rw-r--r-- 1 Sam staff 57524706 May 27 23:50 1SN_4A.snps.tsv.gz -rw-r--r-- 1 Sam staff 72446768 May 27 23:50 1SN_4A.tags.tsv.gz -rw-r--r-- 1 Sam staff 576711 May 28 00:56 1SN_5A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2300146 Jun 9 12:38 1SN_5A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8050023 May 28 00:56 1SN_5A.models.tsv.gz -rw-r--r-- 1 Sam staff 55335171 May 28 00:56 1SN_5A.snps.tsv.gz -rw-r--r-- 1 Sam staff 65656318 May 28 00:56 1SN_5A.tags.tsv.gz -rw-r--r-- 1 Sam staff 628449 May 28 02:12 1SN_6A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2371514 Jun 9 12:40 1SN_6A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8207053 May 28 02:12 1SN_6A.models.tsv.gz -rw-r--r-- 1 Sam staff 56467531 May 28 02:12 1SN_6A.snps.tsv.gz -rw-r--r-- 1 Sam staff 72995159 May 28 02:12 1SN_6A.tags.tsv.gz -rw-r--r-- 1 Sam staff 560702 May 28 03:15 1SN_7A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2215832 Jun 9 12:42 1SN_7A.matches.tsv.gz -rw-r--r-- 1 Sam staff 7702428 May 28 03:15 1SN_7A.models.tsv.gz -rw-r--r-- 1 Sam staff 52959593 May 28 03:15 1SN_7A.snps.tsv.gz -rw-r--r-- 1 Sam staff 65080027 May 28 03:15 1SN_7A.tags.tsv.gz -rw-r--r-- 1 Sam staff 610591 May 28 04:26 1SN_8A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2357559 Jun 9 12:43 1SN_8A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8160485 May 28 04:26 1SN_8A.models.tsv.gz -rw-r--r-- 1 Sam staff 56132050 May 28 04:26 1SN_8A.snps.tsv.gz -rw-r--r-- 1 Sam staff 71909892 May 28 04:26 1SN_8A.tags.tsv.gz -rw-r--r-- 1 Sam staff 611305 May 28 05:41 1SN_9A.alleles.tsv.gz -rw-r--r-- 1 Sam staff 2371371 Jun 9 12:45 1SN_9A.matches.tsv.gz -rw-r--r-- 1 Sam staff 8252751 May 28 05:41 1SN_9A.models.tsv.gz -rw-r--r-- 1 Sam staff 56754889 May 28 05:41 1SN_9A.snps.tsv.gz -rw-r--r-- 1 Sam staff 69383399 May 28 05:41 1SN_9A.tags.tsv.gz -rw-r--r-- 1 Sam staff 110000181 Jun 16 13:03 batch_1.markers.tsv -rw-r--r-- 1 Sam staff 4096 Jun 16 13:03 batch_1.populations.log
%%bash
time /usr/local/bioinformatics/stacks-1.40/populations \
-P /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks \
-M /Volumes/toaster/sam/stacks/oly_BGI_GBS/populations/popmap \
-b 1 \
-k \
-s \
-e apeKI \
--genomic \
--fasta \
--vcf \
-t 8
Fst kernel smoothing: on
Bootstrap resampling: off
Percent samples limit per population: 0
Locus Population limit: 1
Minimum stack depth: 0
Log liklihood filtering: off; threshold: 0
Minor allele frequency cutoff: 0
Maximum observed heterozygosity cutoff: 1
Applying Fst correction: none.
Parsing population map.
Found 96 input file(s).
3 populations found
1HL: 1HL_10A, 1HL_11A, 1HL_12A, 1HL_13A, 1HL_14A, 1HL_15A, 1HL_16A, 1HL_17A, 1HL_19A, 1HL_1A, 1HL_20A, 1HL_21A, 1HL_22A, 1HL_23A, 1HL_24A, 1HL_25A, 1HL_26A, 1HL_27A, 1HL_28A, 1HL_29A, 1HL_2A, 1HL_31A, 1HL_33A, 1HL_34A, 1HL_35A, 1HL_3A, 1HL_4A, 1HL_5A, 1HL_6A, 1HL_7A, 1HL_8A, 1HL_9A
1NF: 1NF_10A, 1NF_11A, 1NF_12A, 1NF_13A, 1NF_14A, 1NF_15A, 1NF_16A, 1NF_17A, 1NF_18A, 1NF_19A, 1NF_1A, 1NF_20A, 1NF_21A, 1NF_22A, 1NF_23A, 1NF_24A, 1NF_25A, 1NF_26A, 1NF_27A, 1NF_28A, 1NF_29A, 1NF_2A, 1NF_30A, 1NF_31A, 1NF_32A, 1NF_33A, 1NF_4A, 1NF_5A, 1NF_6A, 1NF_7A, 1NF_8A, 1NF_9A
1SN: 1SN_10A, 1SN_11A, 1SN_12A, 1SN_13A, 1SN_14A, 1SN_15A, 1SN_16A, 1SN_17A, 1SN_18A, 1SN_19A, 1SN_1A, 1SN_20A, 1SN_21A, 1SN_22A, 1SN_23A, 1SN_24A, 1SN_25A, 1SN_26A, 1SN_27A, 1SN_28A, 1SN_29A, 1SN_2A, 1SN_30A, 1SN_31A, 1SN_32A, 1SN_3A, 1SN_4A, 1SN_5A, 1SN_6A, 1SN_7A, 1SN_8A, 1SN_9A
1 group of populations found
1: 1HL, 1NF, 1SN
Unable to open '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/batch_1.catalog'
Unable to load the catalog '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/batch_1.catalog'
real 0m0.520s
user 0m0.003s
sys 0m0.006s
%%bash
#cstacks command.
time /usr/local/bioinformatics/stacks-1.40/cstacks \
-b 1 \
-o /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/ \
-p 16 \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A \
-s /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A
Number of mismatches allowed between stacks: 1 Loci matched based on sequence identity. Constructing catalog from 96 samples. Initializing new catalog... Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A.alleles.tsv.gz 183160 loci were newly added to the catalog. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_10A [2 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 183160 loci in the catalog, 8110358 kmers in the catalog hash. Merging matches into catalog... 104767 loci were matched to a catalog locus. 1920 loci were matched to a catalog locus using gapped alignments. 92963 loci were newly added to the catalog. 1165 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_11A [3 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 276123 loci in the catalog, 12198042 kmers in the catalog hash. Merging matches into catalog... 105732 loci were matched to a catalog locus. 1670 loci were matched to a catalog locus using gapped alignments. 60766 loci were newly added to the catalog. 1940 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_12A [4 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 336889 loci in the catalog, 14971112 kmers in the catalog hash. Merging matches into catalog... 114432 loci were matched to a catalog locus. 2030 loci were matched to a catalog locus using gapped alignments. 42467 loci were newly added to the catalog. 2544 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_13A [5 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 379356 loci in the catalog, 16860233 kmers in the catalog hash. Merging matches into catalog... 104564 loci were matched to a catalog locus. 1601 loci were matched to a catalog locus using gapped alignments. 27581 loci were newly added to the catalog. 2523 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_14A [6 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 406937 loci in the catalog, 18086563 kmers in the catalog hash. Merging matches into catalog... 112519 loci were matched to a catalog locus. 1974 loci were matched to a catalog locus using gapped alignments. 28316 loci were newly added to the catalog. 2996 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_15A [7 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 435253 loci in the catalog, 19362608 kmers in the catalog hash. Merging matches into catalog... 122195 loci were matched to a catalog locus. 2135 loci were matched to a catalog locus using gapped alignments. 22975 loci were newly added to the catalog. 3062 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_16A [8 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 458228 loci in the catalog, 20360343 kmers in the catalog hash. Merging matches into catalog... 150003 loci were matched to a catalog locus. 3558 loci were matched to a catalog locus using gapped alignments. 34680 loci were newly added to the catalog. 3864 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_17A [9 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 492908 loci in the catalog, 21801899 kmers in the catalog hash. Merging matches into catalog... 157042 loci were matched to a catalog locus. 3886 loci were matched to a catalog locus using gapped alignments. 29567 loci were newly added to the catalog. 4087 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_19A [10 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 522475 loci in the catalog, 23014660 kmers in the catalog hash. Merging matches into catalog... 130965 loci were matched to a catalog locus. 2334 loci were matched to a catalog locus using gapped alignments. 12093 loci were newly added to the catalog. 