%%bash
date
Mon Jun 13 13:53:23 UTC 2016
%%bash
# Running Docker on roadrunner. Prints container ID, instead of host computer name (roaderunner)
hostname
4bc848ecaf48
%%bash
lscpu
Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 2 On-line CPU(s) list: 0,1 Thread(s) per core: 1 Core(s) per socket: 2 Socket(s): 1 Vendor ID: GenuineIntel CPU family: 6 Model: 26 Model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz Stepping: 5 CPU MHz: 2260.998 BogoMIPS: 4521.99 Hypervisor vendor: KVM Virtualization type: full L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 8192K
pwd
u'/notebooks'
cd /data/oly_gbs/
/data/oly_gbs
ls
160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_R1.fq.gz 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_R2.fq.gz
mv 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_R1.fq.gz 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_R1_.fq.gz
mv 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_R2.fq.gz 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_R2_.fq.gz
ls
160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_R1_.fq.gz 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_R2_.fq.gz
cd /analysis/20160609_pyrad/
/analysis/20160609_pyrad
ls
barcodes.txt params.txt
%%bash
cat params.txt
==** parameter inputs for pyRAD version 3.0.66 **======================== affected step ==
./ ## 1. Working directory (all)
/data/oly_gbs/*.gz ## 2. Loc. of non-demultiplexed files (if not line 18) (s1)
/analysis/20160609_pyrad/barcodes.txt ## 3. Loc. of barcode file (if not line 18) (s1)
/usr/local/bioinformatics/vsearch-1.11.1/bin/vsearch ## 4. command (or path) to call vsearch (or usearch) (s3,s6)
/usr/local/bioinformatics/muscle3.8.31_i86darwin64 ## 5. command (or path) to call muscle (s3,s7)
CWGC ## 6. Restriction overhang (e.g., C|TGCAG -> TGCAG) (s1,s2)
16 ## 7. N processors (parallel) (all)
6 ## 8. Mindepth: min coverage for a cluster (s4,s5)
4 ## 9. NQual: max # sites with qual < 20 (or see line 20)(s2)
.88 ## 10. Wclust: clustering threshold as a decimal (s3,s6)
pairgbs ## 11. Datatype: rad,gbs,pairgbs,pairddrad,(others:see docs)(all)
4 ## 12. MinCov: min samples in a final locus (s7)
3 ## 13. MaxSH: max inds with shared hetero site (s7)
oly_gbs_pyrad ## 14. Prefix name for final output (no spaces) (s7)
==== optional params below this line =================================== affected step ==
## 15.opt.: select subset (prefix* only selector) (s2-s7)
## 16.opt.: add-on (outgroup) taxa (list or prefix*) (s6,s7)
## 17.opt.: exclude taxa (list or prefix*) (s7)
## 18.opt.: loc. of de-multiplexed data (s2)
## 19.opt.: maxM: N mismatches in barcodes (def= 1) (s1)
## 20.opt.: phred Qscore offset (def= 33) (s2)
2 ## 21.opt.: filter: def=0=NQual 1=NQual+adapters. 2=strict (s2)
## 22.opt.: a priori E,H (def= 0.001,0.01, if not estimated) (s5)
4 ## 23.opt.: maxN: max Ns in a cons seq (def=5) (s5)
8 ## 24.opt.: maxH: max heterozyg. sites in cons seq (def=5) (s5)
## 25.opt.: ploidy: max alleles in cons seq (def=2;see docs) (s4,s5)
## 26.opt.: maxSNPs: (def=100). Paired (def=100,100) (s7)
## 27.opt.: maxIndels: within-clust,across-clust (def. 3,99) (s3,s7)
## 28.opt.: random number seed (def. 112233) (s3,s6,s7)
## 29.opt.: trim overhang left,right on final loci, def(0,0) (s7)
* ## 30.opt.: output formats: p,n,a,s,v,u,t,m,k,g,* (see docs) (s7)
## 31.opt.: maj. base call at depth>x<mindepth (def.x=mindepth) (s5)
50 ## 32.opt.: keep trimmed reads (def=0). Enter min length. (s2)
## 33.opt.: max stack size (int), def= max(500,mean+2*SD) (s3)
## 34.opt.: minDerep: exclude dereps with <= N copies, def=1 (s3)
## 35.opt.: use hierarchical clustering (def.=0, 1=yes) (s6)
## 36.opt.: repeat masking (def.=1='dust' method, 0=no) (s3,s6)
16 ## 37.opt.: vsearch max threads per job (def.=6; see docs) (s3,s6)
==== optional: list group/clade assignments below this line (see docs) ==================
1HL 5 1HL*
1NF 5 1NF*
1SN 5 1SN*
%%bash
cat barcodes.txt
1NF_1A CTCC 1NF_2A TGCA 1NF_4A ACTA 1NF_5A CAGA 1NF_6A AACT 1NF_7A GCGT 1NF_8A CGAT 1NF_9A GTAA 1NF_10A AGGC 1NF_11A GATC 1NF_12A TCAC 1NF_13A TGCGA 1NF_14A CGCTT 1NF_15A TCACC 1NF_16A CTAGC 1NF_17A ACAAA 1NF_18A TTCTC 1NF_19A AGCCC 1NF_20A GTATT 1NF_21A CTGTA 1NF_22A ACCGT 1NF_23A GCTTA 1NF_24A GGTGT 1NF_25A AGGAT 1NF_26A ATTGA 1NF_27A CATCT 1NF_28A CCTAC 1NF_29A GAGGA 1NF_30A GGAAC 1NF_31A GTCAA 1NF_32A TAATA 1NF_33A TACAT 1SN_1A TCGTT 1SN_2A GGTTGT 1SN_3A CCAGCT 1SN_4A TTCAGA 1SN_5A TAGGAA 1SN_6A GCTCTA 1SN_7A CCACAA 1SN_8A CTTCCA 1SN_9A GAGATA 1SN_10A ATGCCT 1SN_11A AGTGGA 1SN_12A ACCTAA 1SN_13A ATATGT 1SN_14A ATCGTA 1SN_15A CATCGT 1SN_16A CGCGGT 1SN_17A CTATTA 1SN_18A GCCAGT 1SN_19A GGAAGA 1SN_20A GTACTT 1SN_21A GTTGAA 1SN_22A TAACGA 1SN_23A TGGCTA 1SN_24A TATTTTT 1SN_25A CTTGCTT 1SN_26A ATGAAAC 1SN_27A AAAAGTT 1SN_28A GAATTCA 1SN_29A GAACTTC 1SN_30A GGACCTA 1SN_31A GTCGATT 1SN_32A AACGCCT 1HL_1A AATATGC 1HL_2A ACGTGTT 1HL_3A ATTAATT 1HL_4A ATTGGAT 1HL_5A CATAAGT 1HL_6A CGCTGAT 1HL_7A CGGTAGA 1HL_8A CTACGGA 1HL_9A GCGGAAT 1HL_10A TAGCGGA 1HL_11A TCGAAGA 1HL_12A TCTGTGA 1HL_13A TGCTGGA 1HL_14A ACGACTAC 1HL_15A TAGCATGC 1HL_16A TAGGCCAT 1HL_17A TGCAAGGA 1HL_19A TGGTACGT 1HL_20A TCTCAGTC 1HL_21A CCGGATAT 1HL_22A CGCCTTAT 1HL_23A AACCGAGA 1HL_24A ACAGGGAA 1HL_25A ACGTGGTA 1HL_26A CCATGGGT 1HL_27A CGCGGAGA 1HL_28A CGTGTGGT 1HL_29A GCTGTGGA 1HL_31A GGATTGGT 1HL_33A GTGAGGGT 1HL_34A TATCGGGA 1HL_35A TTCCTGGA
%%bash
time pyrad -p params.txt -s 1
cannot find vsearch (or usearch), edit path in param file
------------------------------------------------------------
pyRAD : RADseq for phylogenetics & introgression analyses
------------------------------------------------------------
real 0m2.121s
user 0m0.340s
sys 0m0.120s
%%bash
which vsearch
/usr/local/bioinformatics/vsearch-1.11.1-linux-x86_64/bin/vsearch
%%bash
cat params.txt
==** parameter inputs for pyRAD version 3.0.66 **======================== affected step ==
./ ## 1. Working directory (all)
/data/oly_gbs/*.gz ## 2. Loc. of non-demultiplexed files (if not line 18) (s1)
/analysis/20160609_pyrad/barcodes.txt ## 3. Loc. of barcode file (if not line 18) (s1)
/usr/local/bioinformatics/vsearch-1.11.1-linux-x86_64/bin/vsearch ## 4. command (or path) to call vsearch (or usearch) (s3,s6)
/usr/local/bioinformatics/muscle3.8.31_i86darwin64 ## 5. command (or path) to call muscle (s3,s7)
CWGC ## 6. Restriction overhang (e.g., C|TGCAG -> TGCAG) (s1,s2)
16 ## 7. N processors (parallel) (all)
6 ## 8. Mindepth: min coverage for a cluster (s4,s5)
4 ## 9. NQual: max # sites with qual < 20 (or see line 20)(s2)
.88 ## 10. Wclust: clustering threshold as a decimal (s3,s6)
pairgbs ## 11. Datatype: rad,gbs,pairgbs,pairddrad,(others:see docs)(all)
4 ## 12. MinCov: min samples in a final locus (s7)
3 ## 13. MaxSH: max inds with shared hetero site (s7)
oly_gbs_pyrad ## 14. Prefix name for final output (no spaces) (s7)
==== optional params below this line =================================== affected step ==
## 15.opt.: select subset (prefix* only selector) (s2-s7)
## 16.opt.: add-on (outgroup) taxa (list or prefix*) (s6,s7)
## 17.opt.: exclude taxa (list or prefix*) (s7)
## 18.opt.: loc. of de-multiplexed data (s2)
## 19.opt.: maxM: N mismatches in barcodes (def= 1) (s1)
## 20.opt.: phred Qscore offset (def= 33) (s2)
2 ## 21.opt.: filter: def=0=NQual 1=NQual+adapters. 2=strict (s2)
## 22.opt.: a priori E,H (def= 0.001,0.01, if not estimated) (s5)
4 ## 23.opt.: maxN: max Ns in a cons seq (def=5) (s5)
8 ## 24.opt.: maxH: max heterozyg. sites in cons seq (def=5) (s5)
## 25.opt.: ploidy: max alleles in cons seq (def=2;see docs) (s4,s5)
## 26.opt.: maxSNPs: (def=100). Paired (def=100,100) (s7)
## 27.opt.: maxIndels: within-clust,across-clust (def. 3,99) (s3,s7)
## 28.opt.: random number seed (def. 112233) (s3,s6,s7)
## 29.opt.: trim overhang left,right on final loci, def(0,0) (s7)
* ## 30.opt.: output formats: p,n,a,s,v,u,t,m,k,g,* (see docs) (s7)
