Error in job annotate_sgrnas

Issue #31 new
EPark created an issue

I got this error running MAGECK-VISPR.

Error in job annotate_sgrnas while creating output file annotation/sgrnas.bed. RuleException: CalledProcessError in line 87 of /home/dp159/workflow/Snakefile: Command 'mageck-vispr annotate-library /home/dp159/others/H1.library.txt --sgrna-len 19 --assembly hg38 > annotation/sgrnas.bed 2> logs/annotation/sgrnas.log' returned non-zero exit status 1 File "/home/dp159/workflow/Snakefile", line 87, in __rule_annotate_sgrnas File "/home/dp159/miniconda3/envs/mageck-vispr/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.

Here's the log for sgRNA

Traceback (most recent call last): File "/home/dp159/miniconda3/envs/mageck-vispr/bin/mageck-vispr", line 6, in <module> sys.exit(mageck_vispr.cli.main()) File "/home/dp159/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/mageck_vispr/cli.py", line 163, in main annotation_table=args.annotation_table) File "/home/dp159/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/mageck_vispr/cli.py", line 82, in annotate_library a.annotate() File "/home/dp159/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/mageck_vispr/annotation.py", line 31, in annotate self.sequence_table_import() File "/home/dp159/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/mageck_vispr/annotation.py", line 40, in sequence_table_import elements[2].upper()] IndexError: list index out of range

How would you fix the indexerror? Thank you!

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