3762 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_1A [11 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 534568 loci in the catalog, 23550938 kmers in the catalog hash. Merging matches into catalog... 133591 loci were matched to a catalog locus. 3001 loci were matched to a catalog locus using gapped alignments. 25537 loci were newly added to the catalog. 3818 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_20A [12 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 560105 loci in the catalog, 24630028 kmers in the catalog hash. Merging matches into catalog... 139118 loci were matched to a catalog locus. 2306 loci were matched to a catalog locus using gapped alignments. 14665 loci were newly added to the catalog. 3650 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_21A [13 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 574770 loci in the catalog, 25286839 kmers in the catalog hash. Merging matches into catalog... 119357 loci were matched to a catalog locus. 1986 loci were matched to a catalog locus using gapped alignments. 18370 loci were newly added to the catalog. 3384 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_22A [14 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 593140 loci in the catalog, 26119335 kmers in the catalog hash. Merging matches into catalog... 166710 loci were matched to a catalog locus. 4128 loci were matched to a catalog locus using gapped alignments. 20605 loci were newly added to the catalog. 4709 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_23A [15 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 613745 loci in the catalog, 26949235 kmers in the catalog hash. Merging matches into catalog... 134109 loci were matched to a catalog locus. 2872 loci were matched to a catalog locus using gapped alignments. 19874 loci were newly added to the catalog. 3992 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_24A [16 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 633619 loci in the catalog, 27790155 kmers in the catalog hash. Merging matches into catalog... 153315 loci were matched to a catalog locus. 3495 loci were matched to a catalog locus using gapped alignments. 13258 loci were newly added to the catalog. 4526 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_25A [17 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 646877 loci in the catalog, 28313360 kmers in the catalog hash. Merging matches into catalog... 159952 loci were matched to a catalog locus. 3537 loci were matched to a catalog locus using gapped alignments. 13982 loci were newly added to the catalog. 4425 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_26A [18 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 660859 loci in the catalog, 28867400 kmers in the catalog hash. Merging matches into catalog... 168249 loci were matched to a catalog locus. 3997 loci were matched to a catalog locus using gapped alignments. 13093 loci were newly added to the catalog. 5130 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_27A [19 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 673952 loci in the catalog, 29398942 kmers in the catalog hash. Merging matches into catalog... 172176 loci were matched to a catalog locus. 3040 loci were matched to a catalog locus using gapped alignments. 69769 loci were newly added to the catalog. 3599 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_28A [20 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 743721 loci in the catalog, 30454647 kmers in the catalog hash. Merging matches into catalog... 148578 loci were matched to a catalog locus. 3514 loci were matched to a catalog locus using gapped alignments. 20680 loci were newly added to the catalog. 4649 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_29A [21 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 764401 loci in the catalog, 31346732 kmers in the catalog hash. Merging matches into catalog... 141105 loci were matched to a catalog locus. 3014 loci were matched to a catalog locus using gapped alignments. 16598 loci were newly added to the catalog. 4427 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_2A [22 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 780999 loci in the catalog, 32061535 kmers in the catalog hash. Merging matches into catalog... 143352 loci were matched to a catalog locus. 2868 loci were matched to a catalog locus using gapped alignments. 7799 loci were newly added to the catalog. 4320 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_31A [23 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 788798 loci in the catalog, 32382361 kmers in the catalog hash. Merging matches into catalog... 146883 loci were matched to a catalog locus. 2809 loci were matched to a catalog locus using gapped alignments. 9380 loci were newly added to the catalog. 4296 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_33A [24 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 798178 loci in the catalog, 32759738 kmers in the catalog hash. Merging matches into catalog... 155078 loci were matched to a catalog locus. 3415 loci were matched to a catalog locus using gapped alignments. 10175 loci were newly added to the catalog. 4932 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_34A [25 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 808353 loci in the catalog, 33175470 kmers in the catalog hash. Merging matches into catalog... 153536 loci were matched to a catalog locus. 3254 loci were matched to a catalog locus using gapped alignments. 7917 loci were newly added to the catalog. 4674 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_35A [26 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 816270 loci in the catalog, 33510090 kmers in the catalog hash. Merging matches into catalog... 137936 loci were matched to a catalog locus. 2407 loci were matched to a catalog locus using gapped alignments. 7537 loci were newly added to the catalog. 3907 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_3A [27 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 823807 loci in the catalog, 33828932 kmers in the catalog hash. Merging matches into catalog... 140764 loci were matched to a catalog locus. 2985 loci were matched to a catalog locus using gapped alignments. 14130 loci were newly added to the catalog. 4356 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_4A [28 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 837937 loci in the catalog, 34457967 kmers in the catalog hash. Merging matches into catalog... 122087 loci were matched to a catalog locus. 2133 loci were matched to a catalog locus using gapped alignments. 10821 loci were newly added to the catalog. 3657 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_5A [29 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 848758 loci in the catalog, 34961553 kmers in the catalog hash. Merging matches into catalog... 129697 loci were matched to a catalog locus. 2382 loci were matched to a catalog locus using gapped alignments. 5572 loci were newly added to the catalog. 4095 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_6A [30 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 854330 loci in the catalog, 35183852 kmers in the catalog hash. Merging matches into catalog... 170299 loci were matched to a catalog locus. 4061 loci were matched to a catalog locus using gapped alignments. 55287 loci were newly added to the catalog. 4525 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_7A [31 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 909617 loci in the catalog, 36191260 kmers in the catalog hash. Merging matches into catalog... 136484 loci were matched to a catalog locus. 