Notebook

In [1]:

%%bash
date

Wed Apr  6 13:35:35 PDT 2016

In [2]:

%%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: 137 days 22:26

In [8]:

cd /usr/local/bioinformatics/stacks-1.37

/usr/local/bioinformatics/stacks-1.37

In [9]:

ls

ChangeLog           README              config.h            cstacks*            php/                scripts/            ustacks*
INSTALL             acinclude.m4        config.h.in         estacks*            populations*        sql/
LICENSE             aclocal.m4          config.log          genotypes*          process_radtags*    src/
Makefile            autogen.sh*         config.status*      hstacks*            process_shortreads* sstacks*
Makefile.am         clone_filter*       configure*          kmer_filter*        pstacks*            stamp-h1
Makefile.in         config/             configure.ac        phasedstacks*       rxstacks*           tests/

Test out STACKS process_radtags command to see what happens¶

In [11]:

%%bash
time process_radtags -1 /Volumes/nightingales/O_lurida/20160223_gbs/1HL_10A_1.fq.gz -2 /Volumes/nightingales/O_lurida/20160223_gbs/1HL_10A_2.fq.gz \
-o /Volumes/owl/temp/ -e apeKI -c -q -i gzfastq

No barcodes specified, files will not be demultiplexed.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_10A_1.fq.gz]
  Reading data from:
  /Volumes/nightingales/O_lurida/20160223_gbs/1HL_10A_1.fq.gz and
  /Volumes/nightingales/O_lurida/20160223_gbs/1HL_10A_2.fq.gz
  6373130 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -364015 low quality reads; 6009115 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6373130 total sequences;
  0 ambiguous barcode drops;
  364015 low quality read drops;
  0 ambiguous RAD-Tag drops;
6009115 retained reads.

real	1m41.004s
user	0m52.858s
sys	0m12.562s

List process_radtags output files¶

In [12]:

ls /Volumes/owl/temp/

1HL_10A_1.fq         1HL_10A_1.rem.fq     1HL_10A_2.fq         1HL_10A_2.rem.fq     process_radtags.log

Look at process_radtags log file¶

In [13]:

%%bash
head /Volumes/owl/temp/process_radtags.log

process_radtags -1 /Volumes/nightingales/O_lurida/20160223_gbs/1HL_10A_1.fq.gz -2 /Volumes/nightingales/O_lurida/20160223_gbs/1HL_10A_2.fq.gz -o /Volumes/owl/temp/ -e apeKI -c -q -i gzfastq
process_radtags executed 2016-04-06 13:43:04

File	Retained Reads	Low Quality	Ambiguous Barcodes	Ambiguous RAD-Tag	Total
1HL_10A_1.fq.gz	6009115	364015	0	0	6373130

Total Sequences	6373130
Ambiguous Barcodes	0
Low Quality	364015
Ambiguous RAD-Tag	0

Move to directory with GBS FASTQ files¶

In [15]:

cd /Volumes/nightingales/O_lurida/20160223_gbs/

/Volumes/nightingales/O_lurida/20160223_gbs

Generate a list of each pair of FASTQ files for subsequent processing¶

In [20]:

%%bash
echo *_1.fq.gz

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 UnKnow_1.fq.gz

In [21]:

%%bash
echo *_2.fq.gz

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 UnKnow_2.fq.gz

Use the two lists generated above for cell below to automate running process_radtags on all 96 individuals that were sequenced.¶

Cell below creates two lists, loops through an array and assigns the corresponding FASTQ pairs to the values "i" and "j".¶

The values in "i" and "j" are used in the process_radtags command.¶

In [23]:

%%bash
list1=( 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 )
list2=( 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 )
for pair in "${!list1[@]}"; do
  i=${list1[$pair]}
  j=${list2[$pair]}
  /usr/local/bioinformatics/stacks-1.37/process_radtags -1 $i -2 $j \
-o /Volumes/owl/temp/ -e apeKI -c -q -i gzfastq
done

No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_10A_1.fq.gz]
  Reading data from:
  1HL_10A_1.fq.gz and
  1HL_10A_2.fq.gz
  6373130 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -364015 low quality reads; 6009115 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6373130 total sequences;
  0 ambiguous barcode drops;
  364015 low quality read drops;
  0 ambiguous RAD-Tag drops;
6009115 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_11A_1.fq.gz]
  Reading data from:
  1HL_11A_1.fq.gz and
  1HL_11A_2.fq.gz
  7137006 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -406623 low quality reads; 6730383 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

