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ay-lab / mustache

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
MIT License
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.hic -ch error/Docker update? #51

Closed jaclyn-marie closed 2 years ago

jaclyn-marie commented 2 years ago

Hi @aylab,

I am trying to run mustache right now from a .hic file and it keeps throwing errors due to options not recognized (-st), and -chr needing to have at least one argument. I would like to run for all chromosomes. I tried running -ch all and -ch and I tried inputting multiple chromosomes in different ways (with/without commas and chr) and mustache is unable to proceed. See examples of error messages below:

usage: mustache [-h] [-f F_PATH] -o OUTDIR -r RESOLUTION [-bed BED] [-m MAT] [-b BIASFILE] [-pt PT] [-sz S_Z] [-oc OCTAVES] [-i S] [-p NPROCESSES] -ch CHROMOSOME [-v VERBOSE] mustache: error: unrecognized arguments: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

usage: mustache [-h] [-f F_PATH] -o OUTDIR -r RESOLUTION [-bed BED] [-m MAT] [-b BIASFILE] [-pt PT] [-sz S_Z] [-oc OCTAVES] [-i S] [-p NPROCESSES] -ch CHROMOSOME [-v VERBOSE] mustache: error: unrecognized arguments: chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX

I think this might be due to the version of mustache in the image versus the current available. Are there any plans to update the Dockerfile/Docker Image with the latest version of mustache? It would be greatly appreciated!!

Sincerely, Jaclyn

jaclyn-marie commented 2 years ago

My apologies, calling all chromosomes works with the dovetailg/mustache:latest Docker image.