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Illumina / Cyrius

A tool to genotype CYP2D6 with WGS data
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Issue with file path error? #22

Open joseph-yclam opened 2 years ago

joseph-yclam commented 2 years ago

Hi there,

Is there a way to fix the error where the input file for the sample does not exist?

python star_caller.py --manifest test_filepath --genome 19 --prefix cyr --outDir test_output
WARNING:root:Input file for sample NA23275.bam does not exist.
INFO:root:Writing to json at 2021-11-08 00:30:38.127413
INFO:root:Writing to tsv at 2021-11-08 00:30:38.127615

The test_filepath txt file contains exactly the absolute filepath to the NA23275.bam file. It does not work either for HG00611.bam within the test_data folder either. I have also tried with other bam files that have worked for other PGx programs but am unsure why Cyrius is giving this issue?

xiao-chen-xc commented 2 years ago

The bams in the test_data folder are not WGS bams, so Cyrius won't work if you run it from the command line. Instead the test bams are used for unit testing during development.

Please use a real WGS bam in the manifest file when you run Cyrius from the command line. If that still doesn't work, would you mind showing me one or two lines from your manifest file (the test_filepath txt file)?

joseph-yclam commented 2 years ago

I see, thank you so much! Yes, here is the follow txt file: /CIM_output/CIM005.bam

This file works for other PGx programs but does not for Cyrius? Should it have quotations?

xiao-chen-xc commented 2 years ago

I'm wondering if the path is a relative path, not an absolute path. An absolute path starts from the root directory. If you ls /CIM_output/CIM005.bam, would it work from anywhere outside your current directory? If not, the absolute path should be the output of pwd plus /CIM_output/CIM005.bam.