yu052

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Failed to complete command task: 'rm_individual_seg_files' launched from master workflow,

[pyflow_log.zip](https://github.com/polyactis/Accucopy/files/5560670/pyflow_log.zip) Thanks for your response! I attach the pyflow log files. I have a SNP-sites file for dogs, but I decided to disable the --callRegions because I got a strange...

Failed to complete command task: 'rm_individual_seg_files' launched from master workflow,

I checked that chromosome 33 is indeed in the genome.fa, genome.dict, and genome.fa.fai. It is weird that all the reads in the bam failed to pass the filters, isn't it?...

Failed to complete command task: 'rm_individual_seg_files' launched from master workflow,

Thanks for your response! Actually, I am pretty sure I have good bam files. I checked them in Jbrowse and IGV. Of course, there are mismapped reads, but not much....

Failed to complete command task: 'rm_individual_seg_files' launched from master workflow,

Is it possible to make your program compatible for both format?

Failed to complete command task: 'rm_individual_seg_files' launched from master workflow,

Sorry that I didn't make it clear. I mean the format of the name of the chromosome, chr1 and 1.