evolvedmicrobe
commented
4 years ago Hi @jrknoedler,
Please reach out to support@10xgenomics.com for quick help with his issue. An exit status of -9 means that something sent a SIGKILL to the process, and this may indicate an issue with the cluster configuration, or some other problem, that they'll be able to help you with.
Cheers, Nigel
I'm getting this error message at chunk_reads. Some details: I'm running in cluster mode on a slurm server, and the pipeline has worked with no issues as recently as a few months ago but is now failing on both new and old (i.e. previously working) fastq files. The only differences is I'm using a reference gtf with one entry manually removed, but it seems to be failing before that could possibly have been an issue.
Traceback (most recent call last): File "/scratch/users/knoedler/cellranger-3.1/martian-cs/v3.2.3/adapters/python/martian_shell.py", line 589, in _main stage.main() File "/scratch/users/knoedler/cellranger-3.1/martian-cs/v3.2.3/adapters/python/martian_shell.py", line 554, in main self._run(lambda: self._module.main(args, outs)) File "/scratch/users/knoedler/cellranger-3.1/martian-cs/v3.2.3/adapters/python/martian_shell.py", line 523, in _run cmd() File "/scratch/users/knoedler/cellranger-3.1/martian-cs/v3.2.3/adapters/python/martian_shell.py", line 554, in
self._run(lambda: self._module.main(args, outs))
File "/scratch/users/knoedler/cellranger-3.1/cellranger-cs/3.1/mro/stages/common/chunk_reads/init.py", line 53, in main
tk_subproc.check_call(chunk_reads_args)
File "/scratch/users/knoedler/cellranger-3.1/cellranger-cs/3.1/tenkit/lib/python/tenkit/log_subprocess.py", line 37, in check_call
return subprocess.check_call(*args, **kwargs)
File "/scratch/users/knoedler/cellranger-3.1/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c10/lib/python2.7/subprocess.py", line 186, in check_call
raise CalledProcessError(retcode, cmd)
CalledProcessError: Command '['chunk_reads', '--reads-per-fastq', '5000000', '/scratch/users/knoedler/IntactMalePOA_Kiss1gtftest2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u16d99aa408/files/', 'fastq_chunk', '--martian-args', 'chunk_args.json', '--compress', 'lz4']' returned non-zero exit status -9