unning external command line application. This may print messages to stdout and/or stderr. The commands to be run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist. Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/10_SP_74_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/10_SP_151_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/10_SP_74_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/10_SP_151_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/10_SP_74_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/10_SP_151_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/10_SP_74_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/10_SP_151_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.83 s (15 µs/read; 4.00 M reads/minute). === Summary === Total read pairs processed: 55,472 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 224 (0.4%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 55,472 (100.0%) Total basepairs processed: 30,838,253 bp Read 1: 16,231,654 bp Read 2: 14,606,599 bp Total written (filtered): 30,837,354 bp (100.0%) Read 1: 16,231,654 bp Read 2: 14,605,700 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 224 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 866.8 0 2 4 219 216.7 0 219 5 1 54.2 0 1 6 2 13.5 0 2 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/11_CRT_73_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/11_CRT_150_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/11_CRT_73_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/11_CRT_150_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/11_CRT_73_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/11_CRT_150_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/11_CRT_73_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/11_CRT_150_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.74 s (14 µs/read; 4.26 M reads/minute). === Summary === Total read pairs processed: 52,278 Read 1 with adapter: 1 (0.0%) Read 2 with adapter: 14 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 52,278 (100.0%) Total basepairs processed: 28,856,325 bp Read 1: 15,283,635 bp Read 2: 13,572,690 bp Total written (filtered): 28,856,267 bp (100.0%) Read 1: 15,283,630 bp Read 2: 13,572,637 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 5 1 51.1 0 1 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 14 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 3 816.8 0 3 4 11 204.2 0 11 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/11_SP_72_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/11_SP_149_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/11_SP_72_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/11_SP_149_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/11_SP_72_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/11_SP_149_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/11_SP_72_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/11_SP_149_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.56 s (17 µs/read; 3.56 M reads/minute). === Summary === Total read pairs processed: 33,203 Read 1 with adapter: 1 (0.0%) Read 2 with adapter: 8 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 33,203 (100.0%) Total basepairs processed: 18,372,489 bp Read 1: 9,728,238 bp Read 2: 8,644,251 bp Total written (filtered): 18,372,456 bp (100.0%) Read 1: 9,728,235 bp Read 2: 8,644,221 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 1 518.8 0 1 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 8 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 518.8 0 2 4 6 129.7 0 6 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/12_SP_71_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/12_SP_148_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/12_SP_71_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/12_SP_148_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/12_SP_71_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/12_SP_148_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/12_SP_71_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/12_SP_148_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.93 s (14 µs/read; 4.30 M reads/minute). === Summary === Total read pairs processed: 66,927 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 12 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 66,927 (100.0%) Total basepairs processed: 37,027,400 bp Read 1: 19,509,324 bp Read 2: 17,518,076 bp Total written (filtered): 37,027,343 bp (100.0%) Read 1: 19,509,324 bp Read 2: 17,518,019 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 12 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 1045.7 0 2 4 3 261.4 0 3 5 3 65.4 0 3 6 4 16.3 0 4 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/13_SP_70_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/13_SP_147_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/13_SP_70_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/13_SP_147_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/13_SP_70_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/13_SP_147_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/13_SP_70_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/13_SP_147_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.69 s (15 µs/read; 4.12 M reads/minute). === Summary === Total read pairs processed: 116,139 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 16 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 116,139 (100.0%) Total basepairs processed: 64,958,412 bp Read 1: 33,936,405 bp Read 2: 31,022,007 bp Total written (filtered): 64,958,335 bp (100.0%) Read 1: 33,936,405 bp Read 2: 31,021,930 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 16 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 1814.7 0 2 4 2 453.7 0 2 5 9 113.4 0 9 6 3 28.4 0 3 