2909 loci were matched to a catalog locus using gapped alignments. 10740 loci were newly added to the catalog. 4515 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_8A [32 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 920357 loci in the catalog, 36653013 kmers in the catalog hash. Merging matches into catalog... 151544 loci were matched to a catalog locus. 3363 loci were matched to a catalog locus using gapped alignments. 8733 loci were newly added to the catalog. 4494 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1HL_9A [33 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 929090 loci in the catalog, 37001558 kmers in the catalog hash. Merging matches into catalog... 122531 loci were matched to a catalog locus. 2279 loci were matched to a catalog locus using gapped alignments. 9993 loci were newly added to the catalog. 3893 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_10A [34 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 939083 loci in the catalog, 37471326 kmers in the catalog hash. Merging matches into catalog... 126920 loci were matched to a catalog locus. 2531 loci were matched to a catalog locus using gapped alignments. 9983 loci were newly added to the catalog. 4072 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_11A [35 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 949066 loci in the catalog, 37933610 kmers in the catalog hash. Merging matches into catalog... 124403 loci were matched to a catalog locus. 2594 loci were matched to a catalog locus using gapped alignments. 8261 loci were newly added to the catalog. 3969 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_12A [36 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 957327 loci in the catalog, 38312906 kmers in the catalog hash. Merging matches into catalog... 180145 loci were matched to a catalog locus. 4955 loci were matched to a catalog locus using gapped alignments. 21140 loci were newly added to the catalog. 5949 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_13A [37 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 978467 loci in the catalog, 39266559 kmers in the catalog hash. Merging matches into catalog... 142499 loci were matched to a catalog locus. 3086 loci were matched to a catalog locus using gapped alignments. 11472 loci were newly added to the catalog. 4567 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_14A [38 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 989939 loci in the catalog, 39781739 kmers in the catalog hash. Merging matches into catalog... 140418 loci were matched to a catalog locus. 3066 loci were matched to a catalog locus using gapped alignments. 9934 loci were newly added to the catalog. 4249 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_15A [39 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 999873 loci in the catalog, 40227318 kmers in the catalog hash. Merging matches into catalog... 145386 loci were matched to a catalog locus. 3178 loci were matched to a catalog locus using gapped alignments. 11836 loci were newly added to the catalog. 4712 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_16A [40 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1011709 loci in the catalog, 40768532 kmers in the catalog hash. Merging matches into catalog... 157801 loci were matched to a catalog locus. 4018 loci were matched to a catalog locus using gapped alignments. 13522 loci were newly added to the catalog. 5228 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_17A [41 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1025231 loci in the catalog, 41369702 kmers in the catalog hash. Merging matches into catalog... 113649 loci were matched to a catalog locus. 1942 loci were matched to a catalog locus using gapped alignments. 7197 loci were newly added to the catalog. 3757 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_18A [42 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1032428 loci in the catalog, 41703211 kmers in the catalog hash. Merging matches into catalog... 117852 loci were matched to a catalog locus. 2256 loci were matched to a catalog locus using gapped alignments. 5995 loci were newly added to the catalog. 3775 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_19A [43 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1038423 loci in the catalog, 41974645 kmers in the catalog hash. Merging matches into catalog... 93290 loci were matched to a catalog locus. 1397 loci were matched to a catalog locus using gapped alignments. 2381 loci were newly added to the catalog. 3076 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_1A [44 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1040804 loci in the catalog, 42097979 kmers in the catalog hash. Merging matches into catalog... 139929 loci were matched to a catalog locus. 3082 loci were matched to a catalog locus using gapped alignments. 8321 loci were newly added to the catalog. 4513 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_20A [45 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1049125 loci in the catalog, 42480411 kmers in the catalog hash. Merging matches into catalog... 161973 loci were matched to a catalog locus. 4213 loci were matched to a catalog locus using gapped alignments. 21986 loci were newly added to the catalog. 5227 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_21A [46 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1071111 loci in the catalog, 43514289 kmers in the catalog hash. Merging matches into catalog... 150967 loci were matched to a catalog locus. 3714 loci were matched to a catalog locus using gapped alignments. 10885 loci were newly added to the catalog. 4952 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_22A [47 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1081996 loci in the catalog, 44005193 kmers in the catalog hash. Merging matches into catalog... 168044 loci were matched to a catalog locus. 4230 loci were matched to a catalog locus using gapped alignments. 13881 loci were newly added to the catalog. 5367 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_23A [48 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1095877 loci in the catalog, 44619247 kmers in the catalog hash. Merging matches into catalog... 158547 loci were matched to a catalog locus. 3891 loci were matched to a catalog locus using gapped alignments. 11713 loci were newly added to the catalog. 5102 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_24A [49 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1107590 loci in the catalog, 45148968 kmers in the catalog hash. Merging matches into catalog... 130501 loci were matched to a catalog locus. 2764 loci were matched to a catalog locus using gapped alignments. 5144 loci were newly added to the catalog. 4337 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_25A [50 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1112734 loci in the catalog, 45388350 kmers in the catalog hash. Merging matches into catalog... 162717 loci were matched to a catalog locus. 4143 loci were matched to a catalog locus using gapped alignments. 9781 loci were newly added to the catalog. 5397 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_26A [51 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1122515 loci in the catalog, 45838173 kmers in the catalog hash. Merging matches into catalog... 135980 loci were matched to a catalog locus. 2514 loci were matched to a catalog locus using gapped alignments. 6135 loci were newly added to the catalog. 