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
Comments (3)
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reporter Hi Qiyuan,
Yes. I think my problem was because in my library file, I have space or - symbol in the names of the sgRNA or genes. You can replace them by _. Hope it helps.
Cheers Claire
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Hi, ClaireBear,
Exactly! Thank you so much! @ClaireBear666
Cheers
Qiyuan
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Hi, ClaireBear,
I met similar error as yours. Do you have any updates for the problem solving? Thanks! @ClaireBear666
Best,
Qiyuan