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/14_SP_69_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/14_SP_146_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/14_SP_69_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/14_SP_146_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/14_SP_69_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/14_SP_146_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/14_SP_69_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/14_SP_146_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.10 s (13 µs/read; 4.45 M reads/minute). === Summary === Total read pairs processed: 81,333 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 19 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 81,333 (100.0%) Total basepairs processed: 44,851,183 bp Read 1: 23,777,893 bp Read 2: 21,073,290 bp Total written (filtered): 44,851,108 bp (100.0%) Read 1: 23,777,893 bp Read 2: 21,073,215 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 19 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 3 1270.8 0 3 4 15 317.7 0 15 6 1 19.9 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/16_CRT_68_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/16_CRT_145_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/16_CRT_68_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/16_CRT_145_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/16_CRT_68_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/16_CRT_145_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/16_CRT_68_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/16_CRT_145_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.82 s (15 µs/read; 3.99 M reads/minute). === Summary === Total read pairs processed: 54,607 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 13 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 54,607 (100.0%) Total basepairs processed: 30,427,190 bp Read 1: 15,993,624 bp Read 2: 14,433,566 bp Total written (filtered): 30,427,130 bp (100.0%) Read 1: 15,993,624 bp Read 2: 14,433,506 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 13 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 4 853.2 0 4 4 2 213.3 0 2 5 2 53.3 0 2 6 5 13.3 0 5 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/17_CRT_67_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/17_CRT_144_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/17_CRT_67_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/17_CRT_144_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/17_CRT_67_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/17_CRT_144_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/17_CRT_67_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/17_CRT_144_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.92 s (15 µs/read; 3.97 M reads/minute). === Summary === Total read pairs processed: 60,755 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 13 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 60,755 (100.0%) Total basepairs processed: 33,862,087 bp Read 1: 17,804,753 bp Read 2: 16,057,334 bp Total written (filtered): 33,862,029 bp (100.0%) Read 1: 17,804,753 bp Read 2: 16,057,276 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 13 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 4 949.3 0 4 5 8 59.3 0 8 6 1 14.8 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/21_CRT_65_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/21_CRT_142_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/21_CRT_65_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/21_CRT_142_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/21_CRT_65_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/21_CRT_142_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/21_CRT_65_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/21_CRT_142_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.93 s (14 µs/read; 4.35 M reads/minute). === Summary === Total read pairs processed: 67,117 Read 1 with adapter: 1 (0.0%) Read 2 with adapter: 547 (0.8%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 67,117 (100.0%) Total basepairs processed: 37,433,971 bp Read 1: 19,671,961 bp Read 2: 17,762,010 bp Total written (filtered): 37,432,307 bp (100.0%) Read 1: 19,671,955 bp Read 2: 17,760,352 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 6 1 16.4 0 1 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 547 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 534 1048.7 0 534 4 10 262.2 0 10 5 2 65.5 0 2 6 1 16.4 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/22_CRT_64_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/22_CRT_141_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/22_CRT_64_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/22_CRT_141_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/22_CRT_64_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/22_CRT_141_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/22_CRT_64_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/22_CRT_141_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.83 s (16 µs/read; 3.80 M reads/minute). === Summary === Total read pairs processed: 52,734 Read 1 with adapter: 2 (0.0%) Read 2 with adapter: 28 (0.1%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 52,734 (100.0%) Total basepairs processed: 29,415,837 bp Read 1: 15,469,044 bp Read 2: 13,946,793 bp Total written (filtered): 29,415,716 bp (100.0%) Read 1: 15,469,036 bp Read 2: 13,946,680 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 4 2 206.0 0 2 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 28 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 824.0 0 2 4 23 206.0 0 23 5 3 51.5 0 3 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/23_CRT_63_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/23_CRT_140_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/23_CRT_63_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/23_CRT_140_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/23_CRT_63_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/23_CRT_140_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/23_CRT_63_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/23_CRT_140_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.91 