The number of samples in the --include-samples option do not match rows in design matrix
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)
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reporter -
reporter - marked as trivial
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reporter - changed status to resolved
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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Thank you. It is rally help a lot.
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This ended up being due to an empty line at the end of the design matrix