cutadapt: cutadapt installed via conda igzip error for some fastq files
Only very recently (~2 weeks ago), cutadapt installed via conda has the following error:
This is cutadapt 3.2 with Python 3.8.6
Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC in2438_3_CKDL210000739-2a-AK5142-AK6697_HVHF2DSXY_L2_1.fq.gz
Processing reads on 4 cores in single-end mode ...
[--------->8 ] 00:00:26 5,536,084 reads @ 4.9 µs/read; 12.33 M reads/minuteERROR: Traceback (most recent call last):
File "/opt/conda/envs/test/lib/python3.8/site-packages/cutadapt/pipeline.py", line 560, in run
self.send_to_worker(chunk_index, chunk)
File "/opt/conda/envs/test/lib/python3.8/site-packages/xopen/__init__.py", line 141, in __exit__
self.close()
File "/opt/conda/envs/test/lib/python3.8/site-packages/xopen/__init__.py", line 327, in close
self._raise_if_error(allow_sigterm=allow_sigterm)
File "/opt/conda/envs/test/lib/python3.8/site-packages/xopen/__init__.py", line 350, in _raise_if_error
raise OSError("{} (exit code {})".format(message, retcode))
OSError: igzip: Error while decompressing extra concatenatedgzip files on in2438_3_CKDL210000739-2a-AK5142-AK6697_HVHF2DSXY_L2_1.fq.gz (exit code 1)
ERROR: Traceback (most recent call last):
File "/opt/conda/envs/test/lib/python3.8/site-packages/cutadapt/pipeline.py", line 626, in run
raise e
OSError: igzip: Error while decompressing extra concatenatedgzip files on in2438_3_CKDL210000739-2a-AK5142-AK6697_HVHF2DSXY_L2_1.fq.gz (exit code 1)
Traceback (most recent call last):
File "/opt/conda/envs/test/bin/cutadapt", line 10, in <module>
sys.exit(main_cli())
File "/opt/conda/envs/test/lib/python3.8/site-packages/cutadapt/__main__.py", line 845, in main_cli
main(sys.argv[1:])
File "/opt/conda/envs/test/lib/python3.8/site-packages/cutadapt/__main__.py", line 912, in main
stats = r.run()
File "/opt/conda/envs/test/lib/python3.8/site-packages/cutadapt/pipeline.py", line 824, in run
raise e
OSError: igzip: Error while decompressing extra concatenatedgzip files on in2438_3_CKDL210000739-2a-AK5142-AK6697_HVHF2DSXY_L2_1.fq.gz (exit code 1)
This only happens with some fastq files, only in multi-thread mode (with -j specified), and only with conda-installed cutadapt. I’ve tried version 3.2 and 3.1. I’ve tried rolling back versions of some dependencies including pigz=2.3.4, xopen=1.0.1, dnaio=0.4.4, none of these helps.
I understand this is probably a bioconda problem rather than cutadapt problem. This has also been reported in bioconda recipes repo. So far no solutions. I am hoping maybe cutadapt developers might point me to a few places since you understand the error message better. Thank you.
About this issue
- Original URL
- State: closed
- Created 3 years ago
- Reactions: 1
- Comments: 18 (5 by maintainers)
Yes. Thank you so much for fixing this.
I can confirm that build
ha770c72_2works.