Plugin cutadapt trim paired end giving error

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) [[email protected] 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.

Hi @saitha welcome to :qiime2: !

Is telling you that there are more sequences in file 2 (likely meaning R2 / reverse reads) than in file 1 (R1 / forward reads). The standard format for paired-end reads is that there should be exactly the same number of sequences in the R1 and R2 files. That is, for each read in the forward read file you should have a corresponding read in the reverse read file, and vice versa.

So, the error is letting you know that something is wrong with one or both of the files. You'll have to check with your sequencing / data provider and make sure that these files were not manipulated in any way. Perhaps an incomplete download? Hopefully, you can access the raw sequence files.

-Mike