s (16 µs/read; 3.84 M reads/minute). === Summary === Total read pairs processed: 58,583 Read 1 with adapter: 1 (0.0%) Read 2 with adapter: 51 (0.1%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 58,583 (100.0%) Total basepairs processed: 32,603,240 bp Read 1: 17,145,121 bp Read 2: 15,458,119 bp Total written (filtered): 32,603,040 bp (100.0%) Read 1: 17,145,118 bp Read 2: 15,457,922 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 1 915.4 0 1 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 51 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 11 915.4 0 11 4 37 228.8 0 37 5 2 57.2 0 2 6 1 14.3 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/26_CRT_62_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/26_CRT_139_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/26_CRT_62_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/26_CRT_139_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/26_CRT_62_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/26_CRT_139_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/26_CRT_62_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/26_CRT_139_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.67 s (15 µs/read; 3.88 M reads/minute). === Summary === Total read pairs processed: 43,267 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 3 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 43,267 (100.0%) Total basepairs processed: 23,967,365 bp Read 1: 12,679,371 bp Read 2: 11,287,994 bp Total written (filtered): 23,967,355 bp (100.0%) Read 1: 12,679,371 bp Read 2: 11,287,984 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 3 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 676.0 0 2 4 1 169.0 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/27_CRT_61_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/27_CRT_138_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/27_CRT_61_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/27_CRT_138_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/27_CRT_61_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/27_CRT_138_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/27_CRT_61_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/27_CRT_138_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.15 s (14 µs/read; 4.35 M reads/minute). === Summary === Total read pairs processed: 83,060 Read 1 with adapter: 1 (0.0%) Read 2 with adapter: 5 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 83,060 (100.0%) Total basepairs processed: 46,377,356 bp Read 1: 24,333,111 bp Read 2: 22,044,245 bp Total written (filtered): 46,377,333 bp (100.0%) Read 1: 24,333,108 bp Read 2: 22,044,225 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 1 1297.8 0 1 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 5 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 1297.8 0 2 4 2 324.5 0 2 6 1 20.3 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/28_CRT_60_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/28_CRT_137_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/28_CRT_60_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/28_CRT_137_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/28_CRT_60_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/28_CRT_137_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/28_CRT_60_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/28_CRT_137_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.72 s (15 µs/read; 4.01 M reads/minute). === Summary === Total read pairs processed: 48,192 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 15 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 48,192 (100.0%) Total basepairs processed: 26,739,334 bp Read 1: 14,089,024 bp Read 2: 12,650,310 bp Total written (filtered): 26,739,279 bp (100.0%) Read 1: 14,089,024 bp Read 2: 12,650,255 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 15 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 5 753.0 0 5 4 10 188.2 0 10 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/29_CRT_59_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/29_CRT_136_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/29_CRT_59_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/29_CRT_136_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/29_CRT_59_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/29_CRT_136_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/29_CRT_59_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/29_CRT_136_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.67 s (16 µs/read; 3.72 M reads/minute). === Summary === Total read pairs processed: 103,375 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 12 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 103,375 (100.0%) Total basepairs processed: 57,209,543 bp Read 1: 30,161,700 bp Read 2: 27,047,843 bp Total written (filtered): 57,209,496 bp (100.0%) Read 1: 30,161,700 bp Read 2: 27,047,796 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 12 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 1 1615.2 0 1 4 11 403.8 0 11 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/2_SP_66_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/2_SP_143_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/2_SP_66_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/2_SP_143_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/2_SP_66_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/2_SP_143_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/2_SP_66_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/2_SP_143_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.83 s (16 µs/read; 3.82 M reads/minute). === Summary === Total read pairs processed: 52,779 Read 1 with adapter: 2 (0.0%) Read 2 with adapter: 21 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 52,779 (100.0%) Total basepairs processed: 29,360,789 bp Read 1: 15,432,520 bp Read 2: 13,928,269 bp Total written (filtered): 29,360,698 bp (100.0%) Read 