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

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isadeghi87 opened this issue Mar 20, 2024 · 2 comments

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@isadeghi87
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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
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Dear @caleblareau , have you found the solution?

best
Iman

@Eomesodermin
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Did you find a work around for this issue?

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