Error "Same reference genome file should be used in both 'msisensor scan' and 'msisensor msi' steps!!!"

[sclan]

I have tested the example data from within the test folder for the msi scoring function and I noticed that if I specify any of the following argument, with the default values used, the same error message as seen on the subject line "Same reference genome file should be used in both 'msisensor scan' and 'msisensor msi' steps!!!" shows up with empty output files generated.

-m50 -q3 -s5 -w40

When I don't specify them in the command, the tool seems to work as expected (and have the four non-zero output files generated). But aren't those above arguments with the default values automatically applied if not specified in the command line?

(Example) This one generates the error:
msi -d example.microsate.sites -n example.normal.bam -t example.tumor.bam -e example.bed -f0.05 -i1 -c20 -z0 -m50 -w40 -o output

any input is appreciated.

[ZhaoDanOnGitHub]

Hi, if you only use -n specify normal file, -t specify tumor file and -o output file, the other paraters will use the default values. Ｔhe reason you encounter this problem is because there are no spaces between your parameter symbols and values. The correct way to use is：
msi -d example.microsate.sites -n example.normal.bam -t example.tumor.bam -e example.bed -f 0.05 -c 20 -m 50 -o output.

[ZhaoDanOnGitHub]

In addition, the parameter -f is used in paired data( there are both normal and tumor data) to specify the FDR threshold, the parameter -i is used in tumor only data(there is only tumor data) to specify the minimal comentropy threshold for somatic sites detection.