IndexError: list index out of range

Dear Shirley Liu Lab,

Thanks a lot for developing this awesome tool. I am running the 0.5.3 version for 13 samples of Brunello screens. The demo worked well, but when I start to run my samples, it showed an error (from the MaGeCK->test-> log file):

INFO @ Tue, 18 Dec 2018 15:49:02: Sample index: 0;2;3;4;5;1;6;9;10;11;12;7;8 INFO @ Tue, 18 Dec 2018 15:49:03: Loaded 19113 genes. Traceback (most recent call last): File "/Users/sunc/anaconda3/bin/mageck", line 66, in <module> main(); File "/Users/sunc/anaconda3/bin/mageck", line 43, in main args=crisprseq_parseargs(); File "/Users/sunc/anaconda3/lib/python3.6/site-packages/mageck/argsParser.py", line 244, in crisprseq_parseargs mageckmle_main(parsedargs=args); # ignoring the script path, and the sub command File "/Users/sunc/anaconda3/lib/python3.6/site-packages/mageck/mlemageck.py", line 85, in mageckmle_main cttab_sel[sgid[i]]=sgreadmat[i] IndexError: list index out of range

From the terminal: Error in job mageck_mle while creating output files results/test/brunello.gene_summary.txt, results/test/brunello.sgrna_summary.txt. RuleException: CalledProcessError in line 212 of /Users/sunc/Desktop/Brunello-new/Snakefile: Command 'mageck mle --norm-method median --output-prefix results/test/brunello --genes-var 0 --count-table results/count/all.count.txt --design-matrix designmatrix.txt 2> logs/mageck/test/brunello.log' returned non-zero exit status 1. File "/Users/sunc/Desktop/Brunello-new/Snakefile", line 212, in __rule_mageck_mle File "/Users/sunc/anaconda3/lib/python3.6/concurrent/futures/thread.py", line 56, in run Will exit after finishing currently running jobs. Exiting because a job execution failed. Look above for error message

Your kind support is very much appreciated.

Cheers Claire

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