1: 15,432,514 bp Read 2: 13,928,184 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 824.7 0 2 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 21 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 4 20 206.2 0 20 5 1 51.5 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/30_56_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/30_133_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/30_56_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/30_133_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/30_56_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/30_133_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/30_56_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/30_133_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.91 s (17 µs/read; 3.55 M reads/minute). === Summary === Total read pairs processed: 53,737 Read 1 with adapter: 2 (0.0%) Read 2 with adapter: 29 (0.1%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 53,737 (100.0%) Total basepairs processed: 30,000,168 bp Read 1: 15,695,034 bp Read 2: 14,305,134 bp Total written (filtered): 30,000,045 bp (100.0%) Read 1: 15,695,028 bp Read 2: 14,305,017 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 839.6 0 2 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 29 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 4 28 209.9 0 28 5 1 52.5 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/30_CRT_55_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/30_CRT_132_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/30_CRT_55_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/30_CRT_132_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/30_CRT_55_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/30_CRT_132_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/30_CRT_55_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/30_CRT_132_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.89 s (16 µs/read; 3.65 M reads/minute). === Summary === Total read pairs processed: 54,275 Read 1 with adapter: 2 (0.0%) Read 2 with adapter: 28 (0.1%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 54,275 (100.0%) Total basepairs processed: 30,540,345 bp Read 1: 15,929,886 bp Read 2: 14,610,459 bp Total written (filtered): 30,540,228 bp (100.0%) Read 1: 15,929,880 bp Read 2: 14,610,348 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 848.0 0 2 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 28 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 848.0 0 2 4 25 212.0 0 25 5 1 53.0 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/31_54_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/31_131_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/31_54_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/31_131_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/31_54_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/31_131_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/31_54_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/31_131_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.73 s (16 µs/read; 3.65 M reads/minute). === Summary === Total read pairs processed: 105,285 Read 1 with adapter: 2 (0.0%) Read 2 with adapter: 78 (0.1%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 105,285 (100.0%) Total basepairs processed: 58,326,981 bp Read 1: 30,717,021 bp Read 2: 27,609,960 bp Total written (filtered): 58,326,675 bp (100.0%) Read 1: 30,717,015 bp Read 2: 27,609,660 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 1645.1 0 2 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 78 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 16 1645.1 0 16 4 58 411.3 0 58 5 4 102.8 0 4 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/31_CRT_53_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/31_CRT_130_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/31_CRT_53_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/31_CRT_130_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/31_CRT_53_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/31_CRT_130_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/31_CRT_53_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/31_CRT_130_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.94 s (19 µs/read; 3.16 M reads/minute). === Summary === Total read pairs processed: 49,315 Read 1 with adapter: 1 (0.0%) Read 2 with adapter: 222 (0.5%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 49,315 (100.0%) Total basepairs processed: 27,641,704 bp Read 1: 14,477,577 bp Read 2: 13,164,127 bp Total written (filtered): 27,640,816 bp (100.0%) Read 1: 14,477,573 bp Read 2: 13,163,243 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 4 1 192.6 0 1 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 222 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 4 770.5 0 4 4 218 192.6 0 218 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/32_52_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/32_129_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/32_52_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/32_129_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/32_52_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/32_129_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/32_52_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/32_129_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.00 s (22 µs/read; 2.75 M reads/minute). === Summary === Total read pairs processed: 45,976 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 10 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 45,976 (100.0%) Total basepairs processed: 25,504,996 bp Read 1: 13,423,813 bp Read 2: 12,081,183 bp Total written (filtered): 25,504,958 bp (100.0%) Read 1: 13,423,813 bp Read 2: 12,081,145 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 10 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 3 718.4 0 3 4 6 179.6 0 6 5 1 44.9 