4275 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_27A [52 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1128650 loci in the catalog, 46131694 kmers in the catalog hash. Merging matches into catalog... 138293 loci were matched to a catalog locus. 2816 loci were matched to a catalog locus using gapped alignments. 6326 loci were newly added to the catalog. 4490 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_28A [53 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1134976 loci in the catalog, 46427547 kmers in the catalog hash. Merging matches into catalog... 168267 loci were matched to a catalog locus. 5120 loci were matched to a catalog locus using gapped alignments. 10695 loci were newly added to the catalog. 6158 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_29A [54 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1145671 loci in the catalog, 46882780 kmers in the catalog hash. Merging matches into catalog... 166885 loci were matched to a catalog locus. 4425 loci were matched to a catalog locus using gapped alignments. 10863 loci were newly added to the catalog. 5482 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_2A [55 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1156534 loci in the catalog, 47367943 kmers in the catalog hash. Merging matches into catalog... 146605 loci were matched to a catalog locus. 3450 loci were matched to a catalog locus using gapped alignments. 5613 loci were newly added to the catalog. 4809 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_30A [56 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1162147 loci in the catalog, 47612108 kmers in the catalog hash. Merging matches into catalog... 174655 loci were matched to a catalog locus. 4962 loci were matched to a catalog locus using gapped alignments. 10345 loci were newly added to the catalog. 5979 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_31A [57 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1172492 loci in the catalog, 48049440 kmers in the catalog hash. Merging matches into catalog... 179396 loci were matched to a catalog locus. 4922 loci were matched to a catalog locus using gapped alignments. 10120 loci were newly added to the catalog. 5871 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_32A [58 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1182612 loci in the catalog, 48495086 kmers in the catalog hash. Merging matches into catalog... 147076 loci were matched to a catalog locus. 3288 loci were matched to a catalog locus using gapped alignments. 5840 loci were newly added to the catalog. 4758 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_33A [59 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1188452 loci in the catalog, 48761950 kmers in the catalog hash. Merging matches into catalog... 180719 loci were matched to a catalog locus. 5206 loci were matched to a catalog locus using gapped alignments. 9030 loci were newly added to the catalog. 5950 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_4A [60 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1197482 loci in the catalog, 49163909 kmers in the catalog hash. Merging matches into catalog... 156394 loci were matched to a catalog locus. 3502 loci were matched to a catalog locus using gapped alignments. 7189 loci were newly added to the catalog. 5022 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_5A [61 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1204671 loci in the catalog, 49501494 kmers in the catalog hash. Merging matches into catalog... 141262 loci were matched to a catalog locus. 2738 loci were matched to a catalog locus using gapped alignments. 4166 loci were newly added to the catalog. 4402 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_6A [62 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1208837 loci in the catalog, 49691904 kmers in the catalog hash. Merging matches into catalog... 143824 loci were matched to a catalog locus. 3366 loci were matched to a catalog locus using gapped alignments. 6312 loci were newly added to the catalog. 4795 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_7A [63 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1215149 loci in the catalog, 49987240 kmers in the catalog hash. Merging matches into catalog... 149431 loci were matched to a catalog locus. 3481 loci were matched to a catalog locus using gapped alignments. 7529 loci were newly added to the catalog. 4872 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_8A [64 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1222678 loci in the catalog, 50322455 kmers in the catalog hash. Merging matches into catalog... 167112 loci were matched to a catalog locus. 4449 loci were matched to a catalog locus using gapped alignments. 9174 loci were newly added to the catalog. 5657 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1NF_9A [65 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1231852 loci in the catalog, 50732054 kmers in the catalog hash. Merging matches into catalog... 145884 loci were matched to a catalog locus. 3164 loci were matched to a catalog locus using gapped alignments. 8718 loci were newly added to the catalog. 4607 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_10A [66 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1240570 loci in the catalog, 51124069 kmers in the catalog hash. Merging matches into catalog... 147279 loci were matched to a catalog locus. 3160 loci were matched to a catalog locus using gapped alignments. 6894 loci were newly added to the catalog. 5065 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_11A [67 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1247464 loci in the catalog, 51442197 kmers in the catalog hash. Merging matches into catalog... 180500 loci were matched to a catalog locus. 4985 loci were matched to a catalog locus using gapped alignments. 11519 loci were newly added to the catalog. 6021 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_12A [68 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1258983 loci in the catalog, 51944010 kmers in the catalog hash. Merging matches into catalog... 161533 loci were matched to a catalog locus. 3745 loci were matched to a catalog locus using gapped alignments. 9067 loci were newly added to the catalog. 5216 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_13A [69 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1268050 loci in the catalog, 52364892 kmers in the catalog hash. Merging matches into catalog... 173631 loci were matched to a catalog locus. 4829 loci were matched to a catalog locus using gapped alignments. 9779 loci were newly added to the catalog. 6056 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_14A [70 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1277829 loci in the catalog, 52782712 kmers in the catalog hash. Merging matches into catalog... 144860 loci were matched to a catalog locus. 3201 loci were matched to a catalog locus using gapped alignments. 5758 loci were newly added to the catalog. 4607 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_15A [71 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1283587 loci in the catalog, 53032378 kmers in the catalog hash. Merging matches into catalog... 144771 loci were matched to a catalog locus. 3234 loci were matched to a catalog locus using gapped alignments. 6509 loci were newly added to the catalog. 5154 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_16A [72 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1290096 loci in the catalog, 53312634 kmers in the catalog hash. Merging matches into catalog... 165406 loci were matched to a catalog locus. 4129 loci were matched to a catalog locus using gapped alignments. 