7137006 total sequences;
  0 ambiguous barcode drops;
  406623 low quality read drops;
  0 ambiguous RAD-Tag drops;
6730383 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_12A_1.fq.gz]
  Reading data from:
  1HL_12A_1.fq.gz and
  1HL_12A_2.fq.gz
  5049626 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -287923 low quality reads; 4761703 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5049626 total sequences;
  0 ambiguous barcode drops;
  287923 low quality read drops;
  0 ambiguous RAD-Tag drops;
4761703 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_13A_1.fq.gz]
  Reading data from:
  1HL_13A_1.fq.gz and
  1HL_13A_2.fq.gz
  5352850 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -304892 low quality reads; 5047958 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5352850 total sequences;
  0 ambiguous barcode drops;
  304892 low quality read drops;
  0 ambiguous RAD-Tag drops;
5047958 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_14A_1.fq.gz]
  Reading data from:
  1HL_14A_1.fq.gz and
  1HL_14A_2.fq.gz
  4031222 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -230119 low quality reads; 3801103 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4031222 total sequences;
  0 ambiguous barcode drops;
  230119 low quality read drops;
  0 ambiguous RAD-Tag drops;
3801103 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_15A_1.fq.gz]
  Reading data from:
  1HL_15A_1.fq.gz and
  1HL_15A_2.fq.gz
  4392648 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -250237 low quality reads; 4142411 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4392648 total sequences;
  0 ambiguous barcode drops;
  250237 low quality read drops;
  0 ambiguous RAD-Tag drops;
4142411 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_16A_1.fq.gz]
  Reading data from:
  1HL_16A_1.fq.gz and
  1HL_16A_2.fq.gz
  4666316 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -266126 low quality reads; 4400190 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4666316 total sequences;
  0 ambiguous barcode drops;
  266126 low quality read drops;
  0 ambiguous RAD-Tag drops;
4400190 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_17A_1.fq.gz]
  Reading data from:
  1HL_17A_1.fq.gz and
  1HL_17A_2.fq.gz
  7307522 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -418495 low quality reads; 6889027 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

7307522 total sequences;
  0 ambiguous barcode drops;
  418495 low quality read drops;
  0 ambiguous RAD-Tag drops;
6889027 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_19A_1.fq.gz]
  Reading data from:
  1HL_19A_1.fq.gz and
  1HL_19A_2.fq.gz
  7235968 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -412078 low quality reads; 6823890 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

7235968 total sequences;
  0 ambiguous barcode drops;
  412078 low quality read drops;
  0 ambiguous RAD-Tag drops;
6823890 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_1A_1.fq.gz]
  Reading data from:
  1HL_1A_1.fq.gz and
  1HL_1A_2.fq.gz
  4520860 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -256112 low quality reads; 4264748 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4520860 total sequences;
  0 ambiguous barcode drops;
  256112 low quality read drops;
  0 ambiguous RAD-Tag drops;
4264748 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_20A_1.fq.gz]
  Reading data from:
  1HL_20A_1.fq.gz and
  1HL_20A_2.fq.gz
  5817876 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -330533 low quality reads; 5487343 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5817876 total sequences;
  0 ambiguous barcode drops;
  330533 low quality read drops;
  0 ambiguous RAD-Tag drops;
5487343 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_21A_1.fq.gz]
  Reading data from:
  1HL_21A_1.fq.gz and
  1HL_21A_2.fq.gz
  5183690 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -295100 low quality reads; 4888590 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5183690 total sequences;
  0 ambiguous barcode drops;
  295100 low quality read drops;
  0 ambiguous RAD-Tag drops;
4888590 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_22A_1.fq.gz]
  Reading data from:
  1HL_22A_1.fq.gz and
  1HL_22A_2.fq.gz
  4148458 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -235614 low quality reads; 3912844 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4148458 total sequences;
  0 ambiguous barcode drops;
  235614 low quality read drops;
  0 ambiguous RAD-Tag drops;
3912844 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_23A_1.fq.gz]
  Reading data from:
  1HL_23A_1.fq.gz and
  1HL_23A_2.fq.gz
  7219588 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -412125 low quality reads; 6807463 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

7219588 total sequences;
  0 ambiguous barcode drops;
  412125 low quality read drops;
  0 ambiguous RAD-Tag drops;
6807463 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_24A_1.fq.gz]
  Reading data from:
  1HL_24A_1.fq.gz and
  1HL_24A_2.fq.gz
  5443616 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -309887 low quality reads; 5133729 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5443616 total sequences;
  0 ambiguous barcode drops;
  309887 low quality read drops;
  0 ambiguous RAD-Tag drops;
5133729 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_25A_1.fq.gz]
  Reading data from:
  1HL_25A_1.fq.gz and
  1HL_25A_2.fq.gz
  5915748 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -335814 low quality reads; 5579934 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5915748 total sequences;
  0 ambiguous barcode drops;
  335814 low quality read drops;
  0 ambiguous RAD-Tag drops;
5579934 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_26A_1.fq.gz]
  Reading data from:
  1HL_26A_1.fq.gz and
  1HL_26A_2.fq.gz
  6284738 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -358195 low quality reads; 5926543 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6284738 total sequences;
  0 ambiguous barcode drops;
  358195 low quality read drops;
  0 ambiguous RAD-Tag drops;
5926543 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_27A_1.fq.gz]
  Reading data from:
  1HL_27A_1.fq.gz and
  1HL_27A_2.fq.gz
  6399298 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -365037 low quality reads; 6034261 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6399298 total sequences;
  0 ambiguous barcode drops;
  365037 low quality read drops;
  0 ambiguous RAD-Tag drops;
6034261 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_28A_1.fq.gz]
  Reading data from:
  1HL_28A_1.fq.gz and
  1HL_28A_2.fq.gz
  7540476 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -430416 low quality reads; 7110060 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

