dear all,
I am new to qiime2, maybe it is a silly question, please help me
I downloaded microbiome dataset of 50 samples, running qiime2-2019.10 up to 20 samples no issues, but after that i received the following error
and it shows:
Reads are improperly paired. There are more reads in file 2 than in file 1.
Can you please help. Thanks in advance
Sabitha
(qiime2-2019.10) [wia@tyroneserver SRR12264494]$ qiime cutadapt trim-paired \
--i-demultiplexed-sequences paired-end-demux.qza \
--p-error-rate 0 \
--p-minimum-length 1 \
--o-trimmed-sequences paired-end-trimmed.qza \
--verbose
Running 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 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/1_0_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/1_47_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/1_0_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/1_47_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 --overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/1_0_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/1_47_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/1_0_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/1_47_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8<----------] 00:00:00 62,530 reads @ 12.0 µs/read; 4.98 M reads/minute
Finished in 0.77 s (12 us/read; 4.87 M reads/minute).
=== Summary ===
Total read pairs processed: 62,530
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 62,530 (100.0%)
Total basepairs processed: 32,239,244 bp
Read 1: 16,144,699 bp
Read 2: 16,094,545 bp
Total written (filtered): 32,239,244 bp (100.0%)
Read 1: 16,144,699 bp
Read 2: 16,094,545 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/2_1_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/2_48_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/2_1_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/2_48_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/2_1_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/2_48_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/2_1_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/2_48_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8<----------] 00:00:00 54,911 reads @ 15.7 µs/read; 3.82 M reads/minute
Finished in 0.88 s (16 us/read; 3.73 M reads/minute).
=== Summary ===
Total read pairs processed: 54,911
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 54,911 (100.0%)
Total basepairs processed: 27,991,954 bp
Read 1: 14,018,639 bp
Read 2: 13,973,315 bp
Total written (filtered): 27,991,954 bp (100.0%)
Read 1: 14,018,639 bp
Read 2: 13,973,315 bp
Command: cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/3_2_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/3_49_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/3_2_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/3_49_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/3_2_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/3_49_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/3_2_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/3_49_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8<----------] 00:00:00 61,018 reads @ 16.1 µs/read; 3.72 M reads/minute
Finished in 1.00 s (16 us/read; 3.65 M reads/minute).
=== Summary ===
Total read pairs processed: 61,018
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 61,018 (100.0%)
Total basepairs processed: 36,608,661 bp
Read 1: 18,334,509 bp
Read 2: 18,274,152 bp
Total written (filtered): 36,608,661 bp (100.0%)
Read 1: 18,334,509 bp
Read 2: 18,274,152 bp
Command: cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/4_3_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/4_50_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/4_3_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/4_50_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/4_3_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/4_50_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/4_3_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/4_50_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8=----------] 00:00:01 111,275 reads @ 15.5 µs/read; 3.87 M reads/minute
Finished in 1.74 s (16 us/read; 3.83 M reads/minute).
=== Summary ===
Total read pairs processed: 111,275
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 111,275 (100.0%)
Total basepairs processed: 64,344,902 bp
Read 1: 32,132,072 bp
Read 2: 32,212,830 bp
Total written (filtered): 64,344,902 bp (100.0%)
Read 1: 32,132,072 bp
Read 2: 32,212,830 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/5_4_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/5_51_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/5_4_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/5_51_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/5_4_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/5_51_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/5_4_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/5_51_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8<----------] 00:00:01 52,608 reads @ 19.6 µs/read; 3.07 M reads/minute
Finished in 1.05 s (20 us/read; 3.00 M reads/minute).
=== Summary ===
Total read pairs processed: 52,608
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 52,608 (100.0%)
Total basepairs processed: 28,277,710 bp
Read 1: 14,160,423 bp
Read 2: 14,117,287 bp
Total written (filtered): 28,277,710 bp (100.0%)
Read 1: 14,160,423 bp
Read 2: 14,117,287 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/6_5_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/6_52_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/6_5_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/6_52_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/6_5_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/6_52_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/6_5_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/6_52_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8=----------] 00:00:01 60,383 reads @ 18.6 µs/read; 3.22 M reads/minute
Finished in 1.14 s (19 us/read; 3.17 M reads/minute).
