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niu-lab / msisensor2

Microsatellite instability (MSI) detection for tumor only data.
GNU General Public License v3.0
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Failed Creating DMatrix #1

Open EgirardBioinfo opened 4 years ago

EgirardBioinfo commented 4 years ago

Hi, I have this issue for some samples and not other for the same design. "Failed Creating DMatrix"

I use these parameters : "-c 0 -p 5 -s 3 -M /data/kdi_prod/.kdi/project_workspace_0/1320/acl/01.03/msisensor2/models_hg19"

Do you have an idea of what's going wrong ? Thanks

Beifang commented 4 years ago

It should be caused by too low coverage of the input data. As it happens，that is to say that there is no any site with enough reads for MSI analysis. We will give a warning message in the code soon. We can train a dedicated model for you if you have enough data.

YingYa commented 3 years ago

I have the same issue for some WGS (~60X) samples and not other for the same design. The program at the same site: ...... window: 321 done...:chr3:58500688-58502688 Failed Creating DMatrix

The parameters are : msi -M /path/to/models_hg38 -t /path/to/sample.bam -c 15 -b 4 -o /path/to/sample.MSIsensor2

Does this is possible for WGS data?

Thanks

owehann commented 3 years ago

This possibility cannot be ruled out. In particular, this error started in chr3. Try using paramates ‘-M/-t/-o’ only.