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wwylab / MuSE

Somatic point mutation caller
GNU General Public License v2.0
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Segmentation fault error #15

Closed balayev1 closed 11 months ago

balayev1 commented 11 months ago

Hello, Thank you for making the tool. I'm getting a Segmentation fault error upon running 'MuSE sump' command. I'm currently using MuSE version 2.0.3. The first step of the pipeline (i.e. MuSE call) has finished successfully with called mutations (link below) but second one fails with 'Segmentation fault'. Here is the command used: /home/aventeic/balay011/MuSE/MuSE sump -I /scratch.global/balay011/WGS_skChordomas_Bai/SomaticSNV_calling/work/muse/samples/462/462.MuSE.txt -O 462.MuSE.vcf -G -n 8 Segmentation fault

I'm using following resources: srun -N 1 --cpus-per-task 8 --mem-per-cpu=16gb -t 5:00:00 -p interactive --pty bash

Google drive link to gunzipped file: https://drive.google.com/file/d/1ZhDoFBLdWjFAuHNumpVqY3RBscaMSoYq/view?usp=drive_link

Thanks for your help.

Kind regards, Agshin

jiyunmaths commented 11 months ago

Hi @balayev1, thank you for reporting this issue. I will fix it and update the repo soon.

jiyunmaths commented 11 months ago

Hi @balayev1 , I found why the error occurred. MuSE sump needs a snp database as one of the input. If you have not downloaded it, I refer you to download the Homo_sapiens_assembly38.dbsnp138.vcf.gz and its index file 'Homo_sapiens_assembly38.dbsnp138.vcf.gz.idx' from https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0. Then you can run MuSE sump again use the command home/aventeic/balay011/MuSE/MuSE sump -I /scratch.global/balay011/WGS_skChordomas_Bai/SomaticSNV_calling/work/muse/samples/462/462.MuSE.txt -O 462.MuSE.vcf -G -n 8 -D path_to_Homo_sapiens_assembly38.dbsnp138.vcf.gz. Please let me know if you have more questions. Thanks.

balayev1 commented 11 months ago

Thank you very much for your help!!!