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zeeev / wham

Structural variant detection and association testing
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Bam file not being read #57

Closed drashwinelkar closed 1 year ago

drashwinelkar commented 3 years ago

I am running whamg of the docker container : wham:1.8.0.1.2017.05.03--hd28b015_0 I have provided and index and sorted bam file which is the output of bwa mem with the -R option.

I get the following error when I run whamg- INFO: fasta file: ChAdOx1nCov19_scaffolds_RC.fa INFO: gathering stats (may take some time) for bam: DNA2_wham_sorted.bam terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr Aborted (core dumped)

My read length is 75 bp, paired end sequencing. I tried switching the docker versions but I get the same error, it must be something with my bam file. The bam file is perfectly valid for other SV calling tools that need it.

zeeev commented 1 year ago

My reply is too late to be useful, but it could be a ref file mismatch?