7540476 total sequences;
  0 ambiguous barcode drops;
  430416 low quality read drops;
  0 ambiguous RAD-Tag drops;
7110060 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_29A_1.fq.gz]
  Reading data from:
  1HL_29A_1.fq.gz and
  1HL_29A_2.fq.gz
  6142410 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -351000 low quality reads; 5791410 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6142410 total sequences;
  0 ambiguous barcode drops;
  351000 low quality read drops;
  0 ambiguous RAD-Tag drops;
5791410 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_2A_1.fq.gz]
  Reading data from:
  1HL_2A_1.fq.gz and
  1HL_2A_2.fq.gz
  5516300 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -314684 low quality reads; 5201616 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5516300 total sequences;
  0 ambiguous barcode drops;
  314684 low quality read drops;
  0 ambiguous RAD-Tag drops;
5201616 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_31A_1.fq.gz]
  Reading data from:
  1HL_31A_1.fq.gz and
  1HL_31A_2.fq.gz
  4907506 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -280081 low quality reads; 4627425 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4907506 total sequences;
  0 ambiguous barcode drops;
  280081 low quality read drops;
  0 ambiguous RAD-Tag drops;
4627425 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_33A_1.fq.gz]
  Reading data from:
  1HL_33A_1.fq.gz and
  1HL_33A_2.fq.gz
  5417886 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -308571 low quality reads; 5109315 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5417886 total sequences;
  0 ambiguous barcode drops;
  308571 low quality read drops;
  0 ambiguous RAD-Tag drops;
5109315 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_34A_1.fq.gz]
  Reading data from:
  1HL_34A_1.fq.gz and
  1HL_34A_2.fq.gz
  5798038 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -328771 low quality reads; 5469267 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5798038 total sequences;
  0 ambiguous barcode drops;
  328771 low quality read drops;
  0 ambiguous RAD-Tag drops;
5469267 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_35A_1.fq.gz]
  Reading data from:
  1HL_35A_1.fq.gz and
  1HL_35A_2.fq.gz
  5260626 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -299671 low quality reads; 4960955 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5260626 total sequences;
  0 ambiguous barcode drops;
  299671 low quality read drops;
  0 ambiguous RAD-Tag drops;
4960955 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_3A_1.fq.gz]
  Reading data from:
  1HL_3A_1.fq.gz and
  1HL_3A_2.fq.gz
  4422802 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -252661 low quality reads; 4170141 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4422802 total sequences;
  0 ambiguous barcode drops;
  252661 low quality read drops;
  0 ambiguous RAD-Tag drops;
4170141 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_4A_1.fq.gz]
  Reading data from:
  1HL_4A_1.fq.gz and
  1HL_4A_2.fq.gz
  5142062 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -293734 low quality reads; 4848328 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5142062 total sequences;
  0 ambiguous barcode drops;
  293734 low quality read drops;
  0 ambiguous RAD-Tag drops;
4848328 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_5A_1.fq.gz]
  Reading data from:
  1HL_5A_1.fq.gz and
  1HL_5A_2.fq.gz
  3961332 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -225899 low quality reads; 3735433 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

3961332 total sequences;
  0 ambiguous barcode drops;
  225899 low quality read drops;
  0 ambiguous RAD-Tag drops;
3735433 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_6A_1.fq.gz]
  Reading data from:
  1HL_6A_1.fq.gz and
  1HL_6A_2.fq.gz
  4140102 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -235725 low quality reads; 3904377 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4140102 total sequences;
  0 ambiguous barcode drops;
  235725 low quality read drops;
  0 ambiguous RAD-Tag drops;
3904377 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_7A_1.fq.gz]
  Reading data from:
  1HL_7A_1.fq.gz and
  1HL_7A_2.fq.gz
  5587088 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -318275 low quality reads; 5268813 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5587088 total sequences;
  0 ambiguous barcode drops;
  318275 low quality read drops;
  0 ambiguous RAD-Tag drops;
5268813 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_8A_1.fq.gz]
  Reading data from:
  1HL_8A_1.fq.gz and
  1HL_8A_2.fq.gz
  5088026 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -289492 low quality reads; 4798534 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5088026 total sequences;
  0 ambiguous barcode drops;
  289492 low quality read drops;
  0 ambiguous RAD-Tag drops;
4798534 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1HL_9A_1.fq.gz]
  Reading data from:
  1HL_9A_1.fq.gz and
  1HL_9A_2.fq.gz
  5665890 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -323536 low quality reads; 5342354 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5665890 total sequences;
  0 ambiguous barcode drops;
  323536 low quality read drops;
  0 ambiguous RAD-Tag drops;
5342354 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_10A_1.fq.gz]
  Reading data from:
  1NF_10A_1.fq.gz and
  1NF_10A_2.fq.gz
  4298602 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -246007 low quality reads; 4052595 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4298602 total sequences;
  0 ambiguous barcode drops;
  246007 low quality read drops;
  0 ambiguous RAD-Tag drops;
4052595 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_11A_1.fq.gz]
  Reading data from:
  1NF_11A_1.fq.gz and
  1NF_11A_2.fq.gz
  4533294 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -258322 low quality reads; 4274972 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4533294 total sequences;
  0 ambiguous barcode drops;
  258322 low quality read drops;
  0 ambiguous RAD-Tag drops;
4274972 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_12A_1.fq.gz]
  Reading data from:
  1NF_12A_1.fq.gz and
  1NF_12A_2.fq.gz
  4359846 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -248582 low quality reads; 4111264 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4359846 total sequences;
  0 ambiguous barcode drops;
  248582 low quality read drops;
  0 ambiguous RAD-Tag drops;
4111264 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_13A_1.fq.gz]
  Reading data from:
  1NF_13A_1.fq.gz and
  1NF_13A_2.fq.gz
  7780236 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -443383 low quality reads; 7336853 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

