qiime vsearch join-pairs error: file to small

Hi everyone!

I was wondering if someone could help me with the problem I found. The situation is the following:

I am working with PE samples with are a bit complicated: they are FFPE samples (parafined samples) and their DNA is really fragmented.

This is the reason why I choosed the amazing library q2-sidle. However, it has some requirements that my samples did not comply with:

In the Reads Preparation Section, I have to demultiplexed my sequences (with had been demultiplexed by sample in the sequencing center) into regions. Well, I have used cutadapt + dada2 and I lost all the sequences. So, I decided to try with deblur. In the Moving Pictures, the indications are:

  1. Importing samples into qiime2. (Done).
  2. Cutadapt the samples with the different primers sets to demultiplexed the data into regions. (Done).
  3. Deblur.
    3.1. Join reads (because I am working with Paired End Sequences).
    3.2. Quality filter.
    3.3. Deblur.

Well, in the step 3.1. I got the next error messages:

 Command '['vsearch', '--fastq_mergepairs', '/tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-49-1-FFPE-GsinM_S14_L001_R1_001.fastq.gz', '--reverse', '/tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-49-1-FFPE-GsinM_S14_L001_R2_001.fastq.gz', '--fastqout', '/tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-49-1-FFPE-GsinM_23_L001_R1_001.fastq', '--fastq_ascii', '33', '--fastq_minlen', '1', '--fastq_minovlen', '10', '--fastq_maxdiffs', '10', '--fastq_qmin', '0', '--fastq_qminout', '0', '--fastq_qmax', '41', '--fastq_qmaxout', '41', '--minseqlength', '1', '--fasta_width', '0', '--threads', '1']' returned non-zero exit status 1.

Debug info has been saved to /tmp/qiime2-q2cli-err-q8jddn_o.log

And the command was:

qiime vsearch join-pairs --i-demultiplexed-seqs example_seqs_smurf_R1.qza --o-joined-sequences joined-seqs-smurf-R1.qza

And I looked into the error file and I found the problem: two samples file are too small:

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-1-1-FFPE-GsinM_S36_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-1-1-FFPE-GsinM_S36_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-1-1-FFPE-GsinM_0_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         2  Pairs
         0  Merged (0.0%)
         2  Not merged (100.0%)

Pairs that failed merging due to various reasons:
         1  too few kmers found on same diagonal
         1  alignment score too low, or score drop to high

Statistics of all reads:
    103.75  Mean read length

Statistics of merged reads:
      -nan  Mean fragment length
      -nan  Standard deviation of fragment length
      -nan  Mean expected error in forward sequences
      -nan  Mean expected error in reverse sequences
      -nan  Mean expected error in merged sequences
      -nan  Mean observed errors in merged region of forward sequences
      -nan  Mean observed errors in merged region of reverse sequences
      -nan  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-1-1-FFPE-GsinM_0_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-1-1-FFPE-Tumor-A_S35_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-1-1-FFPE-Tumor-A_S35_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-1-1-FFPE-Tumor-A_1_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         4  Pairs
         2  Merged (50.0%)
         2  Not merged (50.0%)

Pairs that failed merging due to various reasons:
         1  too many differences
         1  alignment score too low, or score drop to high

Statistics of all reads:
    137.88  Mean read length

Statistics of merged reads:
    212.00  Mean fragment length
      0.00  Standard deviation of fragment length
      1.98  Mean expected error in forward sequences
      2.03  Mean expected error in reverse sequences
      1.99  Mean expected error in merged sequences
      2.50  Mean observed errors in merged region of forward sequences
      3.50  Mean observed errors in merged region of reverse sequences
      6.00  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-1-1-FFPE-Tumor-A_1_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-1-1-FFPE-Tumor-B_S33_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-1-1-FFPE-Tumor-B_S33_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-1-1-FFPE-Tumor-B_2_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
        18  Pairs
        10  Merged (55.6%)
         8  Not merged (44.4%)

