msisensor crashes with error "fail to load bam index"

niu-lab / msisensor2

Microsatellite instability (MSI) detection for tumor only data.

GNU General Public License v3.0

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msisensor crashes with error "fail to load bam index" #10

Open kmavrommatis opened 4 years ago

kmavrommatis commented 4 years ago

Hi, msisensor2 may crash wih the error:

[bam_index_load] fail to load BAM index.

even when the index file is available.

I believe this happens when the full path of the bam and bai files contains the string "bam" at some point e.g.

if I have the bam file test.bam, with index test.bai in a directory /opt/test/ everything works. if the directory is /opt/testbamfiles/ I get the above error.

Thanks

owehann commented 4 years ago

Thank you very much for coming up with this question. I have done the same test and got the same feedback. I also change the pathway of bam file, then it works. Thank you again for your advice, and we will try our best to make MSIsensor2 better.