7780236 total sequences;
  0 ambiguous barcode drops;
  443383 low quality read drops;
  0 ambiguous RAD-Tag drops;
7336853 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_14A_1.fq.gz]
  Reading data from:
  1NF_14A_1.fq.gz and
  1NF_14A_2.fq.gz
  5438396 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -309623 low quality reads; 5128773 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5438396 total sequences;
  0 ambiguous barcode drops;
  309623 low quality read drops;
  0 ambiguous RAD-Tag drops;
5128773 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_15A_1.fq.gz]
  Reading data from:
  1NF_15A_1.fq.gz and
  1NF_15A_2.fq.gz
  5108648 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -291298 low quality reads; 4817350 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5108648 total sequences;
  0 ambiguous barcode drops;
  291298 low quality read drops;
  0 ambiguous RAD-Tag drops;
4817350 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_16A_1.fq.gz]
  Reading data from:
  1NF_16A_1.fq.gz and
  1NF_16A_2.fq.gz
  5365896 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -306723 low quality reads; 5059173 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5365896 total sequences;
  0 ambiguous barcode drops;
  306723 low quality read drops;
  0 ambiguous RAD-Tag drops;
5059173 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_17A_1.fq.gz]
  Reading data from:
  1NF_17A_1.fq.gz and
  1NF_17A_2.fq.gz
  6238656 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -356398 low quality reads; 5882258 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6238656 total sequences;
  0 ambiguous barcode drops;
  356398 low quality read drops;
  0 ambiguous RAD-Tag drops;
5882258 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_18A_1.fq.gz]
  Reading data from:
  1NF_18A_1.fq.gz and
  1NF_18A_2.fq.gz
  3500140 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -199756 low quality reads; 3300384 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

3500140 total sequences;
  0 ambiguous barcode drops;
  199756 low quality read drops;
  0 ambiguous RAD-Tag drops;
3300384 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_19A_1.fq.gz]
  Reading data from:
  1NF_19A_1.fq.gz and
  1NF_19A_2.fq.gz
  4073280 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -232401 low quality reads; 3840879 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4073280 total sequences;
  0 ambiguous barcode drops;
  232401 low quality read drops;
  0 ambiguous RAD-Tag drops;
3840879 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_1A_1.fq.gz]
  Reading data from:
  1NF_1A_1.fq.gz and
  1NF_1A_2.fq.gz
  2711520 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -154238 low quality reads; 2557282 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

2711520 total sequences;
  0 ambiguous barcode drops;
  154238 low quality read drops;
  0 ambiguous RAD-Tag drops;
2557282 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_20A_1.fq.gz]
  Reading data from:
  1NF_20A_1.fq.gz and
  1NF_20A_2.fq.gz
  4914052 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -280471 low quality reads; 4633581 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4914052 total sequences;
  0 ambiguous barcode drops;
  280471 low quality read drops;
  0 ambiguous RAD-Tag drops;
4633581 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_21A_1.fq.gz]
  Reading data from:
  1NF_21A_1.fq.gz and
  1NF_21A_2.fq.gz
  6093874 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -347585 low quality reads; 5746289 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6093874 total sequences;
  0 ambiguous barcode drops;
  347585 low quality read drops;
  0 ambiguous RAD-Tag drops;
5746289 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_22A_1.fq.gz]
  Reading data from:
  1NF_22A_1.fq.gz and
  1NF_22A_2.fq.gz
  5790352 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -330821 low quality reads; 5459531 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5790352 total sequences;
  0 ambiguous barcode drops;
  330821 low quality read drops;
  0 ambiguous RAD-Tag drops;
5459531 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_23A_1.fq.gz]
  Reading data from:
  1NF_23A_1.fq.gz and
  1NF_23A_2.fq.gz
  6413484 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -367079 low quality reads; 6046405 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6413484 total sequences;
  0 ambiguous barcode drops;
  367079 low quality read drops;
  0 ambiguous RAD-Tag drops;
6046405 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_24A_1.fq.gz]
  Reading data from:
  1NF_24A_1.fq.gz and
  1NF_24A_2.fq.gz
  6077252 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -345939 low quality reads; 5731313 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6077252 total sequences;
  0 ambiguous barcode drops;
  345939 low quality read drops;
  0 ambiguous RAD-Tag drops;
5731313 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_25A_1.fq.gz]
  Reading data from:
  1NF_25A_1.fq.gz and
  1NF_25A_2.fq.gz
  4406458 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -251905 low quality reads; 4154553 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4406458 total sequences;
  0 ambiguous barcode drops;
  251905 low quality read drops;
  0 ambiguous RAD-Tag drops;
4154553 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_26A_1.fq.gz]
  Reading data from:
  1NF_26A_1.fq.gz and
  1NF_26A_2.fq.gz
  5869588 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -335792 low quality reads; 5533796 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5869588 total sequences;
  0 ambiguous barcode drops;
  335792 low quality read drops;
  0 ambiguous RAD-Tag drops;
5533796 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_27A_1.fq.gz]
  Reading data from:
  1NF_27A_1.fq.gz and
  1NF_27A_2.fq.gz
  4545304 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -259372 low quality reads; 4285932 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4545304 total sequences;
  0 ambiguous barcode drops;
  259372 low quality read drops;
  0 ambiguous RAD-Tag drops;
4285932 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_28A_1.fq.gz]
  Reading data from:
  1NF_28A_1.fq.gz and
  1NF_28A_2.fq.gz
  4689526 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -267109 low quality reads; 4422417 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4689526 total sequences;
  0 ambiguous barcode drops;
  267109 low quality read drops;
  0 ambiguous RAD-Tag drops;
4422417 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_29A_1.fq.gz]
  Reading data from:
  1NF_29A_1.fq.gz and
  1NF_29A_2.fq.gz
  7659962 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -437212 low quality reads; 7222750 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