Pairs that failed merging due to various reasons:
         4  too few kmers found on same diagonal
         4  alignment score too low, or score drop to high

Statistics of all reads:
    135.28  Mean read length

Statistics of merged reads:
    215.10  Mean fragment length
      1.58  Standard deviation of fragment length
      1.33  Mean expected error in forward sequences
      1.64  Mean expected error in reverse sequences
      1.64  Mean expected error in merged sequences
      1.60  Mean observed errors in merged region of forward sequences
      2.90  Mean observed errors in merged region of reverse sequences
      4.50  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-1-1-FFPE-Tumor-B_2_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-13-1-FFPE-Normal_S48_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-13-1-FFPE-Normal_S48_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-13-1-FFPE-Normal_3_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
        79  Pairs
        54  Merged (68.4%)
        25  Not merged (31.6%)

Pairs that failed merging due to various reasons:
         6  too few kmers found on same diagonal
         1  too many differences
        18  alignment score too low, or score drop to high

Statistics of all reads:
    138.18  Mean read length

Statistics of merged reads:
    216.59  Mean fragment length
      1.06  Standard deviation of fragment length
      1.25  Mean expected error in forward sequences
      1.63  Mean expected error in reverse sequences
      1.20  Mean expected error in merged sequences
      2.17  Mean observed errors in merged region of forward sequences
      1.67  Mean observed errors in merged region of reverse sequences
      3.83  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-13-1-FFPE-Normal_3_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-13-1-FFPE-Tumor-B_S50_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-13-1-FFPE-Tumor-B_S50_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-13-1-FFPE-Tumor-B_4_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         6  Pairs
         3  Merged (50.0%)
         3  Not merged (50.0%)

Pairs that failed merging due to various reasons:
         1  too few kmers found on same diagonal
         1  too many differences
         1  alignment score too low, or score drop to high

Statistics of all reads:
    139.17  Mean read length

Statistics of merged reads:
    215.33  Mean fragment length
      2.36  Standard deviation of fragment length
      1.09  Mean expected error in forward sequences
      1.72  Mean expected error in reverse sequences
      1.14  Mean expected error in merged sequences
      0.67  Mean observed errors in merged region of forward sequences
      2.67  Mean observed errors in merged region of reverse sequences
      3.33  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-13-1-FFPE-Tumor-B_4_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-16-1-FFPE-Gmet_S56_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-16-1-FFPE-Gmet_S56_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-16-1-FFPE-Gmet_5_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         2  Pairs
         2  Merged (100.0%)
         0  Not merged (0.0%)

Statistics of all reads:
    138.00  Mean read length

Statistics of merged reads:
    214.50  Mean fragment length
      2.50  Standard deviation of fragment length
      1.95  Mean expected error in forward sequences
      2.36  Mean expected error in reverse sequences
      1.40  Mean expected error in merged sequences
      4.00  Mean observed errors in merged region of forward sequences
      2.00  Mean observed errors in merged region of reverse sequences
      6.00  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-16-1-FFPE-Gmet_5_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-16-1-FFPE-GsinMet_S57_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-16-1-FFPE-GsinMet_S57_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-16-1-FFPE-GsinMet_6_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         4  Pairs
         2  Merged (50.0%)
         2  Not merged (50.0%)

Pairs that failed merging due to various reasons:
         1  too few kmers found on same diagonal
         1  alignment score too low, or score drop to high

Statistics of all reads:
    120.88  Mean read length

Statistics of merged reads:
    213.50  Mean fragment length
      1.50  Standard deviation of fragment length
      1.20  Mean expected error in forward sequences
      1.78  Mean expected error in reverse sequences
      1.84  Mean expected error in merged sequences
      3.00  Mean observed errors in merged region of forward sequences
      2.50  Mean observed errors in merged region of reverse sequences
      5.50  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-16-1-FFPE-GsinMet_6_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-16-1-FFPE-Normal_S52_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-16-1-FFPE-Normal_S52_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-16-1-FFPE-Normal_7_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
        10  Pairs
         6  Merged (60.0%)
         4  Not merged (40.0%)

