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Published 20 hours ago • verified publisher icon caleblareau

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

Open isadeghi87 opened this issue 3 months ago • 1 comments

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 avatar Mar 20 '24 11:03 isadeghi87

Dear @caleblareau , have you found the solution?

best Iman

isadeghi87 avatar Apr 08 '24 08:04 isadeghi87