virtual memory error - scan ref genome

[arorarshi]

I am trying to run msisensor on a few samples from targeted sequencing data. I get an error at the scan step.

Reference genome – b37 GATK version
Command - msisensor scan -d GATKresources/b37/human_g1k_v37.fasta -o msisensor.b37.microsatellites.list

Error –
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted (core dumped)

The virtual memory limit is 8Gb.
The log shows going through all 22 chromsomes.

scanning chomosome 20 done. 152 secs passed
scanning chomosome 21 done. 154 secs passed
scanning chomosome 22 done. 156 secs passed

However the output of scan, file msisensor.b37.microsatellites.list , stops at chromosome 1.
1 46462340 3 57 3 138 202 TGC AGAGG ATAGG
1 46462400 1 0 5 179 539 A AGTAT GACGT
1 46462417

I was able to run the test sample correctly. Any advice will be helpful!
In case you have uploaded the microsatellites list for b37, please let me know.

Thanks!

[ZhaoDanOnGitHub]

Hi,

Because the data of human_f1k_v37.fasta is vary big, your virtual memory is not enough for scan step. Though your virtual memory is 8Gb, I think your virtual memory has been occupied by other programs.I suggest you change another computer with larger memory to run it again.

Thanks

[preciserobot]

I have the same problem on a machine with 16GB of memory. The scanning continues up to chromsome 22 but only chromosome 1 is written.

[Beifang]

Bug fixed. please try again, thanks.

[preciserobot]

Seems to have fixed the issue for me. Many thanks for the fast response!