=== Summary ===
Total read pairs processed: 60,383
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 60,383 (100.0%)
Total basepairs processed: 33,047,979 bp
Read 1: 16,546,171 bp
Read 2: 16,501,808 bp
Total written (filtered): 33,047,979 bp (100.0%)
Read 1: 16,546,171 bp
Read 2: 16,501,808 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/7_6_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/7_53_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/7_6_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/7_53_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/7_6_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/7_53_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/7_6_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/7_53_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8=----------] 00:00:01 56,734 reads @ 19.9 µs/read; 3.01 M reads/minute
Finished in 1.15 s (20 us/read; 2.95 M reads/minute).
=== Summary ===
Total read pairs processed: 56,734
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 56,734 (100.0%)
Total basepairs processed: 30,958,469 bp
Read 1: 15,488,225 bp
Read 2: 15,470,244 bp
Total written (filtered): 30,958,469 bp (100.0%)
Read 1: 15,488,225 bp
Read 2: 15,470,244 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/8_7_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/8_54_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/8_7_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/8_54_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/8_7_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/8_54_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/8_7_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/8_54_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8<----------] 00:00:00 53,281 reads @ 14.0 µs/read; 4.29 M reads/minute
Finished in 0.77 s (14 us/read; 4.17 M reads/minute).
=== Summary ===
Total read pairs processed: 53,281
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 53,281 (100.0%)
Total basepairs processed: 25,527,697 bp
Read 1: 12,785,383 bp
Read 2: 12,742,314 bp
Total written (filtered): 25,527,697 bp (100.0%)
Read 1: 12,785,383 bp
Read 2: 12,742,314 bp
Command: cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/9_8_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/9_55_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/9_8_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/9_55_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/9_8_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/9_55_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/9_8_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/9_55_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8=----------] 00:00:01 77,847 reads @ 16.6 µs/read; 3.61 M reads/minute
Finished in 1.31 s (17 us/read; 3.56 M reads/minute).
=== Summary ===
Total read pairs processed: 77,847
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 77,847 (100.0%)
Total basepairs processed: 46,640,285 bp
Read 1: 23,360,498 bp
Read 2: 23,279,787 bp
Total written (filtered): 46,640,285 bp (100.0%)
Read 1: 23,360,498 bp
Read 2: 23,279,787 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/10_9_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/10_56_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/10_9_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/10_56_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/10_9_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/10_56_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/10_9_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/10_56_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8=----------] 00:00:01 82,593 reads @ 14.0 µs/read; 4.28 M reads/minute
Finished in 1.18 s (14 us/read; 4.21 M reads/minute).
=== Summary ===
Total read pairs processed: 82,593
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 82,593 (100.0%)
Total basepairs processed: 39,790,336 bp
Read 1: 19,924,776 bp
Read 2: 19,865,560 bp
Total written (filtered): 39,790,336 bp (100.0%)
Read 1: 19,924,776 bp
Read 2: 19,865,560 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/11_10_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/11_57_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/11_10_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/11_57_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/11_10_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/11_57_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/11_10_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/11_57_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8<----------] 00:00:00 41,639 reads @ 13.2 µs/read; 4.54 M reads/minute
Finished in 0.58 s (14 us/read; 4.33 M reads/minute).
=== Summary ===
Total read pairs processed: 41,639
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 41,639 (100.0%)
Total basepairs processed: 24,456,674 bp
Read 1: 12,220,132 bp
Read 2: 12,236,542 bp
Total written (filtered): 24,456,674 bp (100.0%)
Read 1: 12,220,132 bp
Read 2: 12,236,542 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/12_11_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/12_58_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/12_11_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/12_58_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/12_11_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/12_58_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/12_11_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/12_58_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8<----------] 00:00:00 72,988 reads @ 13.6 µs/read; 4.41 M reads/minute
Finished in 1.01 s (14 us/read; 4.33 M reads/minute).
