I tried --verbose but I got an error again..
I am attaching the error message below.
qiime vsearch join-pairs --verbose --i-demultiplexed-seqs paired-end-demux.qza --o-joined-sequences demux-joined.qza
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 /var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/qiime2-archive-5e1m62dz/53743d83-7f36-40e8-9029-450453314b27/data/A1_0_L001_R1_001.fastq.gz --reverse /var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/qiime2-archive-5e1m62dz/53743d83-7f36-40e8-9029-450453314b27/data/A1_1_L001_R2_001.fastq.gz --fastqout /var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/q2-SingleLanePerSampleSingleEndFastqDirFmt-i1o16g9g/A1_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
vsearch v2.7.0_macos_x86_64, 8.0GB RAM, 4 cores
Merging reads 100%
199077 Pairs
190464 Merged (95.7%)
8613 Not merged (4.3%)
Pairs that failed merging due to various reasons:
792 too few kmers found on same diagonal
4 potential tandem repeat
1727 too many differences
6080 alignment score too low, or score drop to high
10 staggered read pairs
Statistics of all reads:
250.82 Mean read length
Statistics of merged reads:
454.51 Mean fragment length
13.02 Standard deviation of fragment length
0.62 Mean expected error in forward sequences
0.70 Mean expected error in reverse sequences
0.87 Mean expected error in merged sequences
0.44 Mean observed errors in merged region of forward sequences
0.53 Mean observed errors in merged region of reverse sequences
0.97 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 /var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/q2-SingleLanePerSampleSingleEndFastqDirFmt-i1o16g9g/A1_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 /var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/qiime2-archive-5e1m62dz/53743d83-7f36-40e8-9029-450453314b27/data/A10_8_L001_R1_001.fastq.gz --reverse /var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/qiime2-archive-5e1m62dz/53743d83-7f36-40e8-9029-450453314b27/data/A10_9_L001_R2_001.fastq.gz --fastqout /var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/q2-SingleLanePerSampleSingleEndFastqDirFmt-i1o16g9g/A10_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
vsearch v2.7.0_macos_x86_64, 8.0GB RAM, 4 cores
Merging reads 100%
80574 Pairs
77990 Merged (96.8%)
2584 Not merged (3.2%)
Pairs that failed merging due to various reasons:
165 too few kmers found on same diagonal
640 too many differences
1778 alignment score too low, or score drop to high
1 staggered read pairs
Statistics of all reads:
250.92 Mean read length
Statistics of merged reads:
451.85 Mean fragment length
12.60 Standard deviation of fragment length
0.59 Mean expected error in forward sequences
0.74 Mean expected error in reverse sequences
0.85 Mean expected error in merged sequences
0.37 Mean observed errors in merged region of forward sequences
0.46 Mean observed errors in merged region of reverse sequences
0.83 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 /var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/q2-SingleLanePerSampleSingleEndFastqDirFmt-i1o16g9g/A10_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 /var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/qiime2-archive-5e1m62dz/53743d83-7f36-40e8-9029-450453314b27/data/A11_10_L001_R1_001.fastq.gz --reverse /var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/qiime2-archive-5e1m62dz/53743d83-7f36-40e8-9029-450453314b27/data/A11_11_L001_R2_001.fastq.gz --fastqout /var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/q2-SingleLanePerSampleSingleEndFastqDirFmt-i1o16g9g/A11_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
vsearch v2.7.0_macos_x86_64, 8.0GB RAM, 4 cores
Merging reads 99%
Fatal error: Invalid line 139048 in FASTQ file: Sequence and quality lines must be equally long
Plugin error from vsearch:
Command '['vsearch', '--fastq_mergepairs', '/var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/qiime2-archive-5e1m62dz/53743d83-7f36-40e8-9029-450453314b27/data/A11_10_L001_R1_001.fastq.gz', '--reverse', '/var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/qiime2-archive-5e1m62dz/53743d83-7f36-40e8-9029-450453314b27/data/A11_11_L001_R2_001.fastq.gz', '--fastqout', '/var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/q2-SingleLanePerSampleSingleEndFastqDirFmt-i1o16g9g/A11_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']' returned non-zero exit status 1