## 31.opt.: maj. base call at depth>x<mindepth (def.x=mindepth) (s5)
50 ## 32.opt.: keep trimmed reads (def=0). Enter min length. (s2)
## 33.opt.: max stack size (int), def= max(500,mean+2*SD) (s3)
## 34.opt.: minDerep: exclude dereps with <= N copies, def=1 (s3)
## 35.opt.: use hierarchical clustering (def.=0, 1=yes) (s6)
## 36.opt.: repeat masking (def.=1='dust' method, 0=no) (s3,s6)
16 ## 37.opt.: vsearch max threads per job (def.=6; see docs) (s3,s6)
==== optional: list group/clade assignments below this line (see docs) ==================
1HL 5 1HL*
1NF 5 1NF*
1SN 5 1SN*
%%bash
time pyrad -p params.txt -s 1
cannot find muscle, edit path in input file
------------------------------------------------------------
pyRAD : RADseq for phylogenetics & introgression analyses
------------------------------------------------------------
real 0m0.354s
user 0m0.280s
sys 0m0.060s
%%bash
ls /usr/local/bioinformatics/muscle3.8.31_i86linux64
/usr/local/bioinformatics/muscle3.8.31_i86linux64
%%bash
cat params.txt
==** parameter inputs for pyRAD version 3.0.66 **======================== affected step ==
./ ## 1. Working directory (all)
/data/oly_gbs/*.gz ## 2. Loc. of non-demultiplexed files (if not line 18) (s1)
/analysis/20160609_pyrad/barcodes.txt ## 3. Loc. of barcode file (if not line 18) (s1)
/usr/local/bioinformatics/vsearch-1.11.1-linux-x86_64/bin/vsearch ## 4. command (or path) to call vsearch (or usearch) (s3,s6)
/usr/local/bioinformatics/muscle3.8.31_i86linux64/ ## 5. command (or path) to call muscle (s3,s7)
CWGC ## 6. Restriction overhang (e.g., C|TGCAG -> TGCAG) (s1,s2)
16 ## 7. N processors (parallel) (all)
6 ## 8. Mindepth: min coverage for a cluster (s4,s5)
4 ## 9. NQual: max # sites with qual < 20 (or see line 20)(s2)
.88 ## 10. Wclust: clustering threshold as a decimal (s3,s6)
pairgbs ## 11. Datatype: rad,gbs,pairgbs,pairddrad,(others:see docs)(all)
4 ## 12. MinCov: min samples in a final locus (s7)
3 ## 13. MaxSH: max inds with shared hetero site (s7)
oly_gbs_pyrad ## 14. Prefix name for final output (no spaces) (s7)
==== optional params below this line =================================== affected step ==
## 15.opt.: select subset (prefix* only selector) (s2-s7)
## 16.opt.: add-on (outgroup) taxa (list or prefix*) (s6,s7)
## 17.opt.: exclude taxa (list or prefix*) (s7)
## 18.opt.: loc. of de-multiplexed data (s2)
## 19.opt.: maxM: N mismatches in barcodes (def= 1) (s1)
## 20.opt.: phred Qscore offset (def= 33) (s2)
2 ## 21.opt.: filter: def=0=NQual 1=NQual+adapters. 2=strict (s2)
## 22.opt.: a priori E,H (def= 0.001,0.01, if not estimated) (s5)
4 ## 23.opt.: maxN: max Ns in a cons seq (def=5) (s5)
8 ## 24.opt.: maxH: max heterozyg. sites in cons seq (def=5) (s5)
## 25.opt.: ploidy: max alleles in cons seq (def=2;see docs) (s4,s5)
## 26.opt.: maxSNPs: (def=100). Paired (def=100,100) (s7)
## 27.opt.: maxIndels: within-clust,across-clust (def. 3,99) (s3,s7)
## 28.opt.: random number seed (def. 112233) (s3,s6,s7)
## 29.opt.: trim overhang left,right on final loci, def(0,0) (s7)
* ## 30.opt.: output formats: p,n,a,s,v,u,t,m,k,g,* (see docs) (s7)
## 31.opt.: maj. base call at depth>x<mindepth (def.x=mindepth) (s5)
50 ## 32.opt.: keep trimmed reads (def=0). Enter min length. (s2)
## 33.opt.: max stack size (int), def= max(500,mean+2*SD) (s3)
## 34.opt.: minDerep: exclude dereps with <= N copies, def=1 (s3)
## 35.opt.: use hierarchical clustering (def.=0, 1=yes) (s6)
## 36.opt.: repeat masking (def.=1='dust' method, 0=no) (s3,s6)
16 ## 37.opt.: vsearch max threads per job (def.=6; see docs) (s3,s6)
==== optional: list group/clade assignments below this line (see docs) ==================
1HL 5 1HL*
1NF 5 1NF*
1SN 5 1SN*
%%bash
time pyrad -p params.txt -s 1
cannot find muscle, edit path in input file
------------------------------------------------------------
pyRAD : RADseq for phylogenetics & introgression analyses
------------------------------------------------------------
real 0m0.358s
user 0m0.260s
sys 0m0.080s
%%bash
time pyrad -p params.txt -s 1
warning: CUT site matches within one of the barcodes, I suggest double checking the file to make sure it properly demultiplexes
------------------------------------------------------------
pyRAD : RADseq for phylogenetics & introgression analyses
------------------------------------------------------------
step 1: sorting reads by barcode
.
real 1118m28.900s
user 945m13.910s
sys 42m11.240s
%%bash
head -n 100 stats/s1.sorting.txt
file Nreads cut_found bar_matched 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_.fq.gz 364261046 355811046 354725421 sample true_bar obs_bars N_obs 1SN_27A AAAAGTT AAAAGTT 3325108 1SN_27A AAAAGTT NAAAGTT 8330 1SN_27A AAAAGTT AAAAATT 4748 1SN_27A AAAAGTT ANAAGTT 1455 1SN_27A AAAAGTT AAAATTT 782 1SN_27A AAAAGTT GAAAGTT 739 1SN_27A AAAAGTT AAACGTT 665 1SN_27A AAAAGTT CAAAGTT 617 1SN_27A AAAAGTT AACAGTT 592 1SN_27A AAAAGTT TAAAGTT 558 1SN_27A AAAAGTT AAAAGCT 351 1SN_27A AAAAGTT ACAAGTT 320 1SN_27A AAAAGTT AAAGGTT 284 1SN_27A AAAAGTT AGAAGTT 210 1SN_27A AAAAGTT AAAAGTC 201 1SN_27A AAAAGTT AAGAGTT 176 1SN_27A AAAAGTT AAANGTT 127 1SN_27A AAAAGTT AAAAGGT 106 1SN_27A AAAAGTT AAAAGAT 94 1SN_27A AAAAGTT ATAAGTT 94 1SN_27A AAAAGTT AATAGTT 92 1SN_27A AAAAGTT AAATGTT 80 1SN_27A AAAAGTT AAAACTT 42 1SN_27A AAAAGTT AANAGTT 37 1SN_27A AAAAGTT AAAAGTG 29 1SN_27A AAAAGTT AAAAGTA 27 1SN_27A AAAAGTT AAAAGNT 11 1HL_23A AACCGAGA AACCGAGA 4532975 1HL_23A AACCGAGA NACCGAGA 11670 1HL_23A AACCGAGA AGCCGAGA 3232 1HL_23A AACCGAGA TACCGAGA 2503 1HL_23A AACCGAGA ANCCGAGA 2022 1HL_23A AACCGAGA AACCAAGA 1624 1HL_23A AACCGAGA GACCGAGA 1595 1HL_23A AACCGAGA AACCTAGA 1463 1HL_23A AACCGAGA AATCGAGA 1328 1HL_23A AACCGAGA CACCGAGA 1183 1HL_23A AACCGAGA AACTGAGA 1147 1HL_23A AACCGAGA AACCGCGA 1040 1HL_23A AACCGAGA ACCCGAGA 721 1HL_23A AACCGAGA AACCGAGC 679 1HL_23A AACCGAGA AACCGGGA 486 1HL_23A AACCGAGA AACCGAAA 427 1HL_23A AACCGAGA AACCGAGT 415 1HL_23A AACCGAGA AACAGAGA 398 1HL_23A AACCGAGA AACCGAGG 375 1HL_23A AACCGAGA AACCGTGA 342 1HL_23A AACCGAGA AACCGATA 293 1HL_23A AACCGAGA AAACGAGA 232 1HL_23A AACCGAGA AACNGAGA 214 1HL_23A AACCGAGA ATCCGAGA 187 1HL_23A AACCGAGA AACGGAGA 137 1HL_23A AACCGAGA AACCCAGA 95 1HL_23A AACCGAGA AAGCGAGA 92 1HL_23A AACCGAGA AANCGAGA 54 1HL_23A AACCGAGA AACCGACA 40 1HL_23A AACCGAGA AACCGNGA 20 1SN_32A AACGCCT AACGCCT 3274859 1SN_32A AACGCCT NACGCCT 8278 1SN_32A AACGCCT TACGCCT 2642 1SN_32A AACGCCT GACGCCT 2577 1SN_32A AACGCCT ANCGCCT 1463 1SN_32A AACGCCT AACTCCT 1421 1SN_32A AACGCCT AACACCT 1005 1SN_32A AACGCCT ATCGCCT 958 1SN_32A AACGCCT AATGCCT 860 1SN_32A AACGCCT ACCGCCT 856 1SN_32A AACGCCT AGCGCCT 732 1SN_32A AACGCCT CACGCCT 604 1SN_32A AACGCCT AACGTCT 434 1SN_32A AACGCCT AACGCTT 430 1SN_32A AACGCCT AACGCCC 381 1SN_32A AACGCCT AACGCAT 290 1SN_32A AACGCCT AACGACT 229 1SN_32A AACGCCT AACGGCT 170 1SN_32A AACGCCT AACNCCT 160 1SN_32A AACGCCT AAAGCCT 141 1SN_32A AACGCCT AACCCCT 140 1SN_32A AACGCCT AACGCGT 107 1SN_32A AACGCCT AAGGCCT 94 1SN_32A AACGCCT AACGCCA 79 1SN_32A AACGCCT AACGCCG 45 1SN_32A AACGCCT AANGCCT 28 1SN_32A AACGCCT AACGCNT 13 1NF_6A AACT AACT 3192263 1NF_6A AACT NACT 7691 1NF_6A AACT ANCT 1424 1NF_6A AACT AGCT 963 1NF_6A AACT TACT 873 1NF_6A AACT GACT 791 1NF_6A AACT CACT 717 1NF_6A AACT ATCT 460 1NF_6A AACT AACC 417 1NF_6A AACT ACCT 390 1NF_6A AACT AAGT 289
For this we will use the program PEAR. This step is very important. I can pretty much assure you that you will have many paired end reads in your library that overlap, and if you do not merge these reads they can really mess up your analysis. In this case the vast majority of paired reads are overlapping (~80%), and in fact, the merged reads are the only portion of the data that we will be using for analysis.
