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 paraffin 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:
- Importing samples into qiime2. (Done).
- Cutadapt the samples with the different primers sets to demultiplexed the data into regions. (Done).
- 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