mageck sgrna issue

[liluxiaomeng]

Dear Johannes, I have the same problem with Trunc. When I ran Mageck and failed after count process. You can find the error as below:

Error in job annotate_sgrnas while creating output file annotation/sgrnas.bed. 
RuleException: 
CalledProcessError in line 83 of /datd/liuxiaomeng/project/crispr/analysis/2.mageck_vispr/QC_test3/Snakefile: 
Command 'mageck-vispr annotate-library /datd/liuxiaomeng/project/crispr/download/library/ABlibraryforMageck/Human_GeCKOv2_Library_combine.csv --sgrna-len 20 --assembly hg19 > annotation/sgrnas.bed 2> logs/annotation/sgrnas.log' returned non-zero exit status 1 
File "/datd/liuxiaomeng/project/crispr/analysis/2.mageck_vispr/QC_test3/Snakefile", line 83, in __rule_annotate_sgrnas 
File "/date/liuxiaomeng/software/miniconda3/lib/python3.5/concurrent/futures/thread.py", line 55, in run 
Removing output files of failed job annotate_sgrnas since they might be corrupted: 
annotation/sgrnas.bed 
Will exit after finishing currently running jobs. 
Exiting because a job execution failed. Look above for error message 

[Johannes Köster]

Hi, this looks like a temporal network connection problem. I suggest to try again e.g. today.

[liluxiaomeng]

The problem is solved. Thank you!

[Johannes Köster]

thanks!

[Sandra Schick]

Dear Johannes,

I receive the same error message with one dataset and it is not solved by running it again on another day. Do you have any suggestion?