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caleblareau / mgatk

mgatk: mitochondrial genome analysis toolkit
http://caleblareau.github.io/mgatk
MIT License
101 stars 27 forks source link

Improper folder specification; file missing / extra file present. See documentation #90

Open isadeghi87 opened 6 months ago

isadeghi87 commented 6 months ago

Found bam file: /home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Result/10x_multiomics/CellRanger_ARC/1016715_pool3_hg38/outs/gex_possorted_bam.bam for genotyping. Wed Mar 20 12:38:37 CET 2024: Found file of barcodes to be parsed: /home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Code/bulkWGS/Sadeghi/mgatk/barcodes.tsv Wed Mar 20 12:38:39 CET 2024: User specified mitochondrial genome matches .bam file Wed Mar 20 12:43:06 CET 2024: Finished determining/splitting barcodes for genotyping. Wed Mar 20 12:43:12 CET 2024: Genotyping samples with 20 threads Error in checkGrep(grep(".A.txt", files)) : Improper folder specification; file missing / extra file present. See documentation Calls: importMito -> checkGrep Execution halted

isadeghi87 commented 5 months ago

Dear @caleblareau , have you found the solution?

best Iman

Eomesodermin commented 3 months ago

Did you find a work around for this issue?