Pairs that failed merging due to various reasons:
         4  alignment score too low, or score drop to high

Statistics of all reads:
    139.25  Mean read length

Statistics of merged reads:
    216.33  Mean fragment length
      1.49  Standard deviation of fragment length
      0.85  Mean expected error in forward sequences
      0.97  Mean expected error in reverse sequences
      0.93  Mean expected error in merged sequences
      1.33  Mean observed errors in merged region of forward sequences
      1.50  Mean observed errors in merged region of reverse sequences
      2.83  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-16-1-FFPE-Normal_7_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-16-1-FFPE-TumGrasa_S55_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-16-1-FFPE-TumGrasa_S55_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-16-1-FFPE-TumGrasa_8_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         1  Pairs
         0  Merged (0.0%)
         1  Not merged (100.0%)

Pairs that failed merging due to various reasons:
         1  too few kmers found on same diagonal

Statistics of all reads:
     67.00  Mean read length

Statistics of merged reads:
      -nan  Mean fragment length
      -nan  Standard deviation of fragment length
      -nan  Mean expected error in forward sequences
      -nan  Mean expected error in reverse sequences
      -nan  Mean expected error in merged sequences
      -nan  Mean observed errors in merged region of forward sequences
      -nan  Mean observed errors in merged region of reverse sequences
      -nan  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-16-1-FFPE-TumGrasa_8_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-16-1-FFPE-Tumor-A_S53_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-16-1-FFPE-Tumor-A_S53_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-16-1-FFPE-Tumor-A_9_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         2  Pairs
         0  Merged (0.0%)
         2  Not merged (100.0%)

Pairs that failed merging due to various reasons:
         1  too few kmers found on same diagonal
         1  alignment score too low, or score drop to high

Statistics of all reads:
    103.00  Mean read length

Statistics of merged reads:
      -nan  Mean fragment length
      -nan  Standard deviation of fragment length
      -nan  Mean expected error in forward sequences
      -nan  Mean expected error in reverse sequences
      -nan  Mean expected error in merged sequences
      -nan  Mean observed errors in merged region of forward sequences
      -nan  Mean observed errors in merged region of reverse sequences
      -nan  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-16-1-FFPE-Tumor-A_9_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-16-1-FFPE-Tumor-B_S54_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-16-1-FFPE-Tumor-B_S54_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-16-1-FFPE-Tumor-B_10_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         4  Pairs
         2  Merged (50.0%)
         2  Not merged (50.0%)

Pairs that failed merging due to various reasons:
         2  alignment score too low, or score drop to high

Statistics of all reads:
    139.50  Mean read length

Statistics of merged reads:
    215.00  Mean fragment length
      2.00  Standard deviation of fragment length
      1.03  Mean expected error in forward sequences
      0.76  Mean expected error in reverse sequences
      1.03  Mean expected error in merged sequences
      2.00  Mean observed errors in merged region of forward sequences
      1.00  Mean observed errors in merged region of reverse sequences
      3.00  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-16-1-FFPE-Tumor-B_10_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-17-1-FFPE-Normal_S7_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-17-1-FFPE-Normal_S7_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-17-1-FFPE-Normal_11_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
        18  Pairs
         6  Merged (33.3%)
        12  Not merged (66.7%)

Pairs that failed merging due to various reasons:
         4  too few kmers found on same diagonal
         1  too many differences
         7  alignment score too low, or score drop to high

Statistics of all reads:
    131.11  Mean read length

Statistics of merged reads:
    216.33  Mean fragment length
      1.49  Standard deviation of fragment length
      1.13  Mean expected error in forward sequences
      1.74  Mean expected error in reverse sequences
      1.42  Mean expected error in merged sequences
      2.67  Mean observed errors in merged region of forward sequences
      1.83  Mean observed errors in merged region of reverse sequences
      4.50  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-17-1-FFPE-Normal_11_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-17-1-FFPE-Tumor_S8_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-17-1-FFPE-Tumor_S8_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-17-1-FFPE-Tumor_12_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
        61  Pairs
        43  Merged (70.5%)
        18  Not merged (29.5%)

