split_libraries_fastq.py RuntimeWarning: Mean of empty slice.

[Constantino Schillebeeckx]

When I run the command:

split_libraries_fastq.py -i primerTrimmed50.fastq -b primerTrimmed.index50.fastq -m old_files/Mapping_File_150529_AEF8U.txt --barcode_type 13 --rev_comp_mapping_barcodes -o split_lib

I get a runtime error:

/usr/lib/python2.7/dist-packages/numpy/core/_methods.py:55: RuntimeWarning: Mean of empty slice.
  warnings.warn("Mean of empty slice.", RuntimeWarning)

Unfortunately that numpy error doesn't tell me much more than a mean being calculated on an empty array.  I've previously never had problems with this script.  I'm hoping someone can tell me what I'm doing wrong.

Thanks

[Tony Walters]

Hello Constantino,

Can you try running this with --rev_comp_mapping_barcodes removed? I think in this case, since there is only one read, it's not matching anything, and the zero data left is raising the warning. The seq was assigned to a barcode when I removed --rev_comp_mapping_barcodes and didn't raise the warning.

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[Constantino Schillebeeckx]

Looks like that did the trick!

Even on my full dataset I was getting the runtime error with the --rev_comp_mapping_barcodes option.

Thanks for the help!