Tried different BAM files. Always get Number of sites with enough coverage: 0

[sisyphus-deng]

Greetings,

Here is the command we tried on the test bam file (actually, we also tried the program on our own bam files, and get the same result).

msisensor-ct msi -D -M ./models_hg38 -t ./test/example.cfdna.hg38.bam -o ~/output.prefix

Then we get

*** Summary information ***

Number of total sites: 1459
Number of sites with enough coverage: 0
Number of MSI sites: 0
MSI score(%): 0

Total time consumed:  1 secs

The somatic file is empty and the result file is as below.

Total_Number_of_Sites   Number_of_Somatic_Sites %
0   0   0.00

However, the output.prefix_dis file looks correct.

2733:chr22 29286892 AAAGC 12[T] CTCTT
2734-T: 0 0 0 0 0 0 0 0 25 71 4 86 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2735:chr22 29655716 TGGGC 16[T] GCCTT
2736-T: 0 0 0 0 0 0 0 1 1 3 2 5 9 11 9 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

The T-N paired model seems correct. For example, (I know it is nonsense to use the same bam file as both tumor and normal, but I only would like to test if it can determine the correct coverage) msisensor-ct msi -D -M ./models_hg38 -t ./test/example.cfdna.hg38.bam -n ./test/example.cfdna.hg38.bam -o ~/output.prefix

It can figure out that there are 2 sites with enough coverage.

*** Summary information ***

Number of total sites: 1459
Number of sites with enough coverage: 2
Number of MSI sites: 0
MSI score(%): 0

Total time consumed:  2 secs

Thank you.

[lilicai]

Greetings,

This is a problem with the permissions of the models directory. Change the directory permissions of ./models_hg38 to 777 ,it can run correctly. Refer to the command,

chmod -R 777 ./models_hg38'

I hope that your problem can be solved.

Best wishes .