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/33_51_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/33_128_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/33_51_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/33_128_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/33_51_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/33_128_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/33_51_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/33_128_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.37 s (27 µs/read; 2.26 M reads/minute). === Summary === Total read pairs processed: 51,347 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 28 (0.1%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 51,347 (100.0%) Total basepairs processed: 28,469,071 bp Read 1: 15,030,003 bp Read 2: 13,439,068 bp Total written (filtered): 28,468,960 bp (100.0%) Read 1: 15,030,003 bp Read 2: 13,438,957 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 28 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 1 802.3 0 1 4 27 200.6 0 27 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/34_50_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/34_127_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/34_50_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/34_127_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/34_50_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/34_127_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/34_50_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/34_127_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.48 s (27 µs/read; 2.24 M reads/minute). === Summary === Total read pairs processed: 55,160 Read 1 with adapter: 1 (0.0%) Read 2 with adapter: 15 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 55,160 (100.0%) Total basepairs processed: 30,495,262 bp Read 1: 16,127,247 bp Read 2: 14,368,015 bp Total written (filtered): 30,495,198 bp (100.0%) Read 1: 16,127,242 bp Read 2: 14,367,956 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 5 1 53.9 0 1 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 15 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 1 861.9 0 1 4 14 215.5 0 14 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/35_75_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/35_152_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/35_75_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/35_152_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/35_75_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/35_152_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/35_75_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/35_152_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 4.16 s (22 µs/read; 2.68 M reads/minute). === Summary === Total read pairs processed: 185,756 Read 1 with adapter: 5 (0.0%) Read 2 with adapter: 116 (0.1%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 185,756 (100.0%) Total basepairs processed: 102,155,280 bp Read 1: 54,278,605 bp Read 2: 47,876,675 bp Total written (filtered): 102,154,877 bp (100.0%) Read 1: 54,278,585 bp Read 2: 47,876,292 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 5 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 3 2902.4 0 3 5 1 181.4 0 1 6 1 45.4 0 1 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 116 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 88 2902.4 0 88 4 22 725.6 0 22 5 5 181.4 0 5 6 1 45.4 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/37_49_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/37_126_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/37_49_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/37_126_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/37_49_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/37_126_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/37_49_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/37_126_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.93 s (28 µs/read; 2.16 M reads/minute). === Summary === Total read pairs processed: 69,681 Read 1 with adapter: 1 (0.0%) Read 2 with adapter: 253 (0.4%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 69,681 (100.0%) Total basepairs processed: 38,634,945 bp Read 1: 20,410,431 bp Read 2: 18,224,514 bp Total written (filtered): 38,633,932 bp (100.0%) Read 1: 20,410,428 bp Read 2: 18,223,504 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 1 1088.8 0 1 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 253 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 3 1088.8 0 3 4 249 272.2 0 249 5 1 68.0 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/38_48_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/38_125_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/38_48_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/38_125_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/38_48_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/38_125_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/38_48_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/38_125_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.28 s (23 µs/read; 2.57 M reads/minute). === Summary === Total read pairs processed: 54,945 Read 1 with adapter: 2 (0.0%) Read 2 with adapter: 15 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 54,945 (100.0%) Total basepairs processed: 30,254,001 bp Read 1: 16,096,989 bp Read 2: 14,157,012 bp Total written (filtered): 30,253,917 bp (100.0%) Read 1: 16,096,981 bp Read 2: 14,156,936 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 4 2 214.6 0 2 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 15 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 858.5 0 2 4 5 214.6 0 5 6 7 13.4 0 7 8 1 0.8 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/39_47_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/39_124_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/39_47_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/39_124_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/39_47_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/39_124_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/39_47_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/39_124_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 