The first thing we have to do is unzip the reads.
%%bash
time gunzip ./fastq/*.gz
real 73m48.470s user 18m41.580s sys 20m13.890s
%%bash
lscpu
Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 8 On-line CPU(s) list: 0-7 Thread(s) per core: 1 Core(s) per socket: 8 Socket(s): 1 Vendor ID: GenuineIntel CPU family: 6 Model: 26 Model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz Stepping: 5 CPU MHz: 2260.998 BogoMIPS: 4521.99 Hypervisor vendor: KVM Virtualization type: full L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 8192K
cd /analysis/20160609_pyrad/
/analysis/20160609_pyrad
ls /analysis/20160609_pyrad/fastq/
1HL_10A_R1.fq 1HL_29A_R2.fq 1NF_17A_R1.fq 1NF_4A_R2.fq 1SN_23A_R1.fq 1HL_10A_R2.fq 1HL_2A_R1.fq 1NF_17A_R2.fq 1NF_5A_R1.fq 1SN_23A_R2.fq 1HL_11A_R1.fq 1HL_2A_R2.fq 1NF_18A_R1.fq 1NF_5A_R2.fq 1SN_24A_R1.fq 1HL_11A_R2.fq 1HL_31A_R1.fq 1NF_18A_R2.fq 1NF_6A_R1.fq 1SN_24A_R2.fq 1HL_12A_R1.fq 1HL_31A_R2.fq 1NF_19A_R1.fq 1NF_6A_R2.fq 1SN_25A_R1.fq 1HL_12A_R2.fq 1HL_33A_R1.fq 1NF_19A_R2.fq 1NF_7A_R1.fq 1SN_25A_R2.fq 1HL_13A_R1.fq 1HL_33A_R2.fq 1NF_1A_R1.fq 1NF_7A_R2.fq 1SN_26A_R1.fq 1HL_13A_R2.fq 1HL_34A_R1.fq 1NF_1A_R2.fq 1NF_8A_R1.fq 1SN_26A_R2.fq 1HL_14A_R1.fq 1HL_34A_R2.fq 1NF_20A_R1.fq 1NF_8A_R2.fq 1SN_27A_R1.fq 1HL_14A_R2.fq 1HL_35A_R1.fq 1NF_20A_R2.fq 1NF_9A_R1.fq 1SN_27A_R2.fq 1HL_15A_R1.fq 1HL_35A_R2.fq 1NF_21A_R1.fq 1NF_9A_R2.fq 1SN_28A_R1.fq 1HL_15A_R2.fq 1HL_3A_R1.fq 1NF_21A_R2.fq 1SN_10A_R1.fq 1SN_28A_R2.fq 1HL_16A_R1.fq 1HL_3A_R2.fq 1NF_22A_R1.fq 1SN_10A_R2.fq 1SN_29A_R1.fq 1HL_16A_R2.fq 1HL_4A_R1.fq 1NF_22A_R2.fq 1SN_11A_R1.fq 1SN_29A_R2.fq 1HL_17A_R1.fq 1HL_4A_R2.fq 1NF_23A_R1.fq 1SN_11A_R2.fq 1SN_2A_R1.fq 1HL_17A_R2.fq 1HL_5A_R1.fq 1NF_23A_R2.fq 1SN_12A_R1.fq 1SN_2A_R2.fq 1HL_19A_R1.fq 1HL_5A_R2.fq 1NF_24A_R1.fq 1SN_12A_R2.fq 1SN_30A_R1.fq 1HL_19A_R2.fq 1HL_6A_R1.fq 1NF_24A_R2.fq 1SN_13A_R1.fq 1SN_30A_R2.fq 1HL_1A_R1.fq 1HL_6A_R2.fq 1NF_25A_R1.fq 1SN_13A_R2.fq 1SN_31A_R1.fq 1HL_1A_R2.fq 1HL_7A_R1.fq 1NF_25A_R2.fq 1SN_14A_R1.fq 1SN_31A_R2.fq 1HL_20A_R1.fq 1HL_7A_R2.fq 1NF_26A_R1.fq 1SN_14A_R2.fq 1SN_32A_R1.fq 1HL_20A_R2.fq 1HL_8A_R1.fq 1NF_26A_R2.fq 1SN_15A_R1.fq 1SN_32A_R2.fq 1HL_21A_R1.fq 1HL_8A_R2.fq 1NF_27A_R1.fq 1SN_15A_R2.fq 1SN_3A_R1.fq 1HL_21A_R2.fq 1HL_9A_R1.fq 1NF_27A_R2.fq 1SN_16A_R1.fq 1SN_3A_R2.fq 1HL_22A_R1.fq 1HL_9A_R2.fq 1NF_28A_R1.fq 1SN_16A_R2.fq 1SN_4A_R1.fq 1HL_22A_R2.fq 1NF_10A_R1.fq 1NF_28A_R2.fq 1SN_17A_R1.fq 1SN_4A_R2.fq 1HL_23A_R1.fq 1NF_10A_R2.fq 1NF_29A_R1.fq 1SN_17A_R2.fq 1SN_5A_R1.fq 1HL_23A_R2.fq 1NF_11A_R1.fq 1NF_29A_R2.fq 1SN_18A_R1.fq 1SN_5A_R2.fq 1HL_24A_R1.fq 1NF_11A_R2.fq 1NF_2A_R1.fq 1SN_18A_R2.fq 1SN_6A_R1.fq 1HL_24A_R2.fq 1NF_12A_R1.fq 1NF_2A_R2.fq 1SN_19A_R1.fq 1SN_6A_R2.fq 1HL_25A_R1.fq 1NF_12A_R2.fq 1NF_30A_R1.fq 1SN_19A_R2.fq 1SN_7A_R1.fq 1HL_25A_R2.fq 1NF_13A_R1.fq 1NF_30A_R2.fq 1SN_1A_R1.fq 1SN_7A_R2.fq 1HL_26A_R1.fq 1NF_13A_R2.fq 1NF_31A_R1.fq 1SN_1A_R2.fq 1SN_8A_R1.fq 1HL_26A_R2.fq 1NF_14A_R1.fq 1NF_31A_R2.fq 1SN_20A_R1.fq 1SN_8A_R2.fq 1HL_27A_R1.fq 1NF_14A_R2.fq 1NF_32A_R1.fq 1SN_20A_R2.fq 1SN_9A_R1.fq 1HL_27A_R2.fq 1NF_15A_R1.fq 1NF_32A_R2.fq 1SN_21A_R1.fq 1SN_9A_R2.fq 1HL_28A_R1.fq 1NF_15A_R2.fq 1NF_33A_R1.fq 1SN_21A_R2.fq 1HL_28A_R2.fq 1NF_16A_R1.fq 1NF_33A_R2.fq 1SN_22A_R1.fq 1HL_29A_R1.fq 1NF_16A_R2.fq 1NF_4A_R1.fq 1SN_22A_R2.fq
%%bash
time for gfile in /analysis/20160609_pyrad/fastq/*_R1.fq;
do /usr/local/bioinformatics/pear-0.9.6-bin-64/pear-0.9.6-bin-64 -f $gfile \
-r ${gfile/_R1.fq/_R2.fq} \
-o ${gfile/_R1.fq/} \
-n 33 \
-t 33 \
-q 10 \
-j 20 >> pear.log 2>&1;
done
%%bash
date
Thu Jun 16 20:27:00 UTC 2016
cd /analysis/20160609_pyrad/
/analysis/20160609_pyrad
%%bash
time for gfile in /analysis/20160609_pyrad/fastq/*_R1.fq;
do /usr/local/bioinformatics/pear-0.9.6-bin-64/pear-0.9.6-bin-64 -f $gfile \
-r ${gfile/_R1.fq/_R2.fq} \
-o ${gfile/_R1.fq/} \
-n 33 \
-t 33 \
-q 10 \
-j 20 >> pear.log 2>&1;
done
cd /analysis/20160609_pyrad/
/analysis/20160609_pyrad
ls
barcodes.txt fastq/ params.txt pear.log stats/
cd fastq/
/analysis/20160609_pyrad/fastq
ls
1HL_10A.assembled.fastq 1NF_11A_R1.fq 1HL_10A.discarded.fastq 1NF_11A_R2.fq 1HL_10A.unassembled.forward.fastq 1NF_12A.assembled.fastq 1HL_10A.unassembled.reverse.fastq 1NF_12A.discarded.fastq 1HL_10A_R1.fq 1NF_12A.unassembled.forward.fastq 1HL_10A_R2.fq 1NF_12A.unassembled.reverse.fastq 1HL_11A.assembled.fastq 1NF_12A_R1.fq 1HL_11A.discarded.fastq 1NF_12A_R2.fq 1HL_11A.unassembled.forward.fastq 1NF_13A.assembled.fastq 1HL_11A.unassembled.reverse.fastq 1NF_13A.discarded.fastq 1HL_11A_R1.fq 1NF_13A.unassembled.forward.fastq 1HL_11A_R2.fq 1NF_13A.unassembled.reverse.fastq 1HL_12A.assembled.fastq 1NF_13A_R1.fq 1HL_12A.discarded.fastq 1NF_13A_R2.fq 1HL_12A.unassembled.forward.fastq 1NF_14A.assembled.fastq 1HL_12A.unassembled.reverse.fastq 1NF_14A.discarded.fastq 1HL_12A_R1.fq 1NF_14A.unassembled.forward.fastq 1HL_12A_R2.fq 1NF_14A.unassembled.reverse.fastq 1HL_13A.assembled.fastq 1NF_14A_R1.fq 1HL_13A.discarded.fastq 1NF_14A_R2.fq 1HL_13A.unassembled.forward.fastq 1NF_15A.assembled.fastq 1HL_13A.unassembled.reverse.fastq 1NF_15A.discarded.fastq 1HL_13A_R1.fq 1NF_15A.unassembled.forward.fastq 1HL_13A_R2.fq 1NF_15A.unassembled.reverse.fastq 1HL_14A.assembled.fastq 1NF_15A_R1.fq 1HL_14A.discarded.fastq 1NF_15A_R2.fq 1HL_14A.unassembled.forward.fastq 1NF_16A.assembled.fastq 1HL_14A.unassembled.reverse.fastq 1NF_16A.discarded.fastq 1HL_14A_R1.fq 1NF_16A.unassembled.forward.fastq 1HL_14A_R2.fq 1NF_16A.unassembled.reverse.fastq 1HL_15A.assembled.fastq 1NF_16A_R1.fq 1HL_15A.discarded.fastq 1NF_16A_R2.fq 1HL_15A.unassembled.forward.fastq 1NF_17A.assembled.fastq 1HL_15A.unassembled.reverse.fastq 1NF_17A.discarded.fastq 1HL_15A_R1.fq 1NF_17A.unassembled.forward.fastq 1HL_15A_R2.fq 1NF_17A.unassembled.reverse.fastq 1HL_16A.assembled.fastq 1NF_17A_R1.fq 1HL_16A.discarded.fastq 1NF_17A_R2.fq 1HL_16A.unassembled.forward.fastq 1NF_18A.assembled.fastq 1HL_16A.unassembled.reverse.fastq 1NF_18A.discarded.fastq 1HL_16A_R1.fq 1NF_18A.unassembled.forward.fastq 1HL_16A_R2.fq 1NF_18A.unassembled.reverse.fastq 1HL_17A.assembled.fastq 1NF_18A_R1.fq 1HL_17A.discarded.fastq 1NF_18A_R2.fq 1HL_17A.unassembled.forward.fastq 1NF_19A.assembled.fastq 1HL_17A.unassembled.reverse.fastq 1NF_19A.discarded.fastq 1HL_17A_R1.fq 1NF_19A.unassembled.forward.fastq 1HL_17A_R2.fq 1NF_19A.unassembled.reverse.fastq 1HL_19A.assembled.fastq 1NF_19A_R1.fq 1HL_19A.discarded.fastq 1NF_19A_R2.fq 1HL_19A.unassembled.forward.fastq 1NF_1A.assembled.fastq 1HL_19A.unassembled.reverse.fastq 1NF_1A.discarded.fastq 1HL_19A_R1.fq 1NF_1A.unassembled.forward.fastq 1HL_19A_R2.fq 1NF_1A.unassembled.reverse.fastq 1HL_1A.assembled.fastq 1NF_1A_R1.fq 1HL_1A.discarded.fastq 1NF_1A_R2.fq 1HL_1A.unassembled.forward.fastq 1NF_20A.assembled.fastq 1HL_1A.unassembled.reverse.fastq 1NF_20A.discarded.fastq 1HL_1A_R1.fq 1NF_20A.unassembled.forward.fastq 1HL_1A_R2.fq 1NF_20A.unassembled.reverse.fastq 1HL_20A.assembled.fastq 1NF_20A_R1.fq 1HL_20A.discarded.fastq 1NF_20A_R2.fq 1HL_20A.unassembled.forward.fastq 1NF_21A.assembled.fastq 1HL_20A.unassembled.reverse.fastq 1NF_21A.discarded.fastq 1HL_20A_R1.fq 1NF_21A.unassembled.forward.fastq 1HL_20A_R2.fq 1NF_21A.unassembled.reverse.fastq 1HL_21A.assembled.fastq 1NF_21A_R1.fq 1HL_21A.discarded.fastq 1NF_21A_R2.fq 1HL_21A.unassembled.forward.fastq 1NF_22A.assembled.fastq 1HL_21A.unassembled.reverse.fastq 1NF_22A.discarded.fastq 1HL_21A_R1.fq 1NF_22A.unassembled.forward.fastq 1HL_21A_R2.fq 1NF_22A.unassembled.reverse.fastq 1HL_22A.assembled.fastq 1NF_22A_R1.fq 1HL_22A.discarded.fastq 1NF_22A_R2.fq 1HL_22A.unassembled.forward.fastq 1NF_23A.assembled.fastq 1HL_22A.unassembled.reverse.fastq 1NF_23A.discarded.fastq 1HL_22A_R1.fq 1NF_23A.unassembled.forward.fastq 1HL_22A_R2.fq 1NF_23A.unassembled.reverse.fastq 1HL_23A.assembled.fastq 1NF_23A_R1.fq 1HL_23A.discarded.fastq 1NF_23A_R2.fq 1HL_23A.unassembled.forward.fastq 1NF_24A.assembled.fastq 1HL_23A.unassembled.reverse.fastq 1NF_24A.discarded.fastq 1HL_23A_R1.fq 1NF_24A.unassembled.forward.fastq 1HL_23A_R2.fq 1NF_24A.unassembled.reverse.fastq 1HL_24A.assembled.fastq 1NF_24A_R1.fq 1HL_24A.discarded.fastq 1NF_24A_R2.fq 1HL_24A.unassembled.forward.fastq 1NF_25A.assembled.fastq 1HL_24A.unassembled.reverse.fastq 1NF_25A.discarded.fastq 1HL_24A_R1.fq 1NF_25A.unassembled.forward.fastq 1HL_24A_R2.fq 1NF_25A.unassembled.reverse.fastq 1HL_25A.assembled.fastq 1NF_25A_R1.fq 1HL_25A.discarded.fastq 1NF_25A_R2.fq 1HL_25A.unassembled.forward.fastq 1NF_26A.assembled.fastq 1HL_25A.unassembled.reverse.fastq 1NF_26A.discarded.fastq 1HL_25A_R1.fq 1NF_26A.unassembled.forward.fastq 1HL_25A_R2.fq 1NF_26A.unassembled.reverse.fastq 1HL_26A.assembled.fastq 1NF_26A_R1.fq 1HL_26A.discarded.fastq 1NF_26A_R2.fq 1HL_26A.unassembled.forward.fastq 1NF_27A.assembled.fastq 1HL_26A.unassembled.reverse.fastq 1NF_27A.discarded.fastq 1HL_26A_R1.fq 1NF_27A.unassembled.forward.fastq 1HL_26A_R2.fq 1NF_27A.unassembled.reverse.fastq 1HL_27A.assembled.fastq 1NF_27A_R1.fq 1HL_27A.discarded.fastq 1NF_27A_R2.fq 1HL_27A.unassembled.forward.fastq 1NF_28A.assembled.fastq 1HL_27A.unassembled.reverse.fastq 1NF_28A.discarded.fastq 1HL_27A_R1.fq 1NF_28A.unassembled.forward.fastq 1HL_27A_R2.fq 1NF_28A.unassembled.reverse.fastq 1HL_28A.assembled.fastq 1NF_28A_R1.fq 1HL_28A.discarded.fastq 1NF_28A_R2.fq 1HL_28A.unassembled.forward.fastq 1NF_29A.assembled.fastq 1HL_28A.unassembled.reverse.fastq 1NF_29A.discarded.fastq 1HL_28A_R1.fq 1NF_29A.unassembled.forward.fastq 1HL_28A_R2.fq 1NF_29A.unassembled.reverse.fastq 1HL_29A.assembled.fastq 1NF_29A_R1.fq 1HL_29A.discarded.fastq 1NF_29A_R2.fq 1HL_29A.unassembled.forward.fastq 1NF_2A_R1.fq 1HL_29A.unassembled.reverse.fastq 1NF_2A_R2.fq 1HL_29A_R1.fq 1NF_30A_R1.fq 1HL_29A_R2.fq 1NF_30A_R2.fq 1HL_2A.assembled.fastq 1NF_31A_R1.fq 1HL_2A.discarded.fastq 1NF_31A_R2.fq 1HL_2A.unassembled.forward.fastq 1NF_32A_R1.fq 1HL_2A.unassembled.reverse.fastq 1NF_32A_R2.fq 1HL_2A_R1.fq 1NF_33A_R1.fq 1HL_2A_R2.fq 1NF_33A_R2.fq 1HL_31A.assembled.fastq 1NF_4A_R1.fq 1HL_31A.discarded.fastq 1NF_4A_R2.fq 1HL_31A.unassembled.forward.fastq 1NF_5A_R1.fq 1HL_31A.unassembled.reverse.fastq 1NF_5A_R2.fq 1HL_31A_R1.fq 1NF_6A_R1.fq 1HL_31A_R2.fq 1NF_6A_R2.fq 1HL_33A.assembled.fastq 1NF_7A_R1.fq 1HL_33A.discarded.fastq 1NF_7A_R2.fq 1HL_33A.unassembled.forward.fastq 1NF_8A_R1.fq 1HL_33A.unassembled.reverse.fastq 1NF_8A_R2.fq 1HL_33A_R1.fq 1NF_9A_R1.fq 1HL_33A_R2.fq 1NF_9A_R2.fq 1HL_34A.assembled.fastq 1SN_10A_R1.fq 1HL_34A.discarded.fastq 1SN_10A_R2.fq 1HL_34A.unassembled.forward.fastq 1SN_11A_R1.fq 1HL_34A.unassembled.reverse.fastq 1SN_11A_R2.fq 1HL_34A_R1.fq 1SN_12A_R1.fq 1HL_34A_R2.fq 1SN_12A_R2.fq 1HL_35A.assembled.fastq 1SN_13A_R1.fq 1HL_35A.discarded.fastq 1SN_13A_R2.fq 1HL_35A.unassembled.forward.fastq 1SN_14A_R1.fq 1HL_35A.unassembled.reverse.fastq 1SN_14A_R2.fq 1HL_35A_R1.fq 1SN_15A_R1.fq 1HL_35A_R2.fq 1SN_15A_R2.fq 1HL_3A.assembled.fastq 1SN_16A_R1.fq 1HL_3A.discarded.fastq 1SN_16A_R2.fq 1HL_3A.unassembled.forward.fastq 1SN_17A_R1.fq 1HL_3A.unassembled.reverse.fastq 1SN_17A_R2.fq 1HL_3A_R1.fq 1SN_18A_R1.fq 1HL_3A_R2.fq 1SN_18A_R2.fq 1HL_4A.assembled.fastq 1SN_19A_R1.fq 1HL_4A.discarded.fastq 1SN_19A_R2.fq 1HL_4A.unassembled.forward.fastq 1SN_1A_R1.fq 1HL_4A.unassembled.reverse.fastq 1SN_1A_R2.fq 1HL_4A_R1.fq 1SN_20A_R1.fq 1HL_4A_R2.fq 1SN_20A_R2.fq 1HL_5A.assembled.fastq 1SN_21A_R1.fq 1HL_5A.discarded.fastq 1SN_21A_R2.fq 1HL_5A.unassembled.forward.fastq 1SN_22A_R1.fq 1HL_5A.unassembled.reverse.fastq 1SN_22A_R2.fq 1HL_5A_R1.fq 1SN_23A_R1.fq 1HL_5A_R2.fq 1SN_23A_R2.fq 1HL_6A.assembled.fastq 1SN_24A_R1.fq 1HL_6A.discarded.fastq 1SN_24A_R2.fq 1HL_6A.unassembled.forward.fastq 1SN_25A_R1.fq 1HL_6A.unassembled.reverse.fastq 1SN_25A_R2.fq 1HL_6A_R1.fq 1SN_26A_R1.fq 1HL_6A_R2.fq 1SN_26A_R2.fq 1HL_7A.assembled.fastq 1SN_27A_R1.fq 1HL_7A.discarded.fastq 1SN_27A_R2.fq 1HL_7A.unassembled.forward.fastq 1SN_28A_R1.fq 1HL_7A.unassembled.reverse.fastq 1SN_28A_R2.fq 1HL_7A_R1.fq 1SN_29A_R1.fq 1HL_7A_R2.fq 1SN_29A_R2.fq 1HL_8A.assembled.fastq 1SN_2A_R1.fq 1HL_8A.discarded.fastq 1SN_2A_R2.fq 1HL_8A.unassembled.forward.fastq 1SN_30A_R1.fq 1HL_8A.unassembled.reverse.fastq 1SN_30A_R2.fq 1HL_8A_R1.fq 1SN_31A_R1.fq 1HL_8A_R2.fq 1SN_31A_R2.fq 1HL_9A.assembled.fastq 1SN_32A_R1.fq 1HL_9A.discarded.fastq 1SN_32A_R2.fq 1HL_9A.unassembled.forward.fastq 1SN_3A_R1.fq 1HL_9A.unassembled.reverse.fastq 1SN_3A_R2.fq 1HL_9A_R1.fq 1SN_4A_R1.fq 1HL_9A_R2.fq 1SN_4A_R2.fq 1NF_10A.assembled.fastq 1SN_5A_R1.fq 1NF_10A.discarded.fastq 1SN_5A_R2.fq 1NF_10A.unassembled.forward.fastq 1SN_6A_R1.fq 1NF_10A.unassembled.reverse.fastq 1SN_6A_R2.fq 1NF_10A_R1.fq 1SN_7A_R1.fq 1NF_10A_R2.fq 1SN_7A_R2.fq 1NF_11A.assembled.fastq 1SN_8A_R1.fq 1NF_11A.discarded.fastq 1SN_8A_R2.fq 1NF_11A.unassembled.forward.fastq 1SN_9A_R1.fq 1NF_11A.unassembled.reverse.fastq 1SN_9A_R2.fq
cd ..
/analysis/20160609_pyrad
ls
barcodes.txt fastq/ params.txt pear.log stats/
%%bash
cat pear.log
bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 2: pear: command not found bash: line 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/usr/local/bioinformatics/pear-0.9.6-bin-64/: Is a directory bash: line 2: /usr/local/bioinformatics/pear-0.9.6-bin-64/: Is a directory bash: line 2: /usr/local/bioinformatics/pear-0.9.6-bin-64/: Is a directory bash: line 2: /usr/local/bioinformatics/pear-0.9.6-bin-64/: Is a directory bash: line 2: /usr/local/bioinformatics/pear-0.9.6-bin-64/: Is a directory bash: line 2: /usr/local/bioinformatics/pear-0.9.6-bin-64/: Is a directory ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_10A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_10A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284260 C: 0.220915 G: 0.223558 T: 0.271267 976333 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,890,999 / 4,151,970 (69.630%) Discarded reads ...................: 1,260,971 / 4,151,970 (30.370%) Not assembled reads ...............: 0 / 4,151,970 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_10A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_10A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_10A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_10A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_11A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_11A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284750 C: 0.219094 G: 0.222236 T: 0.273920 1052017 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,088,425 / 4,508,779 (68.498%) Discarded reads ...................: 1,420,354 / 4,508,779 (31.502%) Not assembled reads ...............: 0 / 4,508,779 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_11A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_11A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_11A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_11A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_12A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_12A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.287139 C: 0.219617 G: 0.224007 T: 0.269237 760356 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,323,231 / 3,302,719 (70.343%) Discarded reads ...................: 979,488 / 3,302,719 (29.657%) Not assembled reads ...............: 0 / 3,302,719 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_12A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_12A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_12A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_12A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_13A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_13A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.281475 C: 0.225744 G: 0.229937 T: 0.262844 872487 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,701,305 / 3,778,167 (71.498%) Discarded reads ...................: 1,076,862 / 3,778,167 (28.502%) Not assembled reads ...............: 0 / 3,778,167 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_13A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_13A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_13A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_13A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_14A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_14A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.281942 C: 0.219923 G: 0.228922 T: 0.269212 620505 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,865,526 / 2,687,944 (69.403%) Discarded reads ...................: 822,418 / 2,687,944 (30.597%) Not assembled reads ...............: 0 / 2,687,944 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_14A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_14A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_14A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_14A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_15A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_15A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.286995 C: 0.218292 G: 0.222091 T: 0.272623 629863 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,837,684 / 2,745,386 (66.937%) Discarded reads ...................: 907,702 / 2,745,386 (33.063%) Not assembled reads ...............: 0 / 2,745,386 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_15A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_15A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_15A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_15A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_16A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_16A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284772 C: 0.220373 G: 0.225556 T: 0.269300 704839 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,100,838 / 3,052,493 (68.824%) Discarded reads ...................: 951,655 / 3,052,493 (31.176%) Not assembled reads ...............: 0 / 3,052,493 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_16A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_16A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_16A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_16A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_17A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_17A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285335 C: 0.219349 G: 0.220786 T: 0.274530 1060536 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,106,139 / 4,587,720 (67.706%) Discarded reads ...................: 1,481,581 / 4,587,720 (32.294%) Not assembled reads ...............: 0 / 4,587,720 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_17A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_17A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_17A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_17A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_19A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_19A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.286462 C: 0.221234 G: 0.223039 T: 0.269265 1059693 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,174,884 / 4,607,650 (68.905%) Discarded reads ...................: 1,432,766 / 4,607,650 (31.095%) Not assembled reads ...............: 0 / 4,607,650 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_19A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_19A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_19A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_19A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_1A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_1A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285947 C: 0.218539 G: 0.224484 T: 0.271030 691996 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,098,741 / 3,010,262 (69.720%) Discarded reads ...................: 911,521 / 3,010,262 (30.280%) Not assembled reads ...............: 0 / 3,010,262 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_1A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_1A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_1A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_1A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_20A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_20A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.287080 C: 0.218017 G: 0.225527 T: 0.269376 840036 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,516,582 / 3,692,276 (68.158%) Discarded reads ...................: 1,175,694 / 3,692,276 (31.842%) Not assembled reads ...............: 0 / 3,692,276 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_20A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_20A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_20A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_20A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_21A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_21A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284969 C: 0.220369 G: 0.224433 T: 0.270228 751300 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,203,056 / 3,278,190 (67.203%) Discarded reads ...................: 1,075,134 / 3,278,190 (32.797%) Not assembled reads ...............: 0 / 3,278,190 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_21A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_21A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_21A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_21A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_22A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_22A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.286768 C: 0.218420 G: 0.226207 T: 0.268605 619188 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,807,508 / 2,666,966 (67.774%) Discarded reads ...................: 859,458 / 2,666,966 (32.226%) Not assembled reads ...............: 0 / 2,666,966 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_22A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_22A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_22A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_22A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_23A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_23A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.283043 C: 0.218893 G: 0.223030 T: 0.275034 1053503 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,117,475 / 4,566,989 (68.261%) Discarded reads ...................: 1,449,514 / 4,566,989 (31.739%) Not assembled reads ...............: 0 / 4,566,989 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_23A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_23A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_23A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_23A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_24A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_24A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284089 C: 0.219803 G: 0.220925 T: 0.275182 786608 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,290,319 / 3,418,136 (67.005%) Discarded reads ...................: 1,127,817 / 3,418,136 (32.995%) Not assembled reads ...............: 0 / 3,418,136 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_24A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_24A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_24A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_24A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_25A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_25A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285912 C: 0.220616 G: 0.222195 T: 0.271276 871202 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,606,955 / 3,794,161 (68.710%) Discarded reads ...................: 1,187,206 / 3,794,161 (31.290%) Not assembled reads ...............: 0 / 3,794,161 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_25A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_25A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_25A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_25A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_26A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_26A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.283029 C: 0.223790 G: 0.227327 T: 0.265854 962198 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,915,184 / 4,165,278 (69.988%) Discarded reads ...................: 1,250,094 / 4,165,278 (30.012%) Not assembled reads ...............: 0 / 4,165,278 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_26A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_26A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_26A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_26A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_27A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_27A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.281204 C: 0.223493 G: 0.225397 T: 0.269907 957521 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,887,147 / 4,146,188 (69.634%) Discarded reads ...................: 1,259,041 / 4,146,188 (30.366%) Not assembled reads ...............: 0 / 4,146,188 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_27A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_27A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_27A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_27A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_28A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_28A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285403 C: 0.219129 G: 0.223981 T: 0.271486 1082276 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,182,673 / 4,733,136 (67.242%) Discarded reads ...................: 1,550,463 / 4,733,136 (32.758%) Not assembled reads ...............: 0 / 4,733,136 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_28A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_28A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_28A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_28A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_29A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_29A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.282155 C: 0.226136 G: 0.227452 T: 0.264257 977328 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,004,016 / 4,238,592 (70.873%) Discarded reads ...................: 1,234,576 / 4,238,592 (29.127%) Not assembled reads ...............: 0 / 4,238,592 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_29A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_29A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_29A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_29A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_2A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_2A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.287959 C: 0.219214 G: 0.223470 T: 0.269357 830284 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,525,685 / 3,592,790 (70.299%) Discarded reads ...................: 1,067,105 / 3,592,790 (29.701%) Not assembled reads ...............: 0 / 3,592,790 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_2A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_2A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_2A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_2A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_31A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_31A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.286352 C: 0.223404 G: 0.222343 T: 0.267902 726029 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,203,255 / 3,177,985 (69.329%) Discarded reads ...................: 974,730 / 3,177,985 (30.671%) Not assembled reads ...............: 0 / 3,177,985 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_31A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_31A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_31A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_31A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_33A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_33A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285419 C: 0.224124 G: 0.221250 T: 0.269207 789912 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,357,587 / 3,450,088 (68.334%) Discarded reads ...................: 1,092,501 / 3,450,088 (31.666%) Not assembled reads ...............: 0 / 3,450,088 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_33A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_33A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_33A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_33A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_34A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_34A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.286763 C: 0.219421 G: 0.220701 T: 0.273115 844931 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,461,367 / 3,643,848 (67.549%) Discarded reads ...................: 1,182,481 / 3,643,848 (32.451%) Not assembled reads ...............: 0 / 3,643,848 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_34A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_34A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_34A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_34A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_35A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_35A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.288171 C: 0.218204 G: 0.222090 T: 0.271534 757197 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,222,135 / 3,298,636 (67.365%) Discarded reads ...................: 1,076,501 / 3,298,636 (32.635%) Not assembled reads ...............: 0 / 3,298,636 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_35A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_35A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_35A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_35A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_3A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_3A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.288734 C: 0.216823 G: 0.222551 T: 0.271893 666878 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,994,744 / 2,885,740 (69.124%) Discarded reads ...................: 890,996 / 2,885,740 (30.876%) Not assembled reads ...............: 0 / 2,885,740 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_3A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_3A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_3A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_3A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_4A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_4A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285469 C: 0.221915 G: 0.225571 T: 0.267044 822572 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,492,589 / 3,510,860 (70.997%) Discarded reads ...................: 1,018,271 / 3,510,860 (29.003%) Not assembled reads ...............: 0 / 3,510,860 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_4A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_4A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_4A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_4A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_5A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_5A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284051 C: 0.220209 G: 0.226839 T: 0.268900 635240 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,914,213 / 2,720,076 (70.374%) Discarded reads ...................: 805,863 / 2,720,076 (29.626%) Not assembled reads ...............: 0 / 2,720,076 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_5A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_5A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_5A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_5A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_6A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_6A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285547 C: 0.219469 G: 0.224365 T: 0.270619 609029 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,778,884 / 2,661,086 (66.848%) Discarded reads ...................: 882,202 / 2,661,086 (33.152%) Not assembled reads ...............: 0 / 2,661,086 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_6A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_6A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_6A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_6A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_7A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_7A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.279246 C: 0.221508 G: 0.227431 T: 0.271815 851643 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,555,275 / 3,689,392 (69.260%) Discarded reads ...................: 1,134,117 / 3,689,392 (30.740%) Not assembled reads ...............: 0 / 3,689,392 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_7A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_7A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_7A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_7A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_8A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_8A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.283546 C: 0.220649 G: 0.226514 T: 0.269290 788910 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,330,048 / 3,403,545 (68.459%) Discarded reads ...................: 1,073,497 / 3,403,545 (31.541%) Not assembled reads ...............: 0 / 3,403,545 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_8A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_8A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_8A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_8A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_9A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_9A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.281821 C: 0.223687 G: 0.226621 T: 0.267870 871271 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,620,475 / 3,753,204 (69.820%) Discarded reads ...................: 1,132,729 / 3,753,204 (30.180%) Not assembled reads ...............: 0 / 3,753,204 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_9A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_9A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_9A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_9A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_10A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_10A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284157 C: 0.220971 G: 0.225414 T: 0.269459 664722 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,955,600 / 2,848,504 (68.654%) Discarded reads ...................: 892,904 / 2,848,504 (31.346%) Not assembled reads ...............: 0 / 2,848,504 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_10A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_10A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_10A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_10A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_11A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_11A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.287054 C: 0.217908 G: 0.223626 T: 0.271412 677071 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,004,118 / 2,939,324 (68.183%) Discarded reads ...................: 935,206 / 2,939,324 (31.817%) Not assembled reads ...............: 0 / 2,939,324 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_11A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_11A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_11A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_11A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_12A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_12A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285198 C: 0.218229 G: 0.228122 T: 0.268451 673211 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,051,515 / 2,930,997 (69.994%) Discarded reads ...................: 879,482 / 2,930,997 (30.006%) Not assembled reads ...............: 0 / 2,930,997 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_12A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_12A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_12A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_12A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_13A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_13A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.283198 C: 0.221826 G: 0.226473 T: 0.268503 1200405 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,671,926 / 5,183,236 (70.842%) Discarded reads ...................: 1,511,310 / 5,183,236 (29.158%) Not assembled reads ...............: 0 / 5,183,236 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_13A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_13A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_13A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_13A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_14A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_14A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.288088 C: 0.217760 G: 0.223964 T: 0.270188 801159 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,333,572 / 3,467,126 (67.306%) Discarded reads ...................: 1,133,554 / 3,467,126 (32.694%) Not assembled reads ...............: 0 / 3,467,126 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_14A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_14A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_14A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_14A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_15A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_15A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285599 C: 0.217128 G: 0.227087 T: 0.270186 777701 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,296,320 / 3,344,566 (68.658%) Discarded reads ...................: 1,048,246 / 3,344,566 (31.342%) Not assembled reads ...............: 0 / 3,344,566 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_15A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_15A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_15A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_15A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_16A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_16A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.281531 C: 0.223127 G: 0.231810 T: 0.263532 881970 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,701,311 / 3,813,301 (70.839%) Discarded reads ...................: 1,111,990 / 3,813,301 (29.161%) Not assembled reads ...............: 0 / 3,813,301 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_16A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_16A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_16A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_16A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_17A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_17A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284847 C: 0.215946 G: 0.223492 T: 0.275716 964953 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,846,779 / 4,120,982 (69.080%) Discarded reads ...................: 1,274,203 / 4,120,982 (30.920%) Not assembled reads ...............: 0 / 4,120,982 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_17A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_17A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_17A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_17A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_18A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_18A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.291065 C: 0.214441 G: 0.221778 T: 0.272716 504128 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,469,499 / 2,195,389 (66.936%) Discarded reads ...................: 725,890 / 2,195,389 (33.064%) Not assembled reads ...............: 0 / 2,195,389 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_18A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_18A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_18A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_18A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_19A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_19A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284788 C: 0.218296 G: 0.226489 T: 0.270428 617454 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,775,039 / 2,644,544 (67.121%) Discarded reads ...................: 869,505 / 2,644,544 (32.879%) Not assembled reads ...............: 0 / 2,644,544 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_19A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_19A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_19A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_19A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_1A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_1A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.287105 C: 0.217074 G: 0.226171 T: 0.269650 404635 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,157,346 / 1,743,417 (66.384%) Discarded reads ...................: 586,071 / 1,743,417 (33.616%) Not assembled reads ...............: 0 / 1,743,417 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_1A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_1A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_1A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_1A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_20A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_20A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.288912 C: 0.218564 G: 0.223118 T: 0.269406 752785 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,261,913 / 3,273,230 (69.103%) Discarded reads ...................: 1,011,317 / 3,273,230 (30.897%) Not assembled reads ...............: 0 / 3,273,230 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_20A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_20A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_20A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_20A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_21A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_21A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.283222 C: 0.221884 G: 0.228245 T: 0.266648 931251 