8041 loci were newly added to the catalog. 5346 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_17A [73 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1298137 loci in the catalog, 53662757 kmers in the catalog hash. Merging matches into catalog... 166197 loci were matched to a catalog locus. 4242 loci were matched to a catalog locus using gapped alignments. 9113 loci were newly added to the catalog. 5581 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_18A [74 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1307250 loci in the catalog, 54036847 kmers in the catalog hash. Merging matches into catalog... 165152 loci were matched to a catalog locus. 4052 loci were matched to a catalog locus using gapped alignments. 7876 loci were newly added to the catalog. 5460 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_19A [75 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1315126 loci in the catalog, 54384733 kmers in the catalog hash. Merging matches into catalog... 156453 loci were matched to a catalog locus. 3968 loci were matched to a catalog locus using gapped alignments. 6171 loci were newly added to the catalog. 5339 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_1A [76 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1321297 loci in the catalog, 54658761 kmers in the catalog hash. Merging matches into catalog... 127265 loci were matched to a catalog locus. 2518 loci were matched to a catalog locus using gapped alignments. 6419 loci were newly added to the catalog. 4253 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_20A [77 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1327716 loci in the catalog, 54953438 kmers in the catalog hash. Merging matches into catalog... 178663 loci were matched to a catalog locus. 5150 loci were matched to a catalog locus using gapped alignments. 10472 loci were newly added to the catalog. 6205 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_21A [78 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1338188 loci in the catalog, 55401038 kmers in the catalog hash. Merging matches into catalog... 164476 loci were matched to a catalog locus. 4039 loci were matched to a catalog locus using gapped alignments. 7603 loci were newly added to the catalog. 5764 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_22A [79 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1345791 loci in the catalog, 55735476 kmers in the catalog hash. Merging matches into catalog... 185852 loci were matched to a catalog locus. 5689 loci were matched to a catalog locus using gapped alignments. 10971 loci were newly added to the catalog. 6375 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_23A [80 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1356762 loci in the catalog, 56203922 kmers in the catalog hash. Merging matches into catalog... 119609 loci were matched to a catalog locus. 2098 loci were matched to a catalog locus using gapped alignments. 3898 loci were newly added to the catalog. 3757 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_24A [81 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1360660 loci in the catalog, 56368517 kmers in the catalog hash. Merging matches into catalog... 159202 loci were matched to a catalog locus. 3940 loci were matched to a catalog locus using gapped alignments. 7393 loci were newly added to the catalog. 5336 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_25A [82 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1368053 loci in the catalog, 56678447 kmers in the catalog hash. Merging matches into catalog... 155327 loci were matched to a catalog locus. 3757 loci were matched to a catalog locus using gapped alignments. 5498 loci were newly added to the catalog. 5128 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_26A [83 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1373551 loci in the catalog, 56889919 kmers in the catalog hash. Merging matches into catalog... 146202 loci were matched to a catalog locus. 3132 loci were matched to a catalog locus using gapped alignments. 5530 loci were newly added to the catalog. 4958 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_27A [84 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1379081 loci in the catalog, 57114237 kmers in the catalog hash. Merging matches into catalog... 154046 loci were matched to a catalog locus. 3586 loci were matched to a catalog locus using gapped alignments. 6935 loci were newly added to the catalog. 5061 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_28A [85 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1386016 loci in the catalog, 57398744 kmers in the catalog hash. Merging matches into catalog... 116402 loci were matched to a catalog locus. 2724 loci were matched to a catalog locus using gapped alignments. 7654 loci were newly added to the catalog. 4167 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_29A [86 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1393670 loci in the catalog, 57712433 kmers in the catalog hash. Merging matches into catalog... 162404 loci were matched to a catalog locus. 4017 loci were matched to a catalog locus using gapped alignments. 6502 loci were newly added to the catalog. 5515 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_2A [87 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1400172 loci in the catalog, 57990740 kmers in the catalog hash. Merging matches into catalog... 189111 loci were matched to a catalog locus. 5784 loci were matched to a catalog locus using gapped alignments. 10147 loci were newly added to the catalog. 6410 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_30A [88 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1410319 loci in the catalog, 58394530 kmers in the catalog hash. Merging matches into catalog... 168640 loci were matched to a catalog locus. 4395 loci were matched to a catalog locus using gapped alignments. 7295 loci were newly added to the catalog. 5835 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_31A [89 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1417614 loci in the catalog, 58679011 kmers in the catalog hash. Merging matches into catalog... 142712 loci were matched to a catalog locus. 3169 loci were matched to a catalog locus using gapped alignments. 6733 loci were newly added to the catalog. 4665 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_32A [90 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1424347 loci in the catalog, 58966864 kmers in the catalog hash. Merging matches into catalog... 143387 loci were matched to a catalog locus. 2875 loci were matched to a catalog locus using gapped alignments. 9673 loci were newly added to the catalog. 4429 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_3A [91 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1434020 loci in the catalog, 59413308 kmers in the catalog hash. Merging matches into catalog... 177652 loci were matched to a catalog locus. 4934 loci were matched to a catalog locus using gapped alignments. 6430 loci were newly added to the catalog. 5946 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_4A [92 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1440450 loci in the catalog, 59676746 kmers in the catalog hash. Merging matches into catalog... 171208 loci were matched to a catalog locus. 4199 loci were matched to a catalog locus using gapped alignments. 6895 loci were newly added to the catalog. 5681 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_5A [93 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1447345 loci in the catalog, 59976029 kmers in the catalog hash. Merging matches into catalog... 