IndexError: list index out of range

[YANG QIYUAN]

Hi, when I go through “snakemake -n” then run the vispr analysis, I found the indexError: list index out of range. Could you help me in this case?

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rule mageck_mle:

input: results/count/all.count.txt, designmatrix.txt

output: results/test/NPR-mle.gene_summary.txt, results/test/NPR-mle.sgrna_summary.txt

log: logs/mageck/test/NPR-mle.log

jobid: 10

wildcards: experiment=NPR-mle

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Error in job mageck_mle while creating output files results/test/NPR-mle.gene_summary.txt, results/test/NPR-mle.sgrna_summary.txt.

RuleException:

CalledProcessError in line 212 of /Users/qiyuanyang/Downloads/Yang-crisper/Snakefile:

Command 'mageck mle --norm-method median --output-prefix results/test/NPR-mle --genes-var 0 --count-table results/count/all.count.txt --design-matrix designmatrix.txt 2> logs/mageck/test/NPR-mle.log' returned non-zero exit status 1.

File "/Users/qiyuanyang/Downloads/Yang-crisper/Snakefile", line 212, in __rule_mageck_mle

File "/Users/qiyuanyang/miniconda3/envs/mageck-vispr/lib/python3.6/concurrent/futures/thread.py", line 56, in run

Will exit after finishing currently running jobs.

Analysis complete for Undetermined.fastq

Finished job 5.

10 of 13 steps (77%) done

Will exit after finishing currently running jobs.

Exiting because a job execution failed. Look above for error message

(mageck-vispr) QIYUANs-MBP:Yang-crisper qiyuanyang$

---

here is the log information:

INFO @ Tue, 07 May 2019 20:42:29: Parameters: /Users/qiyuanyang/miniconda3/envs/mageck-vispr/bin/mageck mle --norm-method median --output-prefix results/test/NPR-mle --genes-var 0 --count-table results/count/all.count.txt --design-matrix designmatrix.txt
INFO @ Tue, 07 May 2019 20:42:29: Cannot parse design matrix as a string; try to parse it as a file name ...
INFO @ Tue, 07 May 2019 20:42:29: Design matrix:
INFO @ Tue, 07 May 2019 20:42:29: [[ 1. 0.]
INFO @ Tue, 07 May 2019 20:42:29: [ 1. 0.]
INFO @ Tue, 07 May 2019 20:42:29: [ 1. 1.]
INFO @ Tue, 07 May 2019 20:42:29: [ 1. 1.]
INFO @ Tue, 07 May 2019 20:42:29: [ 1. 1.]
INFO @ Tue, 07 May 2019 20:42:29: [ 1. 1.]
INFO @ Tue, 07 May 2019 20:42:29: [ 1. 1.]
INFO @ Tue, 07 May 2019 20:42:29: [ 1. 1.]
INFO @ Tue, 07 May 2019 20:42:29: [ 1. 0.]]
INFO @ Tue, 07 May 2019 20:42:29: Beta labels:baseline,esc
INFO @ Tue, 07 May 2019 20:42:29: Included samples:Oligo,Plasmid,Day9-R1,Day9-R2,Day9-R3,Day6-R1,Day6-R2,Day6-R3,Undetermined
INFO @ Tue, 07 May 2019 20:42:29: Loaded samples:Oligo;Plasmid;Day9-R1;Day9-R2;Day9-R3;Day6-R1;Day6-R2;Day6-R3;Undetermined
INFO @ Tue, 07 May 2019 20:42:29: Sample index: 6;7;3;4;5;0;1;2;8
INFO @ Tue, 07 May 2019 20:42:29: Loaded 169 genes.
Traceback (most recent call last):
File "/Users/qiyuanyang/miniconda3/envs/mageck-vispr/bin/mageck", line 66, in <module>
main();
File "/Users/qiyuanyang/miniconda3/envs/mageck-vispr/bin/mageck", line 43, in main
args=crisprseq_parseargs();
File "/Users/qiyuanyang/miniconda3/envs/mageck-vispr/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/qiyuanyang/miniconda3/envs/mageck-vispr/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