7659962 total sequences;
  0 ambiguous barcode drops;
  437212 low quality read drops;
  0 ambiguous RAD-Tag drops;
7222750 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_2A_1.fq.gz]
  Reading data from:
  1NF_2A_1.fq.gz and
  1NF_2A_2.fq.gz
  6905862 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -394012 low quality reads; 6511850 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6905862 total sequences;
  0 ambiguous barcode drops;
  394012 low quality read drops;
  0 ambiguous RAD-Tag drops;
6511850 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_30A_1.fq.gz]
  Reading data from:
  1NF_30A_1.fq.gz and
  1NF_30A_2.fq.gz
  5402094 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -308424 low quality reads; 5093670 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5402094 total sequences;
  0 ambiguous barcode drops;
  308424 low quality read drops;
  0 ambiguous RAD-Tag drops;
5093670 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_31A_1.fq.gz]
  Reading data from:
  1NF_31A_1.fq.gz and
  1NF_31A_2.fq.gz
  7123148 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -404772 low quality reads; 6718376 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

7123148 total sequences;
  0 ambiguous barcode drops;
  404772 low quality read drops;
  0 ambiguous RAD-Tag drops;
6718376 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_32A_1.fq.gz]
  Reading data from:
  1NF_32A_1.fq.gz and
  1NF_32A_2.fq.gz
  6955972 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -395341 low quality reads; 6560631 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6955972 total sequences;
  0 ambiguous barcode drops;
  395341 low quality read drops;
  0 ambiguous RAD-Tag drops;
6560631 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_33A_1.fq.gz]
  Reading data from:
  1NF_33A_1.fq.gz and
  1NF_33A_2.fq.gz
  5205902 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -297588 low quality reads; 4908314 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5205902 total sequences;
  0 ambiguous barcode drops;
  297588 low quality read drops;
  0 ambiguous RAD-Tag drops;
4908314 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_4A_1.fq.gz]
  Reading data from:
  1NF_4A_1.fq.gz and
  1NF_4A_2.fq.gz
  7165798 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -408033 low quality reads; 6757765 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

7165798 total sequences;
  0 ambiguous barcode drops;
  408033 low quality read drops;
  0 ambiguous RAD-Tag drops;
6757765 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_5A_1.fq.gz]
  Reading data from:
  1NF_5A_1.fq.gz and
  1NF_5A_2.fq.gz
  5531968 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -314477 low quality reads; 5217491 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5531968 total sequences;
  0 ambiguous barcode drops;
  314477 low quality read drops;
  0 ambiguous RAD-Tag drops;
5217491 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_6A_1.fq.gz]
  Reading data from:
  1NF_6A_1.fq.gz and
  1NF_6A_2.fq.gz
  4847776 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -276286 low quality reads; 4571490 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4847776 total sequences;
  0 ambiguous barcode drops;
  276286 low quality read drops;
  0 ambiguous RAD-Tag drops;
4571490 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_7A_1.fq.gz]
  Reading data from:
  1NF_7A_1.fq.gz and
  1NF_7A_2.fq.gz
  5181014 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -296076 low quality reads; 4884938 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5181014 total sequences;
  0 ambiguous barcode drops;
  296076 low quality read drops;
  0 ambiguous RAD-Tag drops;
4884938 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_8A_1.fq.gz]
  Reading data from:
  1NF_8A_1.fq.gz and
  1NF_8A_2.fq.gz
  5545160 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -316222 low quality reads; 5228938 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5545160 total sequences;
  0 ambiguous barcode drops;
  316222 low quality read drops;
  0 ambiguous RAD-Tag drops;
5228938 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1NF_9A_1.fq.gz]
  Reading data from:
  1NF_9A_1.fq.gz and
  1NF_9A_2.fq.gz
  6760996 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -385656 low quality reads; 6375340 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6760996 total sequences;
  0 ambiguous barcode drops;
  385656 low quality read drops;
  0 ambiguous RAD-Tag drops;
6375340 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_10A_1.fq.gz]
  Reading data from:
  1SN_10A_1.fq.gz and
  1SN_10A_2.fq.gz
  5117334 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -291812 low quality reads; 4825522 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5117334 total sequences;
  0 ambiguous barcode drops;
  291812 low quality read drops;
  0 ambiguous RAD-Tag drops;
4825522 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_11A_1.fq.gz]
  Reading data from:
  1SN_11A_1.fq.gz and
  1SN_11A_2.fq.gz
  5167984 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -295139 low quality reads; 4872845 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5167984 total sequences;
  0 ambiguous barcode drops;
  295139 low quality read drops;
  0 ambiguous RAD-Tag drops;
4872845 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_12A_1.fq.gz]
  Reading data from:
  1SN_12A_1.fq.gz and
  1SN_12A_2.fq.gz
  6847804 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -390395 low quality reads; 6457409 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6847804 total sequences;
  0 ambiguous barcode drops;
  390395 low quality read drops;
  0 ambiguous RAD-Tag drops;
6457409 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_13A_1.fq.gz]
  Reading data from:
  1SN_13A_1.fq.gz and
  1SN_13A_2.fq.gz
  5913982 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -336735 low quality reads; 5577247 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5913982 total sequences;
  0 ambiguous barcode drops;
  336735 low quality read drops;
  0 ambiguous RAD-Tag drops;
5577247 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_14A_1.fq.gz]
  Reading data from:
  1SN_14A_1.fq.gz and
  1SN_14A_2.fq.gz
  7088580 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -403741 low quality reads; 6684839 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