172530 loci were matched to a catalog locus. 4752 loci were matched to a catalog locus using gapped alignments. 7801 loci were newly added to the catalog. 5951 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_6A [94 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1455146 loci in the catalog, 60300566 kmers in the catalog hash. Merging matches into catalog... 163373 loci were matched to a catalog locus. 4111 loci were matched to a catalog locus using gapped alignments. 6957 loci were newly added to the catalog. 5375 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_7A [95 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1462103 loci in the catalog, 60600774 kmers in the catalog hash. Merging matches into catalog... 173497 loci were matched to a catalog locus. 4564 loci were matched to a catalog locus using gapped alignments. 6564 loci were newly added to the catalog. 5630 loci matched more than one catalog locus and were excluded. Processing sample /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_8A [96 of 96] Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A.tags.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A.snps.tsv.gz Parsing /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/1SN_9A.alleles.tsv.gz Searching for sequence matches... Distance allowed between stacks: 1; searching with a k-mer length of 45 (46 k-mers per read); 1 k-mer hits required. 1468667 loci in the catalog, 60878194 kmers in the catalog hash. Merging matches into catalog... 174474 loci were matched to a catalog locus. 4913 loci were matched to a catalog locus using gapped alignments. 7226 loci were newly added to the catalog. 5863 loci matched more than one catalog locus and were excluded. Writing catalog to '/Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks/... done. real 1498m41.735s user 1475m35.020s sys 21m41.917s
ls
1HL_10A.alleles.tsv.gz 1HL_24A.alleles.tsv.gz 1HL_6A.alleles.tsv.gz 1NF_1A.alleles.tsv.gz 1NF_32A.alleles.tsv.gz 1SN_16A.alleles.tsv.gz 1SN_29A.alleles.tsv.gz 1HL_10A.matches.tsv.gz 1HL_24A.matches.tsv.gz 1HL_6A.matches.tsv.gz 1NF_1A.matches.tsv.gz 1NF_32A.matches.tsv.gz 1SN_16A.matches.tsv.gz 1SN_29A.matches.tsv.gz 1HL_10A.models.tsv.gz 1HL_24A.models.tsv.gz 1HL_6A.models.tsv.gz 1NF_1A.models.tsv.gz 1NF_32A.models.tsv.gz 1SN_16A.models.tsv.gz 1SN_29A.models.tsv.gz 1HL_10A.snps.tsv.gz 1HL_24A.snps.tsv.gz 1HL_6A.snps.tsv.gz 1NF_1A.snps.tsv.gz 1NF_32A.snps.tsv.gz 1SN_16A.snps.tsv.gz 1SN_29A.snps.tsv.gz 1HL_10A.tags.tsv.gz 1HL_24A.tags.tsv.gz 1HL_6A.tags.tsv.gz 1NF_1A.tags.tsv.gz 1NF_32A.tags.tsv.gz 1SN_16A.tags.tsv.gz 1SN_29A.tags.tsv.gz 1HL_11A.alleles.tsv.gz 1HL_25A.alleles.tsv.gz 1HL_7A.alleles.tsv.gz 1NF_20A.alleles.tsv.gz 1NF_33A.alleles.tsv.gz 1SN_17A.alleles.tsv.gz 1SN_2A.alleles.tsv.gz 1HL_11A.matches.tsv.gz 1HL_25A.matches.tsv.gz 1HL_7A.matches.tsv.gz 1NF_20A.matches.tsv.gz 1NF_33A.matches.tsv.gz 1SN_17A.matches.tsv.gz 1SN_2A.matches.tsv.gz 1HL_11A.models.tsv.gz 1HL_25A.models.tsv.gz 1HL_7A.models.tsv.gz 1NF_20A.models.tsv.gz 1NF_33A.models.tsv.gz 1SN_17A.models.tsv.gz 1SN_2A.models.tsv.gz 1HL_11A.snps.tsv.gz 1HL_25A.snps.tsv.gz 1HL_7A.snps.tsv.gz 1NF_20A.snps.tsv.gz 1NF_33A.snps.tsv.gz 1SN_17A.snps.tsv.gz 1SN_2A.snps.tsv.gz 1HL_11A.tags.tsv.gz 1HL_25A.tags.tsv.gz 1HL_7A.tags.tsv.gz 1NF_20A.tags.tsv.gz 1NF_33A.tags.tsv.gz 1SN_17A.tags.tsv.gz 1SN_2A.tags.tsv.gz 1HL_12A.alleles.tsv.gz 1HL_26A.alleles.tsv.gz 1HL_8A.alleles.tsv.gz 1NF_21A.alleles.tsv.gz 1NF_4A.alleles.tsv.gz 1SN_18A.alleles.tsv.gz 1SN_30A.alleles.tsv.gz 1HL_12A.matches.tsv.gz 1HL_26A.matches.tsv.gz 1HL_8A.matches.tsv.gz 1NF_21A.matches.tsv.gz 1NF_4A.matches.tsv.gz 1SN_18A.matches.tsv.gz 1SN_30A.matches.tsv.gz 1HL_12A.models.tsv.gz 1HL_26A.models.tsv.gz 1HL_8A.models.tsv.gz 1NF_21A.models.tsv.gz 1NF_4A.models.tsv.gz 1SN_18A.models.tsv.gz 1SN_30A.models.tsv.gz 1HL_12A.snps.tsv.gz 1HL_26A.snps.tsv.gz 1HL_8A.snps.tsv.gz 1NF_21A.snps.tsv.gz 1NF_4A.snps.tsv.gz 1SN_18A.snps.tsv.gz 1SN_30A.snps.tsv.gz 1HL_12A.tags.tsv.gz 1HL_26A.tags.tsv.gz 1HL_8A.tags.tsv.gz 1NF_21A.tags.tsv.gz 1NF_4A.tags.tsv.gz 1SN_18A.tags.tsv.gz 1SN_30A.tags.tsv.gz 1HL_13A.alleles.tsv.gz 1HL_27A.alleles.tsv.gz 1HL_9A.alleles.tsv.gz 1NF_22A.alleles.tsv.gz 1NF_5A.alleles.tsv.gz 1SN_19A.alleles.tsv.gz 1SN_31A.alleles.tsv.gz 1HL_13A.matches.tsv.gz 1HL_27A.matches.tsv.gz 1HL_9A.matches.tsv.gz 1NF_22A.matches.tsv.gz 1NF_5A.matches.tsv.gz 1SN_19A.matches.tsv.gz 1SN_31A.matches.tsv.gz 1HL_13A.models.tsv.gz 1HL_27A.models.tsv.gz 1HL_9A.models.tsv.gz 1NF_22A.models.tsv.gz 1NF_5A.models.tsv.gz 1SN_19A.models.tsv.gz 1SN_31A.models.tsv.gz 1HL_13A.snps.tsv.gz 1HL_27A.snps.tsv.gz 1HL_9A.snps.tsv.gz 1NF_22A.snps.tsv.gz 1NF_5A.snps.tsv.gz 1SN_19A.snps.tsv.gz 1SN_31A.snps.tsv.gz 1HL_13A.tags.tsv.gz 1HL_27A.tags.tsv.gz 1HL_9A.tags.tsv.gz 1NF_22A.tags.tsv.gz 1NF_5A.tags.tsv.gz 1SN_19A.tags.tsv.gz 1SN_31A.tags.tsv.gz 1HL_14A.alleles.tsv.gz 1HL_28A.alleles.tsv.gz 1NF_10A.alleles.tsv.gz 1NF_23A.alleles.tsv.gz 1NF_6A.alleles.tsv.gz 1SN_1A.alleles.tsv.gz 1SN_32A.alleles.tsv.gz 1HL_14A.matches.tsv.gz 1HL_28A.matches.tsv.gz 1NF_10A.matches.tsv.gz 1NF_23A.matches.tsv.gz 1NF_6A.matches.tsv.gz 1SN_1A.matches.tsv.gz 1SN_32A.matches.tsv.gz 1HL_14A.models.tsv.gz 1HL_28A.models.tsv.gz 1NF_10A.models.tsv.gz 1NF_23A.models.tsv.gz 1NF_6A.models.tsv.gz 1SN_1A.models.tsv.gz 1SN_32A.models.tsv.gz 1HL_14A.snps.tsv.gz 1HL_28A.snps.tsv.gz 1NF_10A.snps.tsv.gz 1NF_23A.snps.tsv.gz 1NF_6A.snps.tsv.gz 1SN_1A.snps.tsv.gz 1SN_32A.snps.tsv.gz 1HL_14A.tags.tsv.gz 1HL_28A.tags.tsv.gz 1NF_10A.tags.tsv.gz 1NF_23A.tags.tsv.gz 1NF_6A.tags.tsv.gz 1SN_1A.tags.tsv.gz 1SN_32A.tags.tsv.gz 1HL_15A.alleles.tsv.gz 1HL_29A.alleles.tsv.gz 1NF_11A.alleles.tsv.gz 1NF_24A.alleles.tsv.gz 1NF_7A.alleles.tsv.gz 1SN_20A.alleles.tsv.gz 1SN_3A.alleles.tsv.gz 1HL_15A.matches.tsv.gz 1HL_29A.matches.tsv.gz 1NF_11A.matches.tsv.gz 1NF_24A.matches.tsv.gz 1NF_7A.matches.tsv.gz 1SN_20A.matches.tsv.gz 1SN_3A.matches.tsv.gz 1HL_15A.models.tsv.gz 1HL_29A.models.tsv.gz 1NF_11A.models.tsv.gz 1NF_24A.models.tsv.gz 1NF_7A.models.tsv.gz 1SN_20A.models.tsv.gz 1SN_3A.models.tsv.gz 1HL_15A.snps.tsv.gz 1HL_29A.snps.tsv.gz 1NF_11A.snps.tsv.gz 1NF_24A.snps.tsv.gz 1NF_7A.snps.tsv.gz 1SN_20A.snps.tsv.gz 1SN_3A.snps.tsv.gz 1HL_15A.tags.tsv.gz 1HL_29A.tags.tsv.gz 1NF_11A.tags.tsv.gz 1NF_24A.tags.tsv.gz 1NF_7A.tags.tsv.gz 1SN_20A.tags.tsv.gz 1SN_3A.tags.tsv.gz 1HL_16A.alleles.tsv.gz 1HL_2A.alleles.tsv.gz 1NF_12A.alleles.tsv.gz 1NF_25A.alleles.tsv.gz 1NF_8A.alleles.tsv.gz 1SN_21A.alleles.tsv.gz 1SN_4A.alleles.tsv.gz 1HL_16A.matches.tsv.gz 1HL_2A.matches.tsv.gz 1NF_12A.matches.tsv.gz 1NF_25A.matches.tsv.gz 1NF_8A.matches.tsv.gz 1SN_21A.matches.tsv.gz 1SN_4A.matches.tsv.gz 1HL_16A.models.tsv.gz 1HL_2A.models.tsv.gz 1NF_12A.models.tsv.gz 1NF_25A.models.tsv.gz 1NF_8A.models.tsv.gz 1SN_21A.models.tsv.gz 1SN_4A.models.tsv.gz 1HL_16A.snps.tsv.gz 1HL_2A.snps.tsv.gz 1NF_12A.snps.tsv.gz 1NF_25A.snps.tsv.gz 1NF_8A.snps.tsv.gz 1SN_21A.snps.tsv.gz 1SN_4A.snps.tsv.gz 1HL_16A.tags.tsv.gz 1HL_2A.tags.tsv.gz 1NF_12A.tags.tsv.gz 1NF_25A.tags.tsv.gz 1NF_8A.tags.tsv.gz 1SN_21A.tags.tsv.gz 1SN_4A.tags.tsv.gz 1HL_17A.alleles.tsv.gz 1HL_31A.alleles.tsv.gz 1NF_13A.alleles.tsv.gz 1NF_26A.alleles.tsv.gz 1NF_9A.alleles.tsv.gz 1SN_22A.alleles.tsv.gz 1SN_5A.alleles.tsv.gz 1HL_17A.matches.tsv.gz 1HL_31A.matches.tsv.gz 1NF_13A.matches.tsv.gz 1NF_26A.matches.tsv.gz 1NF_9A.matches.tsv.gz 1SN_22A.matches.tsv.gz 1SN_5A.matches.tsv.gz 1HL_17A.models.tsv.gz 1HL_31A.models.tsv.gz 1NF_13A.models.tsv.gz 1NF_26A.models.tsv.gz 1NF_9A.models.tsv.gz 1SN_22A.models.tsv.gz 1SN_5A.models.tsv.gz 1HL_17A.snps.tsv.gz 