0.98 s (24 µs/read; 2.53 M reads/minute). === Summary === Total read pairs processed: 41,337 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 1 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 41,337 (100.0%) Total basepairs processed: 23,197,568 bp Read 1: 12,118,444 bp Read 2: 11,079,124 bp Total written (filtered): 23,197,564 bp (100.0%) Read 1: 12,118,444 bp Read 2: 11,079,120 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 4 1 161.5 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/3_CRT_58_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/3_CRT_135_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/3_CRT_58_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/3_CRT_135_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/3_CRT_58_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/3_CRT_135_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/3_CRT_58_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/3_CRT_135_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.74 s (23 µs/read; 2.58 M reads/minute). === Summary === Total read pairs processed: 74,725 Read 1 with adapter: 1 (0.0%) Read 2 with adapter: 12 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 74,725 (100.0%) Total basepairs processed: 41,648,949 bp Read 1: 21,864,750 bp Read 2: 19,784,199 bp Total written (filtered): 41,648,905 bp (100.0%) Read 1: 21,864,747 bp Read 2: 19,784,158 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 1 1167.6 0 1 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 12 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 7 1167.6 0 7 4 5 291.9 0 5 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/3_SP_57_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/3_SP_134_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/3_SP_57_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/3_SP_134_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/3_SP_57_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/3_SP_134_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/3_SP_57_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/3_SP_134_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.88 s (24 µs/read; 2.46 M reads/minute). === Summary === Total read pairs processed: 77,182 Read 1 with adapter: 2 (0.0%) Read 2 with adapter: 56 (0.1%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 77,182 (100.0%) Total basepairs processed: 42,666,631 bp Read 1: 22,525,113 bp Read 2: 20,141,518 bp Total written (filtered): 42,666,412 bp (100.0%) Read 1: 22,525,106 bp Read 2: 20,141,306 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 1 1206.0 0 1 4 1 301.5 0 1 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 56 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 15 1206.0 0 15 4 39 301.5 0 39 5 1 75.4 0 1 6 1 18.8 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/4_CRT_76_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/4_CRT_153_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/4_CRT_76_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/4_CRT_153_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/4_CRT_76_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/4_CRT_153_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/4_CRT_76_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/4_CRT_153_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.13 s (23 µs/read; 2.62 M reads/minute). === Summary === Total read pairs processed: 49,384 Read 1 with adapter: 2 (0.0%) Read 2 with adapter: 7 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 49,384 (100.0%) Total basepairs processed: 27,464,795 bp Read 1: 14,397,650 bp Read 2: 13,067,145 bp Total written (filtered): 27,464,760 bp (100.0%) Read 1: 14,397,641 bp Read 2: 13,067,119 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 4 1 192.9 0 1 5 1 48.2 0 1 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 7 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 771.6 0 2 4 5 192.9 0 5 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/4_SP_46_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/4_SP_123_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/4_SP_46_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/4_SP_123_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/4_SP_46_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/4_SP_123_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/4_SP_46_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/4_SP_123_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.23 s (27 µs/read; 2.19 M reads/minute). === Summary === Total read pairs processed: 44,993 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 8 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 44,993 (100.0%) Total basepairs processed: 24,769,662 bp Read 1: 13,186,007 bp Read 2: 11,583,655 bp Total written (filtered): 24,769,629 bp (100.0%) Read 1: 13,186,007 bp Read 2: 11,583,622 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 8 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 1 703.0 0 1 4 6 175.8 0 6 6 1 11.0 0 1 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/5_SP_45_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/5_SP_122_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/5_SP_45_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/5_SP_122_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/5_SP_45_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/5_SP_122_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/5_SP_45_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/5_SP_122_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.48 s (28 µs/read; 2.12 M reads/minute). === Summary === Total read pairs processed: 52,317 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 3 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 52,317 (100.0%) Total basepairs processed: 29,044,470 