7088580 total sequences;
  0 ambiguous barcode drops;
  403741 low quality read drops;
  0 ambiguous RAD-Tag drops;
6684839 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_15A_1.fq.gz]
  Reading data from:
  1SN_15A_1.fq.gz and
  1SN_15A_2.fq.gz
  5012650 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -285801 low quality reads; 4726849 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5012650 total sequences;
  0 ambiguous barcode drops;
  285801 low quality read drops;
  0 ambiguous RAD-Tag drops;
4726849 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_16A_1.fq.gz]
  Reading data from:
  1SN_16A_1.fq.gz and
  1SN_16A_2.fq.gz
  5233932 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -298373 low quality reads; 4935559 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5233932 total sequences;
  0 ambiguous barcode drops;
  298373 low quality read drops;
  0 ambiguous RAD-Tag drops;
4935559 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_17A_1.fq.gz]
  Reading data from:
  1SN_17A_1.fq.gz and
  1SN_17A_2.fq.gz
  5966802 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -339721 low quality reads; 5627081 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5966802 total sequences;
  0 ambiguous barcode drops;
  339721 low quality read drops;
  0 ambiguous RAD-Tag drops;
5627081 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_18A_1.fq.gz]
  Reading data from:
  1SN_18A_1.fq.gz and
  1SN_18A_2.fq.gz
  6497024 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -371120 low quality reads; 6125904 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6497024 total sequences;
  0 ambiguous barcode drops;
  371120 low quality read drops;
  0 ambiguous RAD-Tag drops;
6125904 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_19A_1.fq.gz]
  Reading data from:
  1SN_19A_1.fq.gz and
  1SN_19A_2.fq.gz
  6072926 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -344632 low quality reads; 5728294 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6072926 total sequences;
  0 ambiguous barcode drops;
  344632 low quality read drops;
  0 ambiguous RAD-Tag drops;
5728294 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_1A_1.fq.gz]
  Reading data from:
  1SN_1A_1.fq.gz and
  1SN_1A_2.fq.gz
  6081074 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -344640 low quality reads; 5736434 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6081074 total sequences;
  0 ambiguous barcode drops;
  344640 low quality read drops;
  0 ambiguous RAD-Tag drops;
5736434 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_20A_1.fq.gz]
  Reading data from:
  1SN_20A_1.fq.gz and
  1SN_20A_2.fq.gz
  4310354 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -247242 low quality reads; 4063112 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4310354 total sequences;
  0 ambiguous barcode drops;
  247242 low quality read drops;
  0 ambiguous RAD-Tag drops;
4063112 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_21A_1.fq.gz]
  Reading data from:
  1SN_21A_1.fq.gz and
  1SN_21A_2.fq.gz
  7081236 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -402346 low quality reads; 6678890 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

7081236 total sequences;
  0 ambiguous barcode drops;
  402346 low quality read drops;
  0 ambiguous RAD-Tag drops;
6678890 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_22A_1.fq.gz]
  Reading data from:
  1SN_22A_1.fq.gz and
  1SN_22A_2.fq.gz
  6120730 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -347346 low quality reads; 5773384 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6120730 total sequences;
  0 ambiguous barcode drops;
  347346 low quality read drops;
  0 ambiguous RAD-Tag drops;
5773384 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_23A_1.fq.gz]
  Reading data from:
  1SN_23A_1.fq.gz and
  1SN_23A_2.fq.gz
  7392514 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -421778 low quality reads; 6970736 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

7392514 total sequences;
  0 ambiguous barcode drops;
  421778 low quality read drops;
  0 ambiguous RAD-Tag drops;
6970736 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_24A_1.fq.gz]
  Reading data from:
  1SN_24A_1.fq.gz and
  1SN_24A_2.fq.gz
  3770530 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -213919 low quality reads; 3556611 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