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,903,774 / 4,075,131 (71.256%) Discarded reads ...................: 1,171,357 / 4,075,131 (28.744%) Not assembled reads ...............: 0 / 4,075,131 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_21A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_21A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_21A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_21A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_22A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_22A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284947 C: 0.219154 G: 0.226847 T: 0.269051 879359 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,674,529 / 3,827,463 (69.877%) Discarded reads ...................: 1,152,934 / 3,827,463 (30.123%) Not assembled reads ...............: 0 / 3,827,463 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_22A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_22A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_22A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_22A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_23A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_23A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284968 C: 0.220204 G: 0.227276 T: 0.267552 1015053 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,106,447 / 4,372,177 (71.050%) Discarded reads ...................: 1,265,730 / 4,372,177 (28.950%) Not assembled reads ...............: 0 / 4,372,177 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_23A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_23A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_23A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_23A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_24A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_24A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.288096 C: 0.220296 G: 0.221235 T: 0.270373 889909 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,650,885 / 3,886,155 (68.214%) Discarded reads ...................: 1,235,270 / 3,886,155 (31.786%) Not assembled reads ...............: 0 / 3,886,155 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_24A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_24A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_24A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_24A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_25A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_25A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.287368 C: 0.218703 G: 0.220460 T: 0.273469 638537 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,879,642 / 2,807,991 (66.939%) Discarded reads ...................: 928,349 / 2,807,991 (33.061%) Not assembled reads ...............: 0 / 2,807,991 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_25A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_25A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_25A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_25A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_26A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_26A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.288072 C: 0.217058 G: 0.221301 T: 0.273569 887799 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,616,210 / 3,796,337 (68.914%) Discarded reads ...................: 1,180,127 / 3,796,337 (31.086%) Not assembled reads ...............: 0 / 3,796,337 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_26A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_26A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_26A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_26A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_27A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_27A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285131 C: 0.219412 G: 0.228628 T: 0.266829 707858 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,158,729 / 3,089,535 (69.872%) Discarded reads ...................: 930,806 / 3,089,535 (30.128%) Not assembled reads ...............: 0 / 3,089,535 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_27A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_27A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_27A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_27A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_28A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_28A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.282908 C: 0.220026 G: 0.230713 T: 0.266354 740492 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,221,247 / 3,194,615 (69.531%) Discarded reads ...................: 973,368 / 3,194,615 (30.469%) Not assembled reads ...............: 0 / 3,194,615 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_28A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_28A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_28A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_28A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_29A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_29A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_10A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_10A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284260 C: 0.220915 G: 0.223558 T: 0.271267 976333 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,890,999 / 4,151,970 (69.630%) Discarded reads ...................: 1,260,971 / 4,151,970 (30.370%) Not assembled reads ...............: 0 / 4,151,970 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_10A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_10A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_10A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_10A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_11A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_11A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284750 C: 0.219094 G: 0.222236 T: 0.273920 1052017 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,088,425 / 4,508,779 (68.498%) Discarded reads ...................: 1,420,354 / 4,508,779 (31.502%) Not assembled reads ...............: 0 / 4,508,779 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_11A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_11A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_11A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_11A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_12A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_12A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.287139 C: 0.219617 G: 0.224007 T: 0.269237 760356 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,323,231 / 3,302,719 (70.343%) Discarded reads ...................: 979,488 / 3,302,719 (29.657%) Not assembled reads ...............: 0 / 3,302,719 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_12A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_12A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_12A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_12A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_13A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_13A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.281475 C: 0.225744 G: 0.229937 T: 0.262844 872487 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,701,305 / 3,778,167 (71.498%) Discarded reads ...................: 1,076,862 / 3,778,167 (28.502%) Not assembled reads ...............: 0 / 3,778,167 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_13A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_13A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_13A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_13A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_14A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_14A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.281942 C: 0.219923 G: 0.228922 T: 0.269212 620505 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,865,526 / 2,687,944 (69.403%) Discarded reads ...................: 822,418 / 2,687,944 (30.597%) Not assembled reads ...............: 0 / 2,687,944 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_14A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_14A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_14A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_14A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_15A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_15A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.286995 C: 0.218292 G: 0.222091 T: 0.272623 629863 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,837,684 / 2,745,386 (66.937%) Discarded reads ...................: 907,702 / 2,745,386 (33.063%) Not assembled reads ...............: 0 / 2,745,386 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_15A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_15A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_15A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_15A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_16A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_16A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284772 C: 0.220373 G: 0.225556 T: 0.269300 704839 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,100,838 / 3,052,493 (68.824%) Discarded reads ...................: 951,655 / 3,052,493 (31.176%) Not assembled reads ...............: 0 / 3,052,493 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_16A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_16A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_16A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_16A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_17A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_17A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285335 C: 0.219349 G: 0.220786 T: 0.274530 1060536 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,106,139 / 4,587,720 (67.706%) Discarded reads ...................: 1,481,581 / 4,587,720 (32.294%) Not assembled reads ...............: 0 / 4,587,720 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_17A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_17A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_17A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_17A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_19A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_19A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.286462 C: 0.221234 G: 0.223039 T: 0.269265 1059693 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,174,884 / 4,607,650 (68.905%) Discarded reads ...................: 1,432,766 / 4,607,650 (31.095%) Not assembled reads ...............: 0 / 4,607,650 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_19A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_19A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_19A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_19A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_1A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_1A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285947 C: 0.218539 G: 0.224484 T: 0.271030 691996 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,098,741 / 3,010,262 (69.720%) Discarded reads ...................: 911,521 / 3,010,262 (30.280%) Not assembled reads ...............: 0 / 3,010,262 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_1A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_1A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_1A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_1A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_20A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_20A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.287080 C: 0.218017 G: 0.225527 T: 0.269376 840036 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,516,582 / 3,692,276 (68.158%) Discarded reads ...................: 1,175,694 / 3,692,276 (31.842%) Not assembled reads ...............: 0 / 3,692,276 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_20A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_20A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_20A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_20A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_21A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_21A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284969 C: 0.220369 G: 0.224433 T: 0.270228 751300 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,203,056 / 3,278,190 (67.203%) Discarded reads ...................: 1,075,134 / 3,278,190 (32.797%) Not assembled reads ...............: 0 / 3,278,190 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_21A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_21A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_21A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_21A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_22A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_22A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.286768 C: 0.218420 G: 0.226207 T: 0.268605 619188 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,807,508 / 2,666,966 (67.774%) Discarded reads ...................: 859,458 / 2,666,966 (32.226%) Not assembled reads ...............: 0 / 2,666,966 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_22A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_22A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_22A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_22A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_23A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_23A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.283043 C: 0.218893 G: 0.223030 T: 0.275034 1053503 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,117,475 / 4,566,989 (68.261%) Discarded reads ...................: 1,449,514 / 4,566,989 (31.739%) Not assembled reads ...............: 0 / 4,566,989 