bp Read 1: 15,288,538 bp Read 2: 13,755,932 bp Total written (filtered): 29,044,458 bp (100.0%) Read 1: 15,288,538 bp Read 2: 13,755,920 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 3 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 4 3 204.4 0 3 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/7_CRT_44_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/7_CRT_121_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/7_CRT_44_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/7_CRT_121_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/7_CRT_44_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/7_CRT_121_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/7_CRT_44_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/7_CRT_121_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.31 s (23 µs/read; 2.58 M reads/minute). === Summary === Total read pairs processed: 56,553 Read 1 with adapter: 0 (0.0%) Read 2 with adapter: 33 (0.1%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 56,553 (100.0%) Total basepairs processed: 31,667,137 bp Read 1: 16,582,981 bp Read 2: 15,084,156 bp Total written (filtered): 31,667,007 bp (100.0%) Read 1: 16,582,981 bp Read 2: 15,084,026 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 0 times === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 33 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 2 883.6 0 2 4 31 220.9 0 31 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/7_SP_43_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/7_SP_120_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/7_SP_43_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/7_SP_120_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/7_SP_43_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/7_SP_120_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/7_SP_43_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/7_SP_120_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Finished in 1.44 s (25 µs/read; 2.39 M reads/minute). === Summary === Total read pairs processed: 57,262 Read 1 with adapter: 2 (0.0%) Read 2 with adapter: 9 (0.0%) == Read fate breakdown == Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 57,262 (100.0%) Total basepairs processed: 31,812,595 bp Read 1: 16,766,200 bp Read 2: 15,046,395 bp Total written (filtered): 31,812,558 bp (100.0%) Read 1: 16,766,192 bp Read 2: 15,046,366 bp === First read: Adapter 1 === Sequence: GGCTGACTGACT; Type: regular 5'; Length: 12; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 1 894.7 0 1 5 1 55.9 0 1 === Second read: Adapter 2 === Sequence: CCAATTACCATA; Type: regular 5'; Length: 12; Trimmed: 9 times Minimum overlap: 3 No. of allowed errors: 1-12 bp: 0 Overview of removed sequences length count expect max.err error counts 3 7 894.7 0 7 4 2 223.7 0 2 Command: cutadapt --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/8_CRT_42_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/8_CRT_119_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/8_CRT_42_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/8_CRT_119_L001_R2_001.fastq.gz This is cutadapt 4.1 with Python 3.8.13 Command line parameters: --cores 4 --error-rate 0 --times 1 --overlap 3 --minimum-length 1 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/8_CRT_42_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/8_CRT_119_L001_R2_001.fastq.gz --front GGCTGACTGACT -G CCAATTACCATA /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/8_CRT_42_L001_R1_001.fastq.gz /tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/8_CRT_119_L001_R2_001.fastq.gz Processing paired-end reads on 4 cores ... Traceback (most recent call last): File "/home/julia/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/cutadapt/__main__.py", line 1100, in main stats = r.run() File "/home/julia/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/cutadapt/pipeline.py", line 969, in run writer.write(data, chunk_index) File "/home/julia/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/cutadapt/pipeline.py", line 822, in write self._outfile.write(self._chunks[self._current_index]) File "/home/julia/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/xopen/__init__.py", line 257, in write self._file.write(arg) BrokenPipeError: [Errno 32] Broken pipe During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/julia/anaconda3/envs/qiime2-2022.8/bin/cutadapt", line 10, in sys.exit(main_cli()) File "/home/julia/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/cutadapt/__main__.py", line 1014, in main_cli main(sys.argv[1:]) File "/home/julia/anacoTraceback (most recent call last): File "/home/julia/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__ results = action(**arguments) File "", line 2, in trim_paired File "/home/julia/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable outputs = self._callable_executor_(scope, callable_args, File "/home/julia/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in _callable_executor_ output_views = self._callable(**view_args) File "/home/julia/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_cutadapt/_trim.py", line 189, in trim_paired run_commands(cmds) File "/home/julia/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_cutadapt/_trim.py", line 30, in run_commands subprocess.run(cmd, check=True) File "/home/julia/anaconda3/envs/qiime2-2022.8/lib/python3.8/subprocess.py", line 516, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['cutadapt', '--cores', '4', '--error-rate', '0', '--times', '1', '--overlap', '3', '--minimum-length', '1', '-o', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/8_CRT_42_L001_R1_001.fastq.gz', '-p', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-yacoydj1/8_CRT_119_L001_R2_001.fastq.gz', '--front', 'GGCTGACTGACT', '-G', 'CCAATTACCATA', '/tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/8_CRT_42_L001_R1_001.fastq.gz', '/tmp/qiime2/julia/data/d3792878-a222-46e6-8172-3cb95870805d/data/8_CRT_119_L001_R2_001.fastq.gz']' returned non-zero exit status 120.