Hello!
I've looked through the various posts for the errors related to running cutadapt and I don't believe any of them have the exact same one I am experience so here it goes.
I tried running the following command:
qiime cutadapt trim-paired \
--i-demultiplexed-sequences 16SV4V5_HOME_Run9sequences.qza \
--p-cores 6 \
--p-front-f GTGYCAGCMGCCGCGGTAA \
--p-front-r CCGYCAATTYMTTTRAGTTT \
--p-discard-untrimmed \
--p-no-indels \
--o-trimmed-sequences 16SV4V5_HOME_Run9sequences_trimmed.qza
I get the following error:
Plugin error from cutadapt:
Command '['cutadapt', '--cores', '6', '--error-rate', '0.1', '--times', '1', '--overlap', '3', '--minimum-length', '1', '-o', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-lzba_bh5/QMIC4234_S305_L001_R1_001.fastq.gz', '-p', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-lzba_bh5/QMIC4234_S305_L001_R2_001.fastq.gz', '--front', 'GTGYCAGCMGCCGCGGTAA', '-G', 'CCGYCAATTYMTTTRAGTTT', '--no-indels', '--discard-untrimmed', '/tmp/qiime2-archive-i9777yzm/96590386-0bbd-4f88-9ad9-c842af05584d/data/QMIC4234_S305_L001_R1_001.fastq.gz', '/tmp/qiime2-archive-i9777yzm/96590386-0bbd-4f88-9ad9-c842af05584d/data/QMIC4234_S305_L001_R2_001.fastq.gz']' returned non-zero exit status 1.
Debug info has been saved to /tmp/qiime2-q2cli-err-uja4b8ym.log
I'm attaching the complete log file.
qiime2-q2cli-err-uja4b8ym.txt (689.9 KB)
It runs through many samples and then seems to crash. This is the error given at the end of the log file.
Traceback (most recent call last):
File "/home/colleen.kellogg/miniconda3/envs/qiime2-2020.6/bin/cutadapt", line 10, in <module>
sys.exit(main())
File "/home/colleen.kellogg/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/cutadapt/__main__.py", line 855, in main
stats = r.run()
File "/home/colleen.kellogg/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/cutadapt/pipeline.py", line 645, in __exit__
self.close()
File "/home/colleen.kellogg/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/cutadapt/pipeline.py", line 795, in close
f.close()
File "/home/colleen.kellogg/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/xopen/__init__.py", line 173, in close
"Output {} process terminated with exit code {}".format(self.program, retcode))
OSError: Output pigz process terminated with exit code 28
Traceback (most recent call last):
File "/home/colleen.kellogg/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py", line 329, in __call__
results = action(**arguments)
File "<decorator-gen-551>", line 2, in trim_paired
File "/home/colleen.kellogg/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/home/colleen.kellogg/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/colleen.kellogg/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_cutadapt/_trim.py", line 189, in trim_paired
run_commands(cmds)
File "/home/colleen.kellogg/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_cutadapt/_trim.py", line 30, in run_commands
subprocess.run(cmd, check=True)
File "/home/colleen.kellogg/miniconda3/envs/qiime2-2020.6/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['cutadapt', '--cores', '6', '--error-rate', '0.1', '--times', '1', '--overlap', '3', '--minimum-length', '1', '-o', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-lzba_bh5/QMIC4234_S305_L001_R1_001.fastq.gz', '-p', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-lzba_bh5/QMIC4234_S305_L001_R2_001.fastq.gz', '--front', 'GTGYCAGCMGCCGCGGTAA', '-G', 'CCGYCAATTYMTTTRAGTTT', '--no-indels', '--discard-untrimmed', '/tmp/qiime2-archive-i9777yzm/96590386-0bbd-4f88-9ad9-c842af05584d/data/QMIC4234_S305_L001_R1_001.fastq.gz', '/tmp/qiime2-archive-i9777yzm/96590386-0bbd-4f88-9ad9-c842af05584d/data/QMIC4234_S305_L001_R2_001.fastq.gz']' returned non-zero exit status 1.
seems this may be the pertinent error:
OSError: Output pigz process terminated with exit code 28
Any thoughts about what this problem is here? I'm processing my MiSeq run the same way I have 8 times before, I don't understand what would have changed, especially since I'm using the same version of QIIME2 (version qiime2-2020.6, wasn't sure if i could process newer runs with newer QIIME2 versions and still merge them at the end of the day...)
Thank you in advance for your help!
Colleen