=== Summary ===
Total read pairs processed: 72,988
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 72,988 (100.0%)
Total basepairs processed: 43,395,193 bp
Read 1: 21,722,395 bp
Read 2: 21,672,798 bp
Total written (filtered): 43,395,193 bp (100.0%)
Read 1: 21,722,395 bp
Read 2: 21,672,798 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/13_12_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/13_59_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/13_12_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/13_59_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/13_12_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/13_59_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/13_12_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/13_59_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8<----------] 00:00:00 49,618 reads @ 17.2 µs/read; 3.48 M reads/minute
Finished in 0.88 s (18 us/read; 3.39 M reads/minute).
=== Summary ===
Total read pairs processed: 49,618
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 49,618 (100.0%)
Total basepairs processed: 28,880,604 bp
Read 1: 14,458,287 bp
Read 2: 14,422,317 bp
Total written (filtered): 28,880,604 bp (100.0%)
Read 1: 14,458,287 bp
Read 2: 14,422,317 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/14_13_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/14_60_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/14_13_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/14_60_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/14_13_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/14_60_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/14_13_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/14_60_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8=----------] 00:00:01 97,180 reads @ 14.9 µs/read; 4.01 M reads/minute
Finished in 1.47 s (15 us/read; 3.96 M reads/minute).
=== Summary ===
Total read pairs processed: 97,180
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 97,180 (100.0%)
Total basepairs processed: 54,987,591 bp
Read 1: 27,482,930 bp
Read 2: 27,504,661 bp
Total written (filtered): 54,987,591 bp (100.0%)
Read 1: 27,482,930 bp
Read 2: 27,504,661 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/15_14_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/15_61_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/15_14_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/15_61_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/15_14_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/15_61_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/15_14_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/15_61_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[ 8<---------] 00:00:02 124,364 reads @ 19.3 µs/read; 3.10 M reads/minute
Finished in 2.43 s (20 us/read; 3.07 M reads/minute).
=== Summary ===
Total read pairs processed: 124,364
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 124,364 (100.0%)
Total basepairs processed: 70,186,829 bp
Read 1: 35,026,066 bp
Read 2: 35,160,763 bp
Total written (filtered): 70,186,829 bp (100.0%)
Read 1: 35,026,066 bp
Read 2: 35,160,763 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/16_15_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/16_62_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/16_15_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/16_62_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/16_15_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/16_62_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/16_15_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/16_62_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8=----------] 00:00:01 82,360 reads @ 14.7 µs/read; 4.09 M reads/minute
Finished in 1.23 s (15 us/read; 4.02 M reads/minute).
=== Summary ===
Total read pairs processed: 82,360
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 82,360 (100.0%)
Total basepairs processed: 46,402,449 bp
Read 1: 23,225,892 bp
Read 2: 23,176,557 bp
Total written (filtered): 46,402,449 bp (100.0%)
Read 1: 23,225,892 bp
Read 2: 23,176,557 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/17_16_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/17_63_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/17_16_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/17_63_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/17_16_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/17_63_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/17_16_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/17_63_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8=----------] 00:00:01 88,375 reads @ 16.9 µs/read; 3.56 M reads/minute
Finished in 1.51 s (17 us/read; 3.51 M reads/minute).
=== Summary ===
Total read pairs processed: 88,375
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 88,375 (100.0%)
Total basepairs processed: 51,929,278 bp
Read 1: 25,985,883 bp
Read 2: 25,943,395 bp
Total written (filtered): 51,929,278 bp (100.0%)
Read 1: 25,985,883 bp
Read 2: 25,943,395 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/18_17_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/18_64_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/18_17_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/18_64_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/18_17_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/18_64_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/18_17_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/18_64_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8=----------] 00:00:01 99,979 reads @ 18.9 µs/read; 3.17 M reads/minute
Finished in 1.91 s (19 us/read; 3.14 M reads/minute).
=== Summary ===
Total read pairs processed: 99,979
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 99,979 (100.0%)
Total basepairs processed: 56,891,244 bp
Read 1: 28,426,267 bp
Read 2: 28,464,977 bp
Total written (filtered): 56,891,244 bp (100.0%)
Read 1: 28,426,267 bp
Read 2: 28,464,977 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0\
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/19_18_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/19_65_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/19_18_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/19_65_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/19_18_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/19_65_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/19_18_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/19_65_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8=----------] 00:00:01 92,300 reads @ 13.6 µs/read; 4.40 M reads/minute
Finished in 1.28 s (14 us/read; 4.33 M reads/minute).
