The number of samples in the --include-samples option do not match rows in design matrix

Issue #39 resolved
natallah created an issue

I get the following error when running mageck: INFO @ Tue, 12 Jun 2018 15:36:49: Parameters: /group/bioinfo/apps/apps/miniconda-4.3.21/envs/mageck-vispr/bin/mageck mle --norm-method median --output-prefix resu lts/test/crispr_2018_EKVXandH322M --sgrna-eff-name-column 3 --sgrna-eff-score-column 4 --sgrna-efficiency annotation/sgrnas.bed --genes-var 0 --update-efficiency - -count-table results/count/all.count.txt --design-matrix designmatrix.txt INFO @ Tue, 12 Jun 2018 15:36:55: Cannot parse design matrix as a string; try to parse it as a file name ... ERROR @ Tue, 12 Jun 2018 15:36:55: The number of samples in the --include-samples option do not match rows in design matrix.

However the design matrix and the samples in the .yaml file do indeed match.

Comments (4)

  1. natallah reporter

    It was an empty line at the end of the design matrix causing the issue. Leaving this here in case anyone else runs into a similar issue

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