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_23A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_23A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_23A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_23A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_24A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_24A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284089 C: 0.219803 G: 0.220925 T: 0.275182 786608 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,290,319 / 3,418,136 (67.005%) Discarded reads ...................: 1,127,817 / 3,418,136 (32.995%) Not assembled reads ...............: 0 / 3,418,136 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_24A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_24A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_24A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_24A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_25A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_25A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285912 C: 0.220616 G: 0.222195 T: 0.271276 871202 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,606,955 / 3,794,161 (68.710%) Discarded reads ...................: 1,187,206 / 3,794,161 (31.290%) Not assembled reads ...............: 0 / 3,794,161 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_25A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_25A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_25A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_25A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_26A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_26A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.283029 C: 0.223790 G: 0.227327 T: 0.265854 962198 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,915,184 / 4,165,278 (69.988%) Discarded reads ...................: 1,250,094 / 4,165,278 (30.012%) Not assembled reads ...............: 0 / 4,165,278 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_26A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_26A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_26A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_26A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_27A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_27A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.281204 C: 0.223493 G: 0.225397 T: 0.269907 957521 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,887,147 / 4,146,188 (69.634%) Discarded reads ...................: 1,259,041 / 4,146,188 (30.366%) Not assembled reads ...............: 0 / 4,146,188 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_27A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_27A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_27A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_27A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_28A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_28A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285403 C: 0.219129 G: 0.223981 T: 0.271486 1082276 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,182,673 / 4,733,136 (67.242%) Discarded reads ...................: 1,550,463 / 4,733,136 (32.758%) Not assembled reads ...............: 0 / 4,733,136 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_28A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_28A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_28A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_28A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_29A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_29A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.282155 C: 0.226136 G: 0.227452 T: 0.264257 977328 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,004,016 / 4,238,592 (70.873%) Discarded reads ...................: 1,234,576 / 4,238,592 (29.127%) Not assembled reads ...............: 0 / 4,238,592 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_29A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_29A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_29A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_29A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_2A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_2A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.287959 C: 0.219214 G: 0.223470 T: 0.269357 830284 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,525,685 / 3,592,790 (70.299%) Discarded reads ...................: 1,067,105 / 3,592,790 (29.701%) Not assembled reads ...............: 0 / 3,592,790 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_2A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_2A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_2A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_2A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_31A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_31A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.286352 C: 0.223404 G: 0.222343 T: 0.267902 726029 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,203,255 / 3,177,985 (69.329%) Discarded reads ...................: 974,730 / 3,177,985 (30.671%) Not assembled reads ...............: 0 / 3,177,985 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_31A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_31A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_31A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_31A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_33A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_33A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285419 C: 0.224124 G: 0.221250 T: 0.269207 789912 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,357,587 / 3,450,088 (68.334%) Discarded reads ...................: 1,092,501 / 3,450,088 (31.666%) Not assembled reads ...............: 0 / 3,450,088 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_33A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_33A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_33A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_33A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_34A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_34A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.286763 C: 0.219421 G: 0.220701 T: 0.273115 844931 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,461,367 / 3,643,848 (67.549%) Discarded reads ...................: 1,182,481 / 3,643,848 (32.451%) Not assembled reads ...............: 0 / 3,643,848 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_34A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_34A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_34A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_34A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_35A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_35A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.288171 C: 0.218204 G: 0.222090 T: 0.271534 757197 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,222,135 / 3,298,636 (67.365%) Discarded reads ...................: 1,076,501 / 3,298,636 (32.635%) Not assembled reads ...............: 0 / 3,298,636 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_35A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_35A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_35A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_35A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_3A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_3A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.288734 C: 0.216823 G: 0.222551 T: 0.271893 666878 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,994,744 / 2,885,740 (69.124%) Discarded reads ...................: 890,996 / 2,885,740 (30.876%) Not assembled reads ...............: 0 / 2,885,740 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_3A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_3A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_3A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_3A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_4A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_4A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285469 C: 0.221915 G: 0.225571 T: 0.267044 822572 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,492,589 / 3,510,860 (70.997%) Discarded reads ...................: 1,018,271 / 3,510,860 (29.003%) Not assembled reads ...............: 0 / 3,510,860 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_4A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_4A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_4A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_4A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_5A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_5A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284051 C: 0.220209 G: 0.226839 T: 0.268900 635240 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,914,213 / 2,720,076 (70.374%) Discarded reads ...................: 805,863 / 2,720,076 (29.626%) Not assembled reads ...............: 0 / 2,720,076 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_5A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_5A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_5A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_5A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_6A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_6A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285547 C: 0.219469 G: 0.224365 T: 0.270619 609029 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,778,884 / 2,661,086 (66.848%) Discarded reads ...................: 882,202 / 2,661,086 (33.152%) Not assembled reads ...............: 0 / 2,661,086 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_6A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_6A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_6A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_6A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_7A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_7A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.279246 C: 0.221508 G: 0.227431 T: 0.271815 851643 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,555,275 / 3,689,392 (69.260%) Discarded reads ...................: 1,134,117 / 3,689,392 (30.740%) Not assembled reads ...............: 0 / 3,689,392 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_7A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_7A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_7A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_7A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_8A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_8A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.283546 C: 0.220649 G: 0.226514 T: 0.269290 788910 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,330,048 / 3,403,545 (68.459%) Discarded reads ...................: 1,073,497 / 3,403,545 (31.541%) Not assembled reads ...............: 0 / 3,403,545 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_8A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_8A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_8A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_8A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1HL_9A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1HL_9A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.281821 C: 0.223687 G: 0.226621 T: 0.267870 871271 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,620,475 / 3,753,204 (69.820%) Discarded reads ...................: 1,132,729 / 3,753,204 (30.180%) Not assembled reads ...............: 0 / 3,753,204 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1HL_9A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1HL_9A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1HL_9A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1HL_9A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_10A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_10A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284157 C: 0.220971 G: 0.225414 T: 0.269459 664722 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,955,600 / 2,848,504 (68.654%) Discarded reads ...................: 892,904 / 2,848,504 (31.346%) Not assembled reads ...............: 0 / 2,848,504 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_10A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_10A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_10A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_10A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_11A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_11A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.287054 C: 0.217908 G: 0.223626 T: 0.271412 677071 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,004,118 / 2,939,324 (68.183%) Discarded reads ...................: 935,206 / 2,939,324 (31.817%) Not assembled reads ...............: 0 / 2,939,324 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_11A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_11A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_11A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_11A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_12A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_12A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285198 C: 0.218229 G: 0.228122 T: 0.268451 673211 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,051,515 / 2,930,997 (69.994%) Discarded reads ...................: 879,482 / 2,930,997 (30.006%) Not assembled reads ...............: 0 / 2,930,997 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_12A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_12A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_12A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_12A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_13A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_13A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.283198 C: 0.221826 G: 0.226473 T: 0.268503 1200405 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,671,926 / 5,183,236 (70.842%) Discarded reads ...................: 