1HL_31A.snps.tsv.gz 1NF_13A.snps.tsv.gz 1NF_26A.snps.tsv.gz 1NF_9A.snps.tsv.gz 1SN_22A.snps.tsv.gz 1SN_5A.snps.tsv.gz 1HL_17A.tags.tsv.gz 1HL_31A.tags.tsv.gz 1NF_13A.tags.tsv.gz 1NF_26A.tags.tsv.gz 1NF_9A.tags.tsv.gz 1SN_22A.tags.tsv.gz 1SN_5A.tags.tsv.gz 1HL_19A.alleles.tsv.gz 1HL_33A.alleles.tsv.gz 1NF_14A.alleles.tsv.gz 1NF_27A.alleles.tsv.gz 1SN_10A.alleles.tsv.gz 1SN_23A.alleles.tsv.gz 1SN_6A.alleles.tsv.gz 1HL_19A.matches.tsv.gz 1HL_33A.matches.tsv.gz 1NF_14A.matches.tsv.gz 1NF_27A.matches.tsv.gz 1SN_10A.matches.tsv.gz 1SN_23A.matches.tsv.gz 1SN_6A.matches.tsv.gz 1HL_19A.models.tsv.gz 1HL_33A.models.tsv.gz 1NF_14A.models.tsv.gz 1NF_27A.models.tsv.gz 1SN_10A.models.tsv.gz 1SN_23A.models.tsv.gz 1SN_6A.models.tsv.gz 1HL_19A.snps.tsv.gz 1HL_33A.snps.tsv.gz 1NF_14A.snps.tsv.gz 1NF_27A.snps.tsv.gz 1SN_10A.snps.tsv.gz 1SN_23A.snps.tsv.gz 1SN_6A.snps.tsv.gz 1HL_19A.tags.tsv.gz 1HL_33A.tags.tsv.gz 1NF_14A.tags.tsv.gz 1NF_27A.tags.tsv.gz 1SN_10A.tags.tsv.gz 1SN_23A.tags.tsv.gz 1SN_6A.tags.tsv.gz 1HL_1A.alleles.tsv.gz 1HL_34A.alleles.tsv.gz 1NF_15A.alleles.tsv.gz 1NF_28A.alleles.tsv.gz 1SN_11A.alleles.tsv.gz 1SN_24A.alleles.tsv.gz 1SN_7A.alleles.tsv.gz 1HL_1A.matches.tsv.gz 1HL_34A.matches.tsv.gz 1NF_15A.matches.tsv.gz 1NF_28A.matches.tsv.gz 1SN_11A.matches.tsv.gz 1SN_24A.matches.tsv.gz 1SN_7A.matches.tsv.gz 1HL_1A.models.tsv.gz 1HL_34A.models.tsv.gz 1NF_15A.models.tsv.gz 1NF_28A.models.tsv.gz 1SN_11A.models.tsv.gz 1SN_24A.models.tsv.gz 1SN_7A.models.tsv.gz 1HL_1A.snps.tsv.gz 1HL_34A.snps.tsv.gz 1NF_15A.snps.tsv.gz 1NF_28A.snps.tsv.gz 1SN_11A.snps.tsv.gz 1SN_24A.snps.tsv.gz 1SN_7A.snps.tsv.gz 1HL_1A.tags.tsv.gz 1HL_34A.tags.tsv.gz 1NF_15A.tags.tsv.gz 1NF_28A.tags.tsv.gz 1SN_11A.tags.tsv.gz 1SN_24A.tags.tsv.gz 1SN_7A.tags.tsv.gz 1HL_20A.alleles.tsv.gz 1HL_35A.alleles.tsv.gz 1NF_16A.alleles.tsv.gz 1NF_29A.alleles.tsv.gz 1SN_12A.alleles.tsv.gz 1SN_25A.alleles.tsv.gz 1SN_8A.alleles.tsv.gz 1HL_20A.matches.tsv.gz 1HL_35A.matches.tsv.gz 1NF_16A.matches.tsv.gz 1NF_29A.matches.tsv.gz 1SN_12A.matches.tsv.gz 1SN_25A.matches.tsv.gz 1SN_8A.matches.tsv.gz 1HL_20A.models.tsv.gz 1HL_35A.models.tsv.gz 1NF_16A.models.tsv.gz 1NF_29A.models.tsv.gz 1SN_12A.models.tsv.gz 1SN_25A.models.tsv.gz 1SN_8A.models.tsv.gz 1HL_20A.snps.tsv.gz 1HL_35A.snps.tsv.gz 1NF_16A.snps.tsv.gz 1NF_29A.snps.tsv.gz 1SN_12A.snps.tsv.gz 1SN_25A.snps.tsv.gz 1SN_8A.snps.tsv.gz 1HL_20A.tags.tsv.gz 1HL_35A.tags.tsv.gz 1NF_16A.tags.tsv.gz 1NF_29A.tags.tsv.gz 1SN_12A.tags.tsv.gz 1SN_25A.tags.tsv.gz 1SN_8A.tags.tsv.gz 1HL_21A.alleles.tsv.gz 1HL_3A.alleles.tsv.gz 1NF_17A.alleles.tsv.gz 1NF_2A.alleles.tsv.gz 1SN_13A.alleles.tsv.gz 1SN_26A.alleles.tsv.gz 1SN_9A.alleles.tsv.gz 1HL_21A.matches.tsv.gz 1HL_3A.matches.tsv.gz 1NF_17A.matches.tsv.gz 1NF_2A.matches.tsv.gz 1SN_13A.matches.tsv.gz 1SN_26A.matches.tsv.gz 1SN_9A.matches.tsv.gz 1HL_21A.models.tsv.gz 1HL_3A.models.tsv.gz 1NF_17A.models.tsv.gz 1NF_2A.models.tsv.gz 1SN_13A.models.tsv.gz 1SN_26A.models.tsv.gz 1SN_9A.models.tsv.gz 1HL_21A.snps.tsv.gz 1HL_3A.snps.tsv.gz 1NF_17A.snps.tsv.gz 1NF_2A.snps.tsv.gz 1SN_13A.snps.tsv.gz 1SN_26A.snps.tsv.gz 1SN_9A.snps.tsv.gz 1HL_21A.tags.tsv.gz 1HL_3A.tags.tsv.gz 1NF_17A.tags.tsv.gz 1NF_2A.tags.tsv.gz 1SN_13A.tags.tsv.gz 1SN_26A.tags.tsv.gz 1SN_9A.tags.tsv.gz 1HL_22A.alleles.tsv.gz 1HL_4A.alleles.tsv.gz 1NF_18A.alleles.tsv.gz 1NF_30A.alleles.tsv.gz 1SN_14A.alleles.tsv.gz 1SN_27A.alleles.tsv.gz batch_1.catalog.alleles.tsv.gz 1HL_22A.matches.tsv.gz 1HL_4A.matches.tsv.gz 1NF_18A.matches.tsv.gz 1NF_30A.matches.tsv.gz 1SN_14A.matches.tsv.gz 1SN_27A.matches.tsv.gz batch_1.catalog.snps.tsv.gz 1HL_22A.models.tsv.gz 1HL_4A.models.tsv.gz 1NF_18A.models.tsv.gz 1NF_30A.models.tsv.gz 1SN_14A.models.tsv.gz 1SN_27A.models.tsv.gz batch_1.catalog.tags.tsv.gz 1HL_22A.snps.tsv.gz 1HL_4A.snps.tsv.gz 1NF_18A.snps.tsv.gz 1NF_30A.snps.tsv.gz 1SN_14A.snps.tsv.gz 1SN_27A.snps.tsv.gz batch_1.markers.tsv 1HL_22A.tags.tsv.gz 1HL_4A.tags.tsv.gz 1NF_18A.tags.tsv.gz 1NF_30A.tags.tsv.gz 1SN_14A.tags.tsv.gz 1SN_27A.tags.tsv.gz batch_1.populations.log 1HL_23A.alleles.tsv.gz 1HL_5A.alleles.tsv.gz 1NF_19A.alleles.tsv.gz 1NF_31A.alleles.tsv.gz 1SN_15A.alleles.tsv.gz 1SN_28A.alleles.tsv.gz 1HL_23A.matches.tsv.gz 1HL_5A.matches.tsv.gz 1NF_19A.matches.tsv.gz 1NF_31A.matches.tsv.gz 1SN_15A.matches.tsv.gz 1SN_28A.matches.tsv.gz 1HL_23A.models.tsv.gz 1HL_5A.models.tsv.gz 1NF_19A.models.tsv.gz 1NF_31A.models.tsv.gz 1SN_15A.models.tsv.gz 1SN_28A.models.tsv.gz 1HL_23A.snps.tsv.gz 1HL_5A.snps.tsv.gz 1NF_19A.snps.tsv.gz 1NF_31A.snps.tsv.gz 1SN_15A.snps.tsv.gz 1SN_28A.snps.tsv.gz 1HL_23A.tags.tsv.gz 1HL_5A.tags.tsv.gz 1NF_19A.tags.tsv.gz 1NF_31A.tags.tsv.gz 1SN_15A.tags.tsv.gz 1SN_28A.tags.tsv.gz
%%bash
rm batch_1.populations.log batch_1.markers.tsv
ls
1HL_10A.alleles.tsv.gz 1HL_23A.tags.tsv.gz 1HL_5A.snps.tsv.gz 1NF_19A.models.tsv.gz 1NF_31A.matches.tsv.gz 1SN_15A.alleles.tsv.gz 1SN_27A.tags.tsv.gz 1HL_10A.matches.tsv.gz 1HL_24A.alleles.tsv.gz 1HL_5A.tags.tsv.gz 1NF_19A.snps.tsv.gz 1NF_31A.models.tsv.gz 1SN_15A.matches.tsv.gz 1SN_28A.alleles.tsv.gz 1HL_10A.models.tsv.gz 1HL_24A.matches.tsv.gz 1HL_6A.alleles.tsv.gz 1NF_19A.tags.tsv.gz 1NF_31A.snps.tsv.gz 1SN_15A.models.tsv.gz 1SN_28A.matches.tsv.gz 1HL_10A.snps.tsv.gz 1HL_24A.models.tsv.gz 1HL_6A.matches.tsv.gz 1NF_1A.alleles.tsv.gz 1NF_31A.tags.tsv.gz 1SN_15A.snps.tsv.gz 1SN_28A.models.tsv.gz 1HL_10A.tags.tsv.gz 1HL_24A.snps.tsv.gz 1HL_6A.models.tsv.gz 1NF_1A.matches.tsv.gz 1NF_32A.alleles.tsv.gz 1SN_15A.tags.tsv.gz 1SN_28A.snps.tsv.gz 1HL_11A.alleles.tsv.gz 1HL_24A.tags.tsv.gz 1HL_6A.snps.tsv.gz 1NF_1A.models.tsv.gz 1NF_32A.matches.tsv.gz 1SN_16A.alleles.tsv.gz 1SN_28A.tags.tsv.gz 1HL_11A.matches.tsv.gz 1HL_25A.alleles.tsv.gz 1HL_6A.tags.tsv.gz 1NF_1A.snps.tsv.gz 1NF_32A.models.tsv.gz 1SN_16A.matches.tsv.gz 1SN_29A.alleles.tsv.gz 1HL_11A.models.tsv.gz 1HL_25A.matches.tsv.gz 1HL_7A.alleles.tsv.gz 1NF_1A.tags.tsv.gz 1NF_32A.snps.tsv.gz 1SN_16A.models.tsv.gz 1SN_29A.matches.tsv.gz 1HL_11A.snps.tsv.gz 1HL_25A.models.tsv.gz 1HL_7A.matches.tsv.gz 1NF_20A.alleles.tsv.gz 1NF_32A.tags.tsv.gz 1SN_16A.snps.tsv.gz 1SN_29A.models.tsv.gz 1HL_11A.tags.tsv.gz 1HL_25A.snps.tsv.gz 1HL_7A.models.tsv.gz 1NF_20A.matches.tsv.gz 1NF_33A.alleles.tsv.gz 1SN_16A.tags.tsv.gz 1SN_29A.snps.tsv.gz 1HL_12A.alleles.tsv.gz 1HL_25A.tags.tsv.gz 1HL_7A.snps.tsv.gz 1NF_20A.models.tsv.gz 1NF_33A.matches.tsv.gz 1SN_17A.alleles.tsv.gz 1SN_29A.tags.tsv.gz 1HL_12A.matches.tsv.gz 1HL_26A.alleles.tsv.gz 1HL_7A.tags.tsv.gz 1NF_20A.snps.tsv.gz 1NF_33A.models.tsv.gz 1SN_17A.matches.tsv.gz 1SN_2A.alleles.tsv.gz 1HL_12A.models.tsv.gz 1HL_26A.matches.tsv.gz 1HL_8A.alleles.tsv.gz 1NF_20A.tags.tsv.gz 1NF_33A.snps.tsv.gz 1SN_17A.models.tsv.gz 1SN_2A.matches.tsv.gz 1HL_12A.snps.tsv.gz 1HL_26A.models.tsv.gz 1HL_8A.matches.tsv.gz 1NF_21A.alleles.tsv.gz 1NF_33A.tags.tsv.gz 1SN_17A.snps.tsv.gz 1SN_2A.models.tsv.gz 1HL_12A.tags.tsv.gz 1HL_26A.snps.tsv.gz 1HL_8A.models.tsv.gz 1NF_21A.matches.tsv.gz 1NF_4A.alleles.tsv.gz 1SN_17A.tags.tsv.gz 1SN_2A.snps.tsv.gz 1HL_13A.alleles.tsv.gz 1HL_26A.tags.tsv.gz 1HL_8A.snps.tsv.gz 1NF_21A.models.tsv.gz 1NF_4A.matches.tsv.gz 1SN_18A.alleles.tsv.gz 1SN_2A.tags.tsv.gz 1HL_13A.matches.tsv.gz 1HL_27A.alleles.tsv.gz 1HL_8A.tags.tsv.gz 1NF_21A.snps.tsv.gz 1NF_4A.models.tsv.gz 1SN_18A.matches.tsv.gz 1SN_30A.alleles.tsv.gz 1HL_13A.models.tsv.gz 1HL_27A.matches.tsv.gz 1HL_9A.alleles.tsv.gz 1NF_21A.tags.tsv.gz 1NF_4A.snps.tsv.gz 1SN_18A.models.tsv.gz 1SN_30A.matches.tsv.gz 1HL_13A.snps.tsv.gz 1HL_27A.models.tsv.gz 1HL_9A.matches.tsv.gz 1NF_22A.alleles.tsv.gz 1NF_4A.tags.tsv.gz 1SN_18A.snps.tsv.gz 1SN_30A.models.tsv.gz 1HL_13A.tags.tsv.gz 1HL_27A.snps.tsv.gz 1HL_9A.models.tsv.gz 1NF_22A.matches.tsv.gz 