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liusihan / seGMM

A new tool to infer sex from massively parallel sequencing data.
MIT License
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SegMM running forever #9

Open gopisiva1616 opened 1 year ago

gopisiva1616 commented 1 year ago

Hello, I am trying to determine the gender of a sample from targetted sequencing with the command below and it is just running forever almost a day and I had to kill it. It keeps generating files with weird characters in their names in the Read_stats folder nonstop. seGMM -vcf sample.vcf -i sample.bam -a BAM -t TGS -o $PWD -c xy -s False

I also tried the same using the wes ref file from the repo instead chr x & y with the command below. But it is still the same seGMM -vcf sample.vcf -i sample.bam -a BAM -t TGS -o $PWD -s False -r wes_ref_segmm.txt

Please share your thoughts on this. Thanks.

liusihan commented 1 year ago

Thank you for utilizing seGMM. To accurately determine the gender of samples, a minimum of 10 samples is required. If only a limited number of samples are available for gender prediction, we suggest running seGMM using input files and the provided reference file.

Currently, I am unsure why seGMM took a day to run without encountering any issues or completing the process. As a test, could you please try running seGMM using the 1000G data provided in the test folder? This will help us identify any potential underlying concerns.