/dekupl/dekupl_tmp error

[mndavies286]

Hi

I seem to have been having an issue with the new image that I didn't have with the old image.

The same four files seem to process fine but then I got the error below. I did not have this problem with the previous version when I ran them with a different nomenclature.

My command is:

docker run --rm -v ${PWD}/my-config.json:/dekupl/my-config.json -v ${PWD}/data:/dekupl/data -v ${PWD}/results:/dekupl/results transipedia/dekupl-run --configfile my-config.json -j8 --resources ram=10 -p

Could you suggest what might be happening here?

Best wishes

Matt

jellyfish dump -c DEkupl_result/kmer_counts/SRR7702229.jf | sort -T /dekupl/dekupl_tmp -k 1 -S 3000M --parallel 8| pigz -p 8 -c > DEkupl_result/kmer_counts/SRR7702229.txt.gz sort: cannot create temporary file in '/dekupl/dekupl_tmp': No such file or directory [Fri Feb 8 10:29:22 2019] Error in rule jellyfish_dump: jobid: 0 output: DEkupl_result/kmer_counts/SRR7702229.txt.gz log: DEkupl_result/Logs/SRR7702229_jellyfishDumpRawCounts_exec_time.log

RuleException: CalledProcessError in line 555 of /dekupl/Snakefile: Command ' set -euo pipefail; jellyfish dump -c DEkupl_result/kmer_counts/SRR7702229.jf | sort -T /dekupl/dekupl_tmp -k 1 -S 3000M --parallel 8| pigz -p 8 -c > DEkupl_result/kmer_counts/SRR7702229.txt.gz ' returned non-zero exit status 2. File "/dekupl/Snakefile", line 555, in __rule_jellyfish_dump File "/usr/local/lib/python3.6/concurrent/futures/thread.py", line 56, in run Exiting because a job execution failed. Look above for error message

[jaudoux]

Hi Matt,

Have you deleted the DEkupl_result folder before re-running your command line ? Because if you changed your sample names and re-run the command line with the same output folder, it will generate unexpected errors.

Best, J.

[mndavies286]

Do you mean removing the local /results file? That doesn't seem to make any difference.

[mndavies286]

Sorry, 'folder' not 'file'