Bed file not loading

[PriyaMilne]

Hi,

I am running the msisensor msi command as below:

msisensor msi -d microsatellites.list -n example_normal_bam.bam -t example_tumour_bam.bam –e my_targetedregions.bed -o target_region_msi.tsv

However, it seems like the bed file is not loading, as according to some of the answers that I have seen here, I would expect something like:

loading bed regions ...
loading homopolymer and microsatellite sites ...
Total loading windows: n

However, mine goes straight to:

loading homopolymer and microsatellite sites ...
Total loading windows: 5810
Total loading homopolymer and microsatellites: 1766632

Why is the command not just taking the windows in my bed file? Any help would be very much appreciated.

Thanks.

[ZhaoDanOnGitHub]

@PriyaMilne
I think there may be two reasons for this. First, because the bed file you entered does not exist, the bed file cannot be opened. Second, you do not have the bed file permission. It is recommended that you check if the name of the bed file is spelled correctly and whether you can access file.