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bcgsc / straglr

Tandem repeat expansion detection or genotyping from long-read alignments
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Problem with --trf_args #27

Open ilariastewart opened 8 months ago

ilariastewart commented 8 months ago

No matter what values I assign to --trf_args, I get this error: straglr.py: error: argument --trf_args: expected 7 arguments

For reference, here is the command I am running

sbj=PBMC_XXXX
bam=/mnt/seq/GRCh38/${sbj}/${sbj}.GRCh38.sorted.bam
fa_ref=/mnt/VNTR/VNTR_gene_strglr/hg38.fa
output=PBMC_XXXX_straglr
loci_bed=/mnt/vntr_region_motifs.e.bed

# Provide the TRF arguments, such as Match, Mismatch, Delta, PM, PI, Minscore, MaxPeriod
trf_args="2 7 7 80 10 50 500"

python /mnt/VNTR/VNTR_gene_strglr/straglr-master/straglr.py $bam $fa_ref $output --loci $loci_bed --debug --trf /home/ilaria99/TRF --trf_args $trf_args
readmanchiu commented 8 months ago

I think you are using one of the forks out there, as I noticed from the command line there is a --trf parameter which is not available from Straglr. I did try setting up the trf_args variable like you did and it worked fine. So please use the software from our repo, you can either clone it or install it via Bioconda