Pairs that failed merging due to various reasons:
         1  too few kmers found on same diagonal
         1  too many differences
        16  alignment score too low, or score drop to high

Statistics of all reads:
    139.04  Mean read length

Statistics of merged reads:
    217.00  Mean fragment length
      0.00  Standard deviation of fragment length
      1.54  Mean expected error in forward sequences
      1.85  Mean expected error in reverse sequences
      1.35  Mean expected error in merged sequences
      2.21  Mean observed errors in merged region of forward sequences
      1.86  Mean observed errors in merged region of reverse sequences
      4.07  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-17-1-FFPE-Tumor_12_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-19-1-FFPE-Normal_S15_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-19-1-FFPE-Normal_S15_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-19-1-FFPE-Normal_13_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
        11  Pairs
        10  Merged (90.9%)
         1  Not merged (9.1%)

Pairs that failed merging due to various reasons:
         1  too few kmers found on same diagonal

Statistics of all reads:
    132.18  Mean read length

Statistics of merged reads:
    215.40  Mean fragment length
      2.46  Standard deviation of fragment length
      1.94  Mean expected error in forward sequences
      2.96  Mean expected error in reverse sequences
      2.03  Mean expected error in merged sequences
      2.70  Mean observed errors in merged region of forward sequences
      3.90  Mean observed errors in merged region of reverse sequences
      6.60  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-19-1-FFPE-Normal_13_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-19-1-FFPE-Tumor-A_S16_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-19-1-FFPE-Tumor-A_S16_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-19-1-FFPE-Tumor-A_14_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         7  Pairs
         6  Merged (85.7%)
         1  Not merged (14.3%)

Pairs that failed merging due to various reasons:
         1  too many differences

Statistics of all reads:
    137.57  Mean read length

Statistics of merged reads:
    213.67  Mean fragment length
      2.36  Standard deviation of fragment length
      1.71  Mean expected error in forward sequences
      2.32  Mean expected error in reverse sequences
      1.31  Mean expected error in merged sequences
      1.50  Mean observed errors in merged region of forward sequences
      2.83  Mean observed errors in merged region of reverse sequences
      4.33  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-19-1-FFPE-Tumor-A_14_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-19-1-FFPE-Tumor-B_S17_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-19-1-FFPE-Tumor-B_S17_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-19-1-FFPE-Tumor-B_15_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         1  Pairs
         0  Merged (0.0%)
         1  Not merged (100.0%)

Pairs that failed merging due to various reasons:
         1  too few kmers found on same diagonal

Statistics of all reads:
    140.00  Mean read length

Statistics of merged reads:
      -nan  Mean fragment length
      -nan  Standard deviation of fragment length
      -nan  Mean expected error in forward sequences
      -nan  Mean expected error in reverse sequences
      -nan  Mean expected error in merged sequences
      -nan  Mean observed errors in merged region of forward sequences
      -nan  Mean observed errors in merged region of reverse sequences
      -nan  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-19-1-FFPE-Tumor-B_15_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-33-1-FFPE-Normal_S46_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-33-1-FFPE-Normal_S46_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-33-1-FFPE-Normal_16_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         3  Pairs
         0  Merged (0.0%)
         3  Not merged (100.0%)

Pairs that failed merging due to various reasons:
         2  too few kmers found on same diagonal
         1  alignment score too low, or score drop to high

Statistics of all reads:
    140.17  Mean read length

Statistics of merged reads:
      -nan  Mean fragment length
      -nan  Standard deviation of fragment length
      -nan  Mean expected error in forward sequences
      -nan  Mean expected error in reverse sequences
      -nan  Mean expected error in merged sequences
      -nan  Mean observed errors in merged region of forward sequences
      -nan  Mean observed errors in merged region of reverse sequences
      -nan  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-33-1-FFPE-Normal_16_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-33-1-FFPE-PolipTum_S47_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-33-1-FFPE-PolipTum_S47_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-33-1-FFPE-PolipTum_17_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
        18  Pairs
        10  Merged (55.6%)
         8  Not merged (44.4%)