3770530 total sequences;
  0 ambiguous barcode drops;
  213919 low quality read drops;
  0 ambiguous RAD-Tag drops;
3556611 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_25A_1.fq.gz]
  Reading data from:
  1SN_25A_1.fq.gz and
  1SN_25A_2.fq.gz
  6074178 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -346564 low quality reads; 5727614 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6074178 total sequences;
  0 ambiguous barcode drops;
  346564 low quality read drops;
  0 ambiguous RAD-Tag drops;
5727614 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_26A_1.fq.gz]
  Reading data from:
  1SN_26A_1.fq.gz and
  1SN_26A_2.fq.gz
  5517746 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -314306 low quality reads; 5203440 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5517746 total sequences;
  0 ambiguous barcode drops;
  314306 low quality read drops;
  0 ambiguous RAD-Tag drops;
5203440 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_27A_1.fq.gz]
  Reading data from:
  1SN_27A_1.fq.gz and
  1SN_27A_2.fq.gz
  5215618 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -297965 low quality reads; 4917653 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5215618 total sequences;
  0 ambiguous barcode drops;
  297965 low quality read drops;
  0 ambiguous RAD-Tag drops;
4917653 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_28A_1.fq.gz]
  Reading data from:
  1SN_28A_1.fq.gz and
  1SN_28A_2.fq.gz
  5683174 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -323400 low quality reads; 5359774 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5683174 total sequences;
  0 ambiguous barcode drops;
  323400 low quality read drops;
  0 ambiguous RAD-Tag drops;
5359774 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_29A_1.fq.gz]
  Reading data from:
  1SN_29A_1.fq.gz and
  1SN_29A_2.fq.gz
  4514548 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -256147 low quality reads; 4258401 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4514548 total sequences;
  0 ambiguous barcode drops;
  256147 low quality read drops;
  0 ambiguous RAD-Tag drops;
4258401 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_2A_1.fq.gz]
  Reading data from:
  1SN_2A_1.fq.gz and
  1SN_2A_2.fq.gz
  6160214 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -351022 low quality reads; 5809192 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6160214 total sequences;
  0 ambiguous barcode drops;
  351022 low quality read drops;
  0 ambiguous RAD-Tag drops;
5809192 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_30A_1.fq.gz]
  Reading data from:
  1SN_30A_1.fq.gz and
  1SN_30A_2.fq.gz
  7680406 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -437786 low quality reads; 7242620 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

7680406 total sequences;
  0 ambiguous barcode drops;
  437786 low quality read drops;
  0 ambiguous RAD-Tag drops;
7242620 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_31A_1.fq.gz]
  Reading data from:
  1SN_31A_1.fq.gz and
  1SN_31A_2.fq.gz
  6707430 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -382160 low quality reads; 6325270 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6707430 total sequences;
  0 ambiguous barcode drops;
  382160 low quality read drops;
  0 ambiguous RAD-Tag drops;
6325270 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_32A_1.fq.gz]
  Reading data from:
  1SN_32A_1.fq.gz and
  1SN_32A_2.fq.gz
  5105270 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -290816 low quality reads; 4814454 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5105270 total sequences;
  0 ambiguous barcode drops;
  290816 low quality read drops;
  0 ambiguous RAD-Tag drops;
4814454 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_3A_1.fq.gz]
  Reading data from:
  1SN_3A_1.fq.gz and
  1SN_3A_2.fq.gz
  4884978 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -278712 low quality reads; 4606266 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

4884978 total sequences;
  0 ambiguous barcode drops;
  278712 low quality read drops;
  0 ambiguous RAD-Tag drops;
4606266 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_4A_1.fq.gz]
  Reading data from:
  1SN_4A_1.fq.gz and
  1SN_4A_2.fq.gz
  6589742 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -375779 low quality reads; 6213963 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6589742 total sequences;
  0 ambiguous barcode drops;
  375779 low quality read drops;
  0 ambiguous RAD-Tag drops;
6213963 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_5A_1.fq.gz]
  Reading data from:
  1SN_5A_1.fq.gz and
  1SN_5A_2.fq.gz
  6001704 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -342355 low quality reads; 5659349 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6001704 total sequences;
  0 ambiguous barcode drops;
  342355 low quality read drops;
  0 ambiguous RAD-Tag drops;
5659349 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_6A_1.fq.gz]
  Reading data from:
  1SN_6A_1.fq.gz and
  1SN_6A_2.fq.gz
  6708620 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -383346 low quality reads; 6325274 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6708620 total sequences;
  0 ambiguous barcode drops;
  383346 low quality read drops;
  0 ambiguous RAD-Tag drops;
6325274 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_7A_1.fq.gz]
  Reading data from:
  1SN_7A_1.fq.gz and
  1SN_7A_2.fq.gz
  5929188 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -339301 low quality reads; 5589887 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

5929188 total sequences;
  0 ambiguous barcode drops;
  339301 low quality read drops;
  0 ambiguous RAD-Tag drops;
5589887 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_8A_1.fq.gz]
  Reading data from:
  1SN_8A_1.fq.gz and
  1SN_8A_2.fq.gz
  6539620 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -372582 low quality reads; 6167038 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6539620 total sequences;
  0 ambiguous barcode drops;
  372582 low quality read drops;
  0 ambiguous RAD-Tag drops;
6167038 retained reads.
No barcodes specified, files will not be demultiplexed.
Processing paired-end data.
Using Phred+33 encoding for quality scores.
Found 1 paired input file(s).
Barcode type unspecified, assuming unbarcoded data.
Processing file 1 of 1 [1SN_9A_1.fq.gz]
  Reading data from:
  1SN_9A_1.fq.gz and
  1SN_9A_2.fq.gz
  6354410 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -361967 low quality reads; 5992443 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/Volumes/owl/temp/process_radtags.log'

6354410 total sequences;
  0 ambiguous barcode drops;
  361967 low quality read drops;
  0 ambiguous RAD-Tag drops;
5992443 retained reads.

