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tfwillems / HipSTR

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
GNU General Public License v2.0
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Argument list too long #62

Closed SergeyPhys closed 5 years ago

SergeyPhys commented 5 years ago

Hi Thomas,

When I start HipSTR with ~6000 BAM files, I receive the error: "Argument list too long". I found that HipSTR works when number of BAM files is less or about 4000. Could you please change the maximum number of BAM files?

Thanks in advance!

Sergey

tfwillems commented 5 years ago

Hi Sergey,

I don't impose a maximum limit on the number of BAM files that can be provided, so I suspect this error is produced by your scripting environment/operating system, not HipSTR.

Have you tried doing --bam-files bam_list.txt instead of --bams BAM1,BAM2,BAM3...BAM6000. Here, bam_list.txt would be a text file that contains 6000 lines, one per file name.

SergeyPhys commented 5 years ago

Hi Thomas,

Thanks for suggestion! It works!