Error at MLE stage

[Alexander Raeside]

Hello

I am able to run Mageck-vispr through the Mageck count stage but the pipeline appears to crash at the mle stage in loop function within the mageckCountNorm.py program.

Below is the log from the mle.log file and the error message within the command like

INFO  @ Thu, 17 Jan 2019 15:24:59: Parameters: /home/alex/miniconda2/envs/vispr-mageck/bin/mageck mle --norm-method median --output-prefix results/test/SL-mle --genes-var 0 --count-table results/count/all.count.txt --threads 8 --design-matrix finedesign.txt 
/home/alex/miniconda2/envs/vispr-mageck/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
INFO  @ Thu, 17 Jan 2019 15:25:02: Cannot parse design matrix as a string; try to parse it as a file name ... 
INFO  @ Thu, 17 Jan 2019 15:25:02: Design matrix: 
INFO  @ Thu, 17 Jan 2019 15:25:02: [[1. 0. 0.] 
INFO  @ Thu, 17 Jan 2019 15:25:02:  [1. 1. 0.] 
INFO  @ Thu, 17 Jan 2019 15:25:02:  [1. 1. 0.] 
INFO  @ Thu, 17 Jan 2019 15:25:02:  [1. 0. 0.] 
INFO  @ Thu, 17 Jan 2019 15:25:02:  [1. 0. 1.] 
INFO  @ Thu, 17 Jan 2019 15:25:02:  [1. 0. 1.]] 
INFO  @ Thu, 17 Jan 2019 15:25:02: Beta labels:baseline,d9,d15 
INFO  @ Thu, 17 Jan 2019 15:25:02: Included samples:REF-CAS9,D9-WT,D9-CAS9,REF-WT,d15-WT,d15-CAS9 
INFO  @ Thu, 17 Jan 2019 15:25:02: Loaded samples:REF-CAS9;D9-WT;D9-CAS9;REF-WT;d15-WT;d15-CAS9 
INFO  @ Thu, 17 Jan 2019 15:25:02: Sample index: 3;0;2;4;1;5 
INFO  @ Thu, 17 Jan 2019 15:25:02: Loaded 886 genes. 
Traceback (most recent call last):
  File "/home/alex/miniconda2/envs/vispr-mageck/bin/mageck", line 66, in <module>
    main();
  File "/home/alex/miniconda2/envs/vispr-mageck/bin/mageck", line 43, in main
    args=crisprseq_parseargs();
  File "/home/alex/miniconda2/envs/vispr-mageck/lib/python3.5/site-packages/mageck/argsParser.py", line 244, in crisprseq_parseargs
    mageckmle_main(parsedargs=args); # ignoring the script path, and the sub command
  File "/home/alex/miniconda2/envs/vispr-mageck/lib/python3.5/site-packages/mageck/mlemageck.py", line 88, in mageckmle_main
    size_f=normalizeCounts(cttab_sel,method=args.norm_method,returnfactor=True,reversefactor=True,controlsgfile=args.control_sgrna)
  File "/home/alex/miniconda2/envs/vispr-mageck/lib/python3.5/site-packages/mageck/mageckCountNorm.py", line 119, in normalizeCounts
    samplefactor=mageckcount_gettotalnormfactor(ctable_nm)
  File "/home/alex/miniconda2/envs/vispr-mageck/lib/python3.5/site-packages/mageck/mageckCountNorm.py", line 24, in mageckcount_gettotalnormfactor
    sumsample=[sumsample[i]+v[i] for i in range(n)]
  File "/home/alex/miniconda2/envs/vispr-mageck/lib/python3.5/site-packages/mageck/mageckCountNorm.py", line 24, in <listcomp>
    sumsample=[sumsample[i]+v[i] for i in range(n)]
TypeError: unsupported operand type(s) for +: 'float' and 'list'

here is the error

Error in rule mageck_mle: jobid: 7 output: results/test/SL-mle.gene_summary.txt, results/test/SL-mle.sgrna_summary.txt log: logs/mageck/test/SL-mle.log

RuleException: CalledProcessError in line 212 of /home/alex/Bioinformatics_projects/Crispr_Pooled_Screen/blue_magic/Snakefile: Command ' set -euo pipefail; mageck mle --norm-method median --output-prefix results/test/SL-mle --genes-var 0 --count-table results/count/all.count.txt --threads 8 --design-matrix finedesign.txt 2> logs/mageck/test/SL-mle.log ' returned non-zero exit status 1 File "/home/alex/Bioinformatics_projects/Crispr_Pooled_Screen/blue_magic/Snakefile", line 212, in __rule_mageck_mle File "/home/alex/miniconda2/envs/vispr-mageck/lib/python3.5/concurrent/futures/thread.py", line 55, in run Will exit after finishing currently running jobs. Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/alex/Bioinformatics_projects/Crispr_Pooled_Screen/blue_magic/.snakemake/log/2019-01-17T141712.121120.snakemake.log

Any help would be deeply appreciated.

Thank you,

Alex