Concatenate output files into single FASTQ file.¶

Create four lists - each of the four output files generated per individual¶

In [28]:

cd /Volumes/owl/temp/

/Volumes/owl/temp

In [29]:

%%bash
echo *A_1.1.fq.gz

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

In [30]:

%%bash
echo *A_1.rem.1.fq.gz

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

In [31]:

%%bash
echo *A_2.2.fq.gz

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

In [32]:

%%bash
echo *A_2.rem.2.fq.gz

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

Store the four lists generated above as variables¶

Loop through each component of each list as arrays and store the value from each list in independent variables¶

Concatenate the four corresponding files into a single FASTQ GZIP file¶

Use parameter expansion to adjust name of output file by replacing "_1.1" from list1 filenames with nothing (i.e. delete "_1.1").¶

In [33]:

%%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 )

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

In [35]:

%%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

Create de novo stacks¶

In [1]:

cd /Volumes/owl/temp/

/Volumes/owl/temp

In [ ]:

%%bash
#Runs ustacks and appends sql ID to each file for downstream analysis.
sql_id=0
for i in *A.fq.gz; do
  ((sql_id++))
  /usr/local/bioinformatics/stacks-1.37/ustacks -t gzfastq -f $i -o ./stacks -i $sql_id -d -r -p 16
  
done

In [ ]:

ls ./stacks/

In [ ]:

pwd

Create stacks catalog (cstacks)¶

In [ ]:

cd ./stacks/

List file names and format for subsequent use in cstacks command¶

In [ ]:

%%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 following cstacks command.
for fname in *; do printf " %s\n" "-s ${fname%%.*} \\" >> tmp.txt; done
cat tmp.txt | uniq
rm tmp.txt

In [ ]:

%%bash
#cstacks command.
time /usr/local/bioinformatics/stacks-1.37/cstacks -b 1 -o . \
-p 16 \
-s 1HL_10A \
-s 1HL_11A \
-s 1HL_12A \
-s 1HL_13A \
-s 1HL_14A \
-s 1HL_15A \
-s 1HL_16A \
-s 1HL_17A \
-s 1HL_19A \
-s 1HL_1A \
-s 1HL_20A \
-s 1HL_21A \
-s 1HL_22A \
-s 1HL_23A \
-s 1HL_24A \
-s 1HL_25A \
-s 1HL_26A \
-s 1HL_27A \
-s 1HL_28A \
-s 1HL_29A \
-s 1HL_2A \
-s 1HL_31A \
-s 1HL_33A \
-s 1HL_34A \
-s 1HL_35A \
-s 1HL_3A \
-s 1HL_4A \
-s 1HL_5A \
-s 1HL_6A \
-s 1HL_7A \
-s 1HL_8A \
-s 1HL_9A \
-s 1NF_10A \
-s 1NF_11A \
-s 1NF_12A \
-s 1NF_13A \
-s 1NF_14A \
-s 1NF_15A \
-s 1NF_16A \
-s 1NF_17A \
-s 1NF_18A \
-s 1NF_19A \
-s 1NF_1A \
-s 1NF_20A \
-s 1NF_21A \
-s 1NF_22A \
-s 1NF_23A \
-s 1NF_24A \
-s 1NF_25A \
-s 1NF_26A \
-s 1NF_27A \
-s 1NF_28A \
-s 1NF_29A \
-s 1NF_2A \
-s 1NF_30A \
-s 1NF_31A \
-s 1NF_32A \
-s 1NF_33A \
-s 1NF_4A \
-s 1NF_5A \
-s 1NF_6A \
-s 1NF_7A \
-s 1NF_8A \
-s 1NF_9A \
-s 1SN_10A \
-s 1SN_11A \
-s 1SN_12A \
-s 1SN_13A \
-s 1SN_14A \
-s 1SN_15A \
-s 1SN_16A \
-s 1SN_17A \
-s 1SN_18A \
-s 1SN_19A \
-s 1SN_1A \
-s 1SN_20A \
-s 1SN_21A \
-s 1SN_22A \
-s 1SN_23A \
-s 1SN_24A \
-s 1SN_25A \
-s 1SN_26A \
-s 1SN_27A \
-s 1SN_28A \
-s 1SN_29A \
-s 1SN_2A \
-s 1SN_30A \
-s 1SN_31A \
-s 1SN_32A \
-s 1SN_3A \
-s 1SN_4A \
-s 1SN_5A \
-s 1SN_6A \
-s 1SN_7A \
-s 1SN_8A \
-s 1SN_9A

In [ ]: