Running into CalledProcessError

[Ishan Goyal]

I have been repeatedly running into this same Called Process Error. When I check the log files, it gives me the following debugging message:

"usage: mageck [-h] [-v] {count,test,pathway,plot,mle} ... mageck: error: unrecognized arguments: Check Line 7a Check Line 7a.log"

I have tried using both the designmatrix and manually entering the treatment and control files to no avail. Please let me know what can be done.

[Mailis]

I have been running into a similar issue Error in job mageck_mle while creating output files results/test/NI.gene_summary.txt, results/test/NI.sgrna_summary.txt. RuleException: CalledProcessError in line 151 of /home/MINTS/mm2032/Documents/vispr/Snakefile: Command 'mageck mle --norm-method median --output-prefix results/test/NI --sgrna-eff-name-column 3 --sgrna-eff-score-column 4 --sgrna-efficiency annotation/sgrnas.bed --genes-var 0 --count-table results/count/all.count.txt --design-matrix designmatrix.txt 2> logs/mageck/test/NI.log' returned non-zero exit status 1 File "/home/MINTS/mm2032/Documents/vispr/Snakefile", line 151, in __rule_mageck_mle File "/home/MINTS/mm2032/miniconda3/lib/python3.5/concurrent/futures/thread.py", line 55, in run Will exit after finishing currently running jobs. Exiting because a job execution failed. Look above for error message

Any suggestions?? Best wishes Mailis

[Johannes Köster]

You should have a look at the log file. It will show the actual error.