search

KCCG / mity

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data
MIT License
36 stars 3 forks source link

Error in gsort #18

Closed Pharmacogenetecist closed 2 years ago

Pharmacogenetecist commented 2 years ago

I get the following error when running mity call

mity call \

--prefix transplant \ --out-folder-path "output/" \ --region MT:1:500 \ --normalise \ "x.bam" \ "x2.bam" \ "x3.bam" Found dependency: /home/ec2-user/anaconda3/envs/MITY/bin/freebayes Found dependency: /home/ec2-user/anaconda3/envs/MITY/bin/gsort Found dependency: /home/ec2-user/anaconda3/envs/MITY/bin/tabix Found dependency: /home/ec2-user/anaconda3/envs/MITY/bin/bgzip Found dependency: /home/ec2-user/anaconda3/envs/MITY/bin/python Found dependency: /home/ec2-user/anaconda3/envs/MITY/bin/mity mity version 0.4.0 Calling mitochondrial variants Running FreeBayes in sensitive mode No variants in VCF with specified chromosome/s Writing normalised vcf: /transplant.mity.vcf.gz gsort version 0.1.4 2022/10/05 21:09:15 error from gsort.Sorterror reading/writing header: error peaking for header: EOF

Pharmacogenetecist commented 2 years ago

Never mind, found my error: Was the MT:1:500 Should be MT: 1-500