Pairs that failed merging due to various reasons:
         3  too few kmers found on same diagonal
         1  too many differences
         4  alignment score too low, or score drop to high

Statistics of all reads:
    134.64  Mean read length

Statistics of merged reads:
    214.40  Mean fragment length
      2.94  Standard deviation of fragment length
      1.38  Mean expected error in forward sequences
      1.94  Mean expected error in reverse sequences
      1.42  Mean expected error in merged sequences
      2.00  Mean observed errors in merged region of forward sequences
      1.80  Mean observed errors in merged region of reverse sequences
      3.80  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-33-1-FFPE-PolipTum_17_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-40-1-FFPE-GsinM_S11_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-40-1-FFPE-GsinM_S11_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-40-1-FFPE-GsinM_18_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         3  Pairs
         1  Merged (33.3%)
         2  Not merged (66.7%)

Pairs that failed merging due to various reasons:
         1  too many differences
         1  alignment score too low, or score drop to high

Statistics of all reads:
    140.33  Mean read length

Statistics of merged reads:
    207.00  Mean fragment length
      0.00  Standard deviation of fragment length
      1.81  Mean expected error in forward sequences
      4.32  Mean expected error in reverse sequences
      1.82  Mean expected error in merged sequences
      2.00  Mean observed errors in merged region of forward sequences
      3.00  Mean observed errors in merged region of reverse sequences
      5.00  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-40-1-FFPE-GsinM_18_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-40-1-FFPE-Normal_S9_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-40-1-FFPE-Normal_S9_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-40-1-FFPE-Normal_19_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         1  Pairs
         1  Merged (100.0%)
         0  Not merged (0.0%)

Statistics of all reads:
    136.50  Mean read length

Statistics of merged reads:
    211.00  Mean fragment length
      0.00  Standard deviation of fragment length
      3.44  Mean expected error in forward sequences
      2.99  Mean expected error in reverse sequences
      3.81  Mean expected error in merged sequences
      4.00  Mean observed errors in merged region of forward sequences
      5.00  Mean observed errors in merged region of reverse sequences
      9.00  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-40-1-FFPE-Normal_19_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-40-1-FFPE-Tumor_S10_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-40-1-FFPE-Tumor_S10_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-40-1-FFPE-Tumor_20_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
        28  Pairs
        20  Merged (71.4%)
         8  Not merged (28.6%)

Pairs that failed merging due to various reasons:
         3  too many differences
         5  alignment score too low, or score drop to high

Statistics of all reads:
    137.50  Mean read length

Statistics of merged reads:
    213.60  Mean fragment length
      2.91  Standard deviation of fragment length
      1.65  Mean expected error in forward sequences
      2.07  Mean expected error in reverse sequences
      1.54  Mean expected error in merged sequences
      2.15  Mean observed errors in merged region of forward sequences
      2.40  Mean observed errors in merged region of reverse sequences
      4.55  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-40-1-FFPE-Tumor_20_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-47-1-FFPE-Normal_S44_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-47-1-FFPE-Normal_S44_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-47-1-FFPE-Normal_21_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         9  Pairs
         3  Merged (33.3%)
         6  Not merged (66.7%)

Pairs that failed merging due to various reasons:
         1  too few kmers found on same diagonal
         2  too many differences
         3  alignment score too low, or score drop to high

Statistics of all reads:
    131.33  Mean read length

Statistics of merged reads:
    213.67  Mean fragment length
      2.36  Standard deviation of fragment length
      1.58  Mean expected error in forward sequences
      2.03  Mean expected error in reverse sequences
      1.50  Mean expected error in merged sequences
      2.33  Mean observed errors in merged region of forward sequences
      1.67  Mean observed errors in merged region of reverse sequences
      4.00  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-47-1-FFPE-Normal_21_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-47-1-FFPE-Tumor_S45_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-47-1-FFPE-Tumor_S45_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-47-1-FFPE-Tumor_22_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch

Merging reads 100%
         3  Pairs
         1  Merged (33.3%)
         2  Not merged (66.7%)

Pairs that failed merging due to various reasons:
         1  too few kmers found on same diagonal
         1  too many differences

Statistics of all reads:
    113.83  Mean read length

Statistics of merged reads:
    212.00  Mean fragment length
      0.00  Standard deviation of fragment length
      0.66  Mean expected error in forward sequences
      0.91  Mean expected error in reverse sequences
      1.39  Mean expected error in merged sequences
      2.00  Mean observed errors in merged region of forward sequences
      3.00  Mean observed errors in merged region of reverse sequences
      5.00  Mean observed errors in merged region
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: gzip /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-47-1-FFPE-Tumor_22_L001_R1_001.fastq

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-49-1-FFPE-GsinM_S14_L001_R1_001.fastq.gz --reverse /tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-49-1-FFPE-GsinM_S14_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-49-1-FFPE-GsinM_23_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout 0 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

vsearch v2.7.0_linux_x86_64, 15.1GB RAM, 16 cores
https://github.com/torognes/vsearch



**Fatal error: File too small**
Traceback (most recent call last):
  File "/home/elsa/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/commands.py", line 329, in __call__
    results = action(**arguments)
  File "<decorator-gen-193>", line 2, in join_pairs
  File "/home/elsa/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 244, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/home/elsa/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 390, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/home/elsa/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_vsearch/_join_pairs.py", line 56, in join_pairs
    _, result = _join_pairs_w_command_output(
  File "/home/elsa/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_vsearch/_join_pairs.py", line 147, in _join_pairs_w_command_output
    run_command(cmd)
  File "/home/elsa/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_vsearch/_cluster_features.py", line 33, in run_command
    subprocess.run(cmd, check=True)
  File "/home/elsa/miniconda3/envs/qiime2-2021.4/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['vsearch', '--fastq_mergepairs', '/tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-49-1-FFPE-GsinM_S14_L001_R1_001.fastq.gz', '--reverse', '/tmp/qiime2-archive-9awiowi8/2dfa1b64-b0fa-42b3-aedb-9f81ed069ca5/data/CCR-49-1-FFPE-GsinM_S14_L001_R2_001.fastq.gz', '--fastqout', '/tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-gq_a5tbf/CCR-49-1-FFPE-GsinM_23_L001_R1_001.fastq', '--fastq_ascii', '33', '--fastq_minlen', '1', '--fastq_minovlen', '10', '--fastq_maxdiffs', '10', '--fastq_qmin', '0', '--fastq_qminout', '0', '--fastq_qmax', '41', '--fastq_qmaxout', '41', '--minseqlength', '1', '--fasta_width', '0', '--threads', '1']' returned non-zero exit status 1.

How can I proceed? I need the outputs that the dada2 or the deblur commands give to continue with the q2-sidle tutorial.

(I know I could re-imported the samples without these two files, but I would prefer avoid this solution if I can).

Thank you!!

Best,

Elsa

Hello Elsa,

I think that's the best way forward right now. Newer versions of vsearch will happily work with empty files (see issue 366), but the version of vsearch that comes with Qiime2 does not support that yet.

Sorry for the inconvenience. Let us know if you have other questions about running q2-sidle!

Colin

2 Likes

Hi @colinbrislawn,

Ok, if I find another solution I will reply this post!!

Thank for your help!

Elsa

Hello Elsa,

OK, let me know what you find!

I was talking with some of the mods about this problem (hey mods :wave:), and they suggested to take another look at ready quality. It looks like the majority of your reads are filtered out before they even get to the joining step. It might be worthwhile to revisit the cutadapt or deblur steps, maybe using only your forward reads if they have the highest quality.

Colin

3 Likes