stat.mageck2

[yeroslaviz]

when running stat.mageck from the template file I get an error message

INFO  @ Fri, 16 Mar 2018 11:28:47: Parameters: /usr/local/bin/mageck test --count-table /local/Assa/projects/GuanW.sgRNAScreening/TRAILscreen-ANALYSIS-MAGeCK-RAW_MAGeCK_sgRNA.tab --treatment-id 0,1 --control-id 2,3 --norm-method median --sort-criteria neg --gene-test-fdr-threshold 0.05 --adjust-method fdr --output-prefix TRAILscreen-ANALYSIS-MAGeCK-RAW 
INFO  @ Fri, 16 Mar 2018 11:28:47: Welcome to MAGeCK v0.5.7. Command: test 
INFO  @ Fri, 16 Mar 2018 11:28:47: Loading count table from /local/Assa/projects/GuanW.sgRNAScreening/TRAILscreen-ANALYSIS-MAGeCK-RAW_MAGeCK_sgRNA.tab  
INFO  @ Fri, 16 Mar 2018 11:28:47: Processing 1 lines.. 
WARNING @ Fri, 16 Mar 2018 11:28:47: Line 1 of the read count table has fewer than 3 columns. Skip this line ... 
Traceback (most recent call last):
  File "/usr/local/bin/mageck", line 66, in <module>
    main();
  File "/usr/local/bin/mageck", line 51, in main
    magecktest_main(args);
  File "/usr/local/lib/python2.7/dist-packages/mageck/crisprFunction.py", line 562, in magecktest_main
    mapres=getcounttablefromfile(args.count_table)
  File "/usr/local/lib/python2.7/dist-packages/mageck/mageckCount.py", line 372, in getcounttablefromfile
    geneid=field[1]
IndexError: list index out of range

This happens bacause the file used as inout to mageck (= count table) is not tab-delimited.
in the stat,mageck function in lines 39-40 the file is created.

  write.table(dataset.combined, file = dataset.combined.file, 
    row.names = FALSE, quote = FALSE)

here you just need to add the sep= "\t" parameter.

than mageck runs with no errors.

Assa