1NF_5A.alleles.tsv.gz 1SN_18A.tags.tsv.gz 1SN_30A.snps.tsv.gz 1HL_14A.alleles.tsv.gz 1HL_27A.tags.tsv.gz 1HL_9A.snps.tsv.gz 1NF_22A.models.tsv.gz 1NF_5A.matches.tsv.gz 1SN_19A.alleles.tsv.gz 1SN_30A.tags.tsv.gz 1HL_14A.matches.tsv.gz 1HL_28A.alleles.tsv.gz 1HL_9A.tags.tsv.gz 1NF_22A.snps.tsv.gz 1NF_5A.models.tsv.gz 1SN_19A.matches.tsv.gz 1SN_31A.alleles.tsv.gz 1HL_14A.models.tsv.gz 1HL_28A.matches.tsv.gz 1NF_10A.alleles.tsv.gz 1NF_22A.tags.tsv.gz 1NF_5A.snps.tsv.gz 1SN_19A.models.tsv.gz 1SN_31A.matches.tsv.gz 1HL_14A.snps.tsv.gz 1HL_28A.models.tsv.gz 1NF_10A.matches.tsv.gz 1NF_23A.alleles.tsv.gz 1NF_5A.tags.tsv.gz 1SN_19A.snps.tsv.gz 1SN_31A.models.tsv.gz 1HL_14A.tags.tsv.gz 1HL_28A.snps.tsv.gz 1NF_10A.models.tsv.gz 1NF_23A.matches.tsv.gz 1NF_6A.alleles.tsv.gz 1SN_19A.tags.tsv.gz 1SN_31A.snps.tsv.gz 1HL_15A.alleles.tsv.gz 1HL_28A.tags.tsv.gz 1NF_10A.snps.tsv.gz 1NF_23A.models.tsv.gz 1NF_6A.matches.tsv.gz 1SN_1A.alleles.tsv.gz 1SN_31A.tags.tsv.gz 1HL_15A.matches.tsv.gz 1HL_29A.alleles.tsv.gz 1NF_10A.tags.tsv.gz 1NF_23A.snps.tsv.gz 1NF_6A.models.tsv.gz 1SN_1A.matches.tsv.gz 1SN_32A.alleles.tsv.gz 1HL_15A.models.tsv.gz 1HL_29A.matches.tsv.gz 1NF_11A.alleles.tsv.gz 1NF_23A.tags.tsv.gz 1NF_6A.snps.tsv.gz 1SN_1A.models.tsv.gz 1SN_32A.matches.tsv.gz 1HL_15A.snps.tsv.gz 1HL_29A.models.tsv.gz 1NF_11A.matches.tsv.gz 1NF_24A.alleles.tsv.gz 1NF_6A.tags.tsv.gz 1SN_1A.snps.tsv.gz 1SN_32A.models.tsv.gz 1HL_15A.tags.tsv.gz 1HL_29A.snps.tsv.gz 1NF_11A.models.tsv.gz 1NF_24A.matches.tsv.gz 1NF_7A.alleles.tsv.gz 1SN_1A.tags.tsv.gz 1SN_32A.snps.tsv.gz 1HL_16A.alleles.tsv.gz 1HL_29A.tags.tsv.gz 1NF_11A.snps.tsv.gz 1NF_24A.models.tsv.gz 1NF_7A.matches.tsv.gz 1SN_20A.alleles.tsv.gz 1SN_32A.tags.tsv.gz 1HL_16A.matches.tsv.gz 1HL_2A.alleles.tsv.gz 1NF_11A.tags.tsv.gz 1NF_24A.snps.tsv.gz 1NF_7A.models.tsv.gz 1SN_20A.matches.tsv.gz 1SN_3A.alleles.tsv.gz 1HL_16A.models.tsv.gz 1HL_2A.matches.tsv.gz 1NF_12A.alleles.tsv.gz 1NF_24A.tags.tsv.gz 1NF_7A.snps.tsv.gz 1SN_20A.models.tsv.gz 1SN_3A.matches.tsv.gz 1HL_16A.snps.tsv.gz 1HL_2A.models.tsv.gz 1NF_12A.matches.tsv.gz 1NF_25A.alleles.tsv.gz 1NF_7A.tags.tsv.gz 1SN_20A.snps.tsv.gz 1SN_3A.models.tsv.gz 1HL_16A.tags.tsv.gz 1HL_2A.snps.tsv.gz 1NF_12A.models.tsv.gz 1NF_25A.matches.tsv.gz 1NF_8A.alleles.tsv.gz 1SN_20A.tags.tsv.gz 1SN_3A.snps.tsv.gz 1HL_17A.alleles.tsv.gz 1HL_2A.tags.tsv.gz 1NF_12A.snps.tsv.gz 1NF_25A.models.tsv.gz 1NF_8A.matches.tsv.gz 1SN_21A.alleles.tsv.gz 1SN_3A.tags.tsv.gz 1HL_17A.matches.tsv.gz 1HL_31A.alleles.tsv.gz 1NF_12A.tags.tsv.gz 1NF_25A.snps.tsv.gz 1NF_8A.models.tsv.gz 1SN_21A.matches.tsv.gz 1SN_4A.alleles.tsv.gz 1HL_17A.models.tsv.gz 1HL_31A.matches.tsv.gz 1NF_13A.alleles.tsv.gz 1NF_25A.tags.tsv.gz 1NF_8A.snps.tsv.gz 1SN_21A.models.tsv.gz 1SN_4A.matches.tsv.gz 1HL_17A.snps.tsv.gz 1HL_31A.models.tsv.gz 1NF_13A.matches.tsv.gz 1NF_26A.alleles.tsv.gz 1NF_8A.tags.tsv.gz 1SN_21A.snps.tsv.gz 1SN_4A.models.tsv.gz 1HL_17A.tags.tsv.gz 1HL_31A.snps.tsv.gz 1NF_13A.models.tsv.gz 1NF_26A.matches.tsv.gz 1NF_9A.alleles.tsv.gz 1SN_21A.tags.tsv.gz 1SN_4A.snps.tsv.gz 1HL_19A.alleles.tsv.gz 1HL_31A.tags.tsv.gz 1NF_13A.snps.tsv.gz 1NF_26A.models.tsv.gz 1NF_9A.matches.tsv.gz 1SN_22A.alleles.tsv.gz 1SN_4A.tags.tsv.gz 1HL_19A.matches.tsv.gz 1HL_33A.alleles.tsv.gz 1NF_13A.tags.tsv.gz 1NF_26A.snps.tsv.gz 1NF_9A.models.tsv.gz 1SN_22A.matches.tsv.gz 1SN_5A.alleles.tsv.gz 1HL_19A.models.tsv.gz 1HL_33A.matches.tsv.gz 1NF_14A.alleles.tsv.gz 1NF_26A.tags.tsv.gz 1NF_9A.snps.tsv.gz 1SN_22A.models.tsv.gz 1SN_5A.matches.tsv.gz 1HL_19A.snps.tsv.gz 1HL_33A.models.tsv.gz 1NF_14A.matches.tsv.gz 1NF_27A.alleles.tsv.gz 1NF_9A.tags.tsv.gz 1SN_22A.snps.tsv.gz 1SN_5A.models.tsv.gz 1HL_19A.tags.tsv.gz 1HL_33A.snps.tsv.gz 1NF_14A.models.tsv.gz 1NF_27A.matches.tsv.gz 1SN_10A.alleles.tsv.gz 1SN_22A.tags.tsv.gz 1SN_5A.snps.tsv.gz 1HL_1A.alleles.tsv.gz 1HL_33A.tags.tsv.gz 1NF_14A.snps.tsv.gz 1NF_27A.models.tsv.gz 1SN_10A.matches.tsv.gz 1SN_23A.alleles.tsv.gz 1SN_5A.tags.tsv.gz 1HL_1A.matches.tsv.gz 1HL_34A.alleles.tsv.gz 1NF_14A.tags.tsv.gz 1NF_27A.snps.tsv.gz 1SN_10A.models.tsv.gz 1SN_23A.matches.tsv.gz 1SN_6A.alleles.tsv.gz 1HL_1A.models.tsv.gz 1HL_34A.matches.tsv.gz 1NF_15A.alleles.tsv.gz 1NF_27A.tags.tsv.gz 1SN_10A.snps.tsv.gz 1SN_23A.models.tsv.gz 1SN_6A.matches.tsv.gz 1HL_1A.snps.tsv.gz 1HL_34A.models.tsv.gz 1NF_15A.matches.tsv.gz 1NF_28A.alleles.tsv.gz 1SN_10A.tags.tsv.gz 1SN_23A.snps.tsv.gz 1SN_6A.models.tsv.gz 1HL_1A.tags.tsv.gz 1HL_34A.snps.tsv.gz 1NF_15A.models.tsv.gz 1NF_28A.matches.tsv.gz 1SN_11A.alleles.tsv.gz 1SN_23A.tags.tsv.gz 1SN_6A.snps.tsv.gz 1HL_20A.alleles.tsv.gz 1HL_34A.tags.tsv.gz 1NF_15A.snps.tsv.gz 1NF_28A.models.tsv.gz 1SN_11A.matches.tsv.gz 1SN_24A.alleles.tsv.gz 1SN_6A.tags.tsv.gz 1HL_20A.matches.tsv.gz 1HL_35A.alleles.tsv.gz 1NF_15A.tags.tsv.gz 1NF_28A.snps.tsv.gz 1SN_11A.models.tsv.gz 1SN_24A.matches.tsv.gz 1SN_7A.alleles.tsv.gz 1HL_20A.models.tsv.gz 1HL_35A.matches.tsv.gz 1NF_16A.alleles.tsv.gz 1NF_28A.tags.tsv.gz 1SN_11A.snps.tsv.gz 1SN_24A.models.tsv.gz 1SN_7A.matches.tsv.gz 1HL_20A.snps.tsv.gz 1HL_35A.models.tsv.gz 1NF_16A.matches.tsv.gz 1NF_29A.alleles.tsv.gz 1SN_11A.tags.tsv.gz 1SN_24A.snps.tsv.gz 1SN_7A.models.tsv.gz 1HL_20A.tags.tsv.gz 1HL_35A.snps.tsv.gz 1NF_16A.models.tsv.gz 1NF_29A.matches.tsv.gz 1SN_12A.alleles.tsv.gz 1SN_24A.tags.tsv.gz 1SN_7A.snps.tsv.gz 1HL_21A.alleles.tsv.gz 1HL_35A.tags.tsv.gz 1NF_16A.snps.tsv.gz 1NF_29A.models.tsv.gz 1SN_12A.matches.tsv.gz 1SN_25A.alleles.tsv.gz 1SN_7A.tags.tsv.gz 1HL_21A.matches.tsv.gz 1HL_3A.alleles.tsv.gz 1NF_16A.tags.tsv.gz 1NF_29A.snps.tsv.gz 1SN_12A.models.tsv.gz 1SN_25A.matches.tsv.gz 1SN_8A.alleles.tsv.gz 1HL_21A.models.tsv.gz 1HL_3A.matches.tsv.gz 1NF_17A.alleles.tsv.gz 1NF_29A.tags.tsv.gz 1SN_12A.snps.tsv.gz 1SN_25A.models.tsv.gz 1SN_8A.matches.tsv.gz 1HL_21A.snps.tsv.gz 1HL_3A.models.tsv.gz 1NF_17A.matches.tsv.gz 1NF_2A.alleles.tsv.gz 1SN_12A.tags.tsv.gz 1SN_25A.snps.tsv.gz 1SN_8A.models.tsv.gz 1HL_21A.tags.tsv.gz 1HL_3A.snps.tsv.gz 1NF_17A.models.tsv.gz 1NF_2A.matches.tsv.gz 1SN_13A.alleles.tsv.gz 1SN_25A.tags.tsv.gz 1SN_8A.snps.tsv.gz 1HL_22A.alleles.tsv.gz 1HL_3A.tags.tsv.gz 1NF_17A.snps.tsv.gz 1NF_2A.models.tsv.gz 1SN_13A.matches.tsv.gz 1SN_26A.alleles.tsv.gz 1SN_8A.tags.tsv.gz 1HL_22A.matches.tsv.gz 1HL_4A.alleles.tsv.gz 1NF_17A.tags.tsv.gz 1NF_2A.snps.tsv.gz 1SN_13A.models.tsv.gz 1SN_26A.matches.tsv.gz 1SN_9A.alleles.tsv.gz 1HL_22A.models.tsv.gz 1HL_4A.matches.tsv.gz 1NF_18A.alleles.tsv.gz 1NF_2A.tags.tsv.gz 1SN_13A.snps.tsv.gz 1SN_26A.models.tsv.gz 1SN_9A.matches.tsv.gz 1HL_22A.snps.tsv.gz 1HL_4A.models.tsv.gz 1NF_18A.matches.tsv.gz 1NF_30A.alleles.tsv.gz 1SN_13A.tags.tsv.gz 1SN_26A.snps.tsv.gz 1SN_9A.models.tsv.gz 1HL_22A.tags.tsv.gz 1HL_4A.snps.tsv.gz 1NF_18A.models.tsv.gz 1NF_30A.matches.tsv.gz 1SN_14A.alleles.tsv.gz 1SN_26A.tags.tsv.gz 1SN_9A.snps.tsv.gz 1HL_23A.alleles.tsv.gz 1HL_4A.tags.tsv.gz 1NF_18A.snps.tsv.gz 1NF_30A.models.tsv.gz 1SN_14A.matches.tsv.gz 1SN_27A.alleles.tsv.gz 1SN_9A.tags.tsv.gz 1HL_23A.matches.tsv.gz 1HL_5A.alleles.tsv.gz 1NF_18A.tags.tsv.gz 1NF_30A.snps.tsv.gz 1SN_14A.models.tsv.gz 1SN_27A.matches.tsv.gz batch_1.catalog.alleles.tsv.gz 1HL_23A.models.tsv.gz 1HL_5A.matches.tsv.gz 1NF_19A.alleles.tsv.gz 1NF_30A.tags.tsv.gz 1SN_14A.snps.tsv.gz 1SN_27A.models.tsv.gz batch_1.catalog.snps.tsv.gz 1HL_23A.snps.tsv.gz 1HL_5A.models.tsv.gz 1NF_19A.matches.tsv.gz 1NF_31A.alleles.tsv.gz 1SN_14A.tags.tsv.gz 1SN_27A.snps.tsv.gz batch_1.catalog.tags.tsv.gz
%%bash
time /usr/local/bioinformatics/stacks-1.40/populations \
-P /Volumes/toaster/sam/stacks/oly_BGI_GBS/stacks \
-M /Volumes/toaster/sam/stacks/oly_BGI_GBS/populations/popmap \
-b 1 \
-k \
-s \
-e apeKI \
--genomic \
--fasta \
--vcf \
-t 8