=== Summary ===
Total read pairs processed: 92,300
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 92,300 (100.0%)
Total basepairs processed: 52,912,810 bp
Read 1: 26,466,858 bp
Read 2: 26,445,952 bp
Total written (filtered): 52,912,810 bp (100.0%)
Read 1: 26,466,858 bp
Read 2: 26,445,952 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/20_19_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/20_66_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/20_19_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/20_66_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/20_19_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/20_66_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/20_19_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/20_66_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8=----------] 00:00:01 76,560 reads @ 18.6 µs/read; 3.23 M reads/minute
Finished in 1.45 s (19 us/read; 3.17 M reads/minute).
=== Summary ===
Total read pairs processed: 76,560
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 76,560 (100.0%)
Total basepairs processed: 42,646,073 bp
Read 1: 21,291,906 bp
Read 2: 21,354,167 bp
Total written (filtered): 42,646,073 bp (100.0%)
Read 1: 21,291,906 bp
Read 2: 21,354,167 bp
Command:
cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/21_20_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/21_67_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/21_20_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/21_67_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters:
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/21_20_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/21_67_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/21_20_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/21_67_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
[8=----------] 00:00:01 76,219 reads @ 16.7 µs/read; 3.59 M reads/minute
Finished in 1.30 s (17 us/read; 3.53 M reads/minute).
=== Summary ===
Total read pairs processed: 76,219
Read 1 with adapter: 0 (0.0%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 0 (0.0%)
Pairs written (passing filters): 76,219 (100.0%)
Total basepairs processed: 43,212,267 bp
Read 1: 21,591,094 bp
Read 2: 21,621,173 bp
Total written (filtered): 43,212,267 bp (100.0%)
Read 1: 21,591,094 bp
Read 2: 21,621,173 bp
Command: cutadapt \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/22_21_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/22_68_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/22_21_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/22_68_L001_R2_001.fastq.gz
This is cutadapt 2.6 with Python 3.6.7
Command line parameters: \
--cores 1 \
--error-rate 0.0 \
--times 1 \
--overlap 3 \
--minimum-length 1 \
-o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/22_21_L001_R1_001.fastq.gz \
-p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/22_68_L001_R2_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/22_21_L001_R1_001.fastq.gz \
/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/22_68_L001_R2_001.fastq.gz
Processing reads on 1 core in paired-end mode ...
cutadapt: error:
Error in sequence file at unknown line: Reads are improperly paired.
There are more reads in file 2 than in file 1.
Traceback (most recent call last):
File "/home/wia/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in __call__
results = action(**arguments)
File "</home/wia/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-465>", line 2, in trim_paired
File "/home/wia/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home/wia/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/wia/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_cutadapt/_trim.py", line 189, in trim_paired
run_commands(cmds)
File "/home/wia/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_cutadapt/_trim.py", line 30, in run_commands
subprocess.run(cmd, check=True)
File "/home/wia/miniconda3/envs/qiime2-2019.10/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['cutadapt', '--cores', '1', '--error-rate', '0.0', '--times', '1', '--overlap', '3', '--minimum-length', '1', '-o', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/22_21_L001_R1_001.fastq.gz', '-p', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/22_68_L001_R2_001.fastq.gz', '/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/22_21_L001_R1_001.fastq.gz', '/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/22_68_L001_R2_001.fastq.gz']' returned non-zero exit status 1.
Plugin error from cutadapt:
Command '['cutadapt', '--cores', '1', '--error-rate', '0.0', '--times', '1', '--overlap', '3', '--minimum-length', '1', '-o', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/22_21_L001_R1_001.fastq.gz', '-p', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-flw2_938/22_68_L001_R2_001.fastq.gz', '/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/22_21_L001_R1_001.fastq.gz', '/tmp/qiime2-archive-l0pw87b_/cfa75f02-88b3-4dce-ad13-dde7649c4008/data/22_68_L001_R2_001.fastq.gz']' returned non-zero exit status 1.
See above for debug info.