1,511,310 / 5,183,236 (29.158%) Not assembled reads ...............: 0 / 5,183,236 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_13A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_13A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_13A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_13A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_14A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_14A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.288088 C: 0.217760 G: 0.223964 T: 0.270188 801159 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,333,572 / 3,467,126 (67.306%) Discarded reads ...................: 1,133,554 / 3,467,126 (32.694%) Not assembled reads ...............: 0 / 3,467,126 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_14A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_14A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_14A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_14A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_15A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_15A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285599 C: 0.217128 G: 0.227087 T: 0.270186 777701 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,296,320 / 3,344,566 (68.658%) Discarded reads ...................: 1,048,246 / 3,344,566 (31.342%) Not assembled reads ...............: 0 / 3,344,566 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_15A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_15A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_15A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_15A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_16A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_16A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.281531 C: 0.223127 G: 0.231810 T: 0.263532 881970 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,701,311 / 3,813,301 (70.839%) Discarded reads ...................: 1,111,990 / 3,813,301 (29.161%) Not assembled reads ...............: 0 / 3,813,301 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_16A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_16A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_16A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_16A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_17A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_17A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284847 C: 0.215946 G: 0.223492 T: 0.275716 964953 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,846,779 / 4,120,982 (69.080%) Discarded reads ...................: 1,274,203 / 4,120,982 (30.920%) Not assembled reads ...............: 0 / 4,120,982 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_17A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_17A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_17A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_17A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_18A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_18A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.291065 C: 0.214441 G: 0.221778 T: 0.272716 504128 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,469,499 / 2,195,389 (66.936%) Discarded reads ...................: 725,890 / 2,195,389 (33.064%) Not assembled reads ...............: 0 / 2,195,389 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_18A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_18A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_18A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_18A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_19A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_19A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284788 C: 0.218296 G: 0.226489 T: 0.270428 617454 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,775,039 / 2,644,544 (67.121%) Discarded reads ...................: 869,505 / 2,644,544 (32.879%) Not assembled reads ...............: 0 / 2,644,544 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_19A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_19A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_19A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_19A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_1A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_1A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.287105 C: 0.217074 G: 0.226171 T: 0.269650 404635 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,157,346 / 1,743,417 (66.384%) Discarded reads ...................: 586,071 / 1,743,417 (33.616%) Not assembled reads ...............: 0 / 1,743,417 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_1A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_1A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_1A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_1A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_20A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_20A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.288912 C: 0.218564 G: 0.223118 T: 0.269406 752785 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,261,913 / 3,273,230 (69.103%) Discarded reads ...................: 1,011,317 / 3,273,230 (30.897%) Not assembled reads ...............: 0 / 3,273,230 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_20A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_20A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_20A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_20A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_21A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_21A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.283222 C: 0.221884 G: 0.228245 T: 0.266648 931251 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,903,774 / 4,075,131 (71.256%) Discarded reads ...................: 1,171,357 / 4,075,131 (28.744%) Not assembled reads ...............: 0 / 4,075,131 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_21A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_21A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_21A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_21A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_22A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_22A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284947 C: 0.219154 G: 0.226847 T: 0.269051 879359 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,674,529 / 3,827,463 (69.877%) Discarded reads ...................: 1,152,934 / 3,827,463 (30.123%) Not assembled reads ...............: 0 / 3,827,463 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_22A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_22A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_22A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_22A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_23A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_23A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.284968 C: 0.220204 G: 0.227276 T: 0.267552 1015053 uncalled bases Assemblying reads: 100% Assembled reads ...................: 3,106,447 / 4,372,177 (71.050%) Discarded reads ...................: 1,265,730 / 4,372,177 (28.950%) Not assembled reads ...............: 0 / 4,372,177 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_23A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_23A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_23A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_23A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_24A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_24A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.288096 C: 0.220296 G: 0.221235 T: 0.270373 889909 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,650,885 / 3,886,155 (68.214%) Discarded reads ...................: 1,235,270 / 3,886,155 (31.786%) Not assembled reads ...............: 0 / 3,886,155 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_24A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_24A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_24A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_24A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_25A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_25A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.287368 C: 0.218703 G: 0.220460 T: 0.273469 638537 uncalled bases Assemblying reads: 100% Assembled reads ...................: 1,879,642 / 2,807,991 (66.939%) Discarded reads ...................: 928,349 / 2,807,991 (33.061%) Not assembled reads ...............: 0 / 2,807,991 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_25A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_25A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_25A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_25A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_26A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_26A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.288072 C: 0.217058 G: 0.221301 T: 0.273569 887799 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,616,210 / 3,796,337 (68.914%) Discarded reads ...................: 1,180,127 / 3,796,337 (31.086%) Not assembled reads ...............: 0 / 3,796,337 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_26A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_26A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_26A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_26A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_27A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_27A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.285131 C: 0.219412 G: 0.228628 T: 0.266829 707858 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,158,729 / 3,089,535 (69.872%) Discarded reads ...................: 930,806 / 3,089,535 (30.128%) Not assembled reads ...............: 0 / 3,089,535 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_27A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_27A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_27A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_27A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_28A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_28A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....: DONE A: 0.282908 C: 0.220026 G: 0.230713 T: 0.266354 740492 uncalled bases Assemblying reads: 100% Assembled reads ...................: 2,221,247 / 3,194,615 (69.531%) Discarded reads ...................: 973,368 / 3,194,615 (30.469%) Not assembled reads ...............: 0 / 3,194,615 (0.000%) Assembled reads file...............: /analysis/20160609_pyrad/fastq/1NF_28A.assembled.fastq Discarded reads file...............: /analysis/20160609_pyrad/fastq/1NF_28A.discarded.fastq Unassembled forward reads file.....: /analysis/20160609_pyrad/fastq/1NF_28A.unassembled.forward.fastq Unassembled reverse reads file.....: /analysis/20160609_pyrad/fastq/1NF_28A.unassembled.reverse.fastq ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.6 [January 15, 2015] Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 Forward reads file.................: /analysis/20160609_pyrad/fastq/1NF_29A_R1.fq Reverse reads file.................: /analysis/20160609_pyrad/fastq/1NF_29A_R2.fq PHRED..............................: 33 Using empirical frequencies........: YES Statistical method.................: OES Maximum assembly length............: 999999 Minimum assembly length............: 33 p-value............................: 0.010000 Quality score threshold (trimming).: 10 Minimum read size after trimming...: 33 Maximal ratio of uncalled bases....: 1.000000 Minimum overlap....................: 10 Scoring method.....................: Scaled score Threads............................: 20 Allocating memory..................: 200,000,000 bytes Computing empirical frequencies....:
%%bash
date
Wed Jun 29 18:10:08 UTC 2016
%%bash
#Rename previous pear.log so new log info isn't appended to previous file
mv pear.log pear.log.20160609
ls
barcodes.txt fastq/ params.txt pear.log.20160609 stats/
%%bash
time for gfile in /analysis/20160609_pyrad/fastq/*_R1.fq;
do /usr/local/bioinformatics/pear-0.9.6-bin-64/pear-0.9.6-bin-64 -f $gfile \
-r ${gfile/_R1.fq/_R2.fq} \
-o ${gfile/_R1.fq/} \
-n 33 \
-t 33 \
-q 10 \
-j 20 >> pear.log 2>&1;
done
cd /analysis/20160609_pyrad/
/analysis/20160609_pyrad
ls
barcodes.txt fastq/ params.txt pear.log pear.log.20160609 stats/
rm pear.log
ls
barcodes.txt fastq/ params.txt pear.log.20160609 stats/
%%bash
time for gfile in /analysis/20160609_pyrad/fastq/*_R1.fq;
do /usr/local/bioinformatics/pear-0.9.6-bin-64/pear-0.9.6-bin-64 -f $gfile \
-r ${gfile/_R1.fq/_R2.fq} \
-o ${gfile/_R1.fq/} \
-n 33 \
-t 33 \
-q 10 \
-j 20 >> pear.log 2>&1;
done
%%bash
date
Thu Jun 30 15:23:02 PDT 2016
%%bash
system_profiler SPSoftwareDataType
Software:
System Software Overview:
System Version: OS X 10.11.5 (15F34)
Kernel Version: Darwin 15.5.0
Boot Volume: boot_drive
Boot Mode: Normal
Computer Name: roadrunner
User Name: sam (sam)
Secure Virtual Memory: Enabled
System Integrity Protection: Enabled
Time since boot: 35 minutes
%%bash
#Uses grep to exclude lines that display serial number and hardware UUID
system_profiler SPHardwareDataType | grep -v [SH][ea]
Model Name: Xserve
Model Identifier: Xserve3,1
Processor Name: Quad-Core Intel Xeon
Processor Speed: 2.26 GHz
Number of Processors: 2
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache (per Processor): 8 MB
Memory: 48 GB
Processor Interconnect Speed: 5.86 GT/s
Boot ROM Version: XS31.0081.B04
SMC Version (system): 1.43f4
LOM Revision: 1.1.8
cd /Users/sam/analysis/20160609_pyrad/
/Users/sam/analysis/20160609_pyrad
ls
barcodes.txt params.txt pear.log.20160609 fastq/ pear.log stats/
%%bash
mv pear.log pear.log.20160629
ls
barcodes.txt params.txt pear.log.20160629 fastq/ pear.log.20160609 stats/
%%bash
time for gfile in /Users/sam/analysis/20160609_pyrad/fastq/*_R1.fq;
do pear -f $gfile \
-r ${gfile/_R1.fq/_R2.fq} \
-o ${gfile/_R1.fq/} \
-n 33 \
-t 33 \
-q 10 \
-j 20 >> pear.log 2>&1;
done