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sudmantlab / loco-pipe

loco-pipe is an automated Snakemake pipeline that streamlines a set of essential population genomic analyses for low-coverage whole genome sequencing (lcWGS) data
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error reading likelihood genotype matrix 'combined.subsetted.lgm': failed to parse matrix size #4

Open avdanurag opened 1 month ago

avdanurag commented 1 month ago

Hi,

Thank you for developing this wonderful workflow.

I am trying to run loco-pipe workflow with 169 maize samples (BAMs). After the workflow is 47 % complete I get following error I would really appreciate your help about the issue :

Error in rule run_ohana_global: jobid: 319 input: /storage/Anurag/INVITE/pub_data/INVITE_DATA/160-INVITE-WGS/angsd/results/LC_WGS/ohana/global/combined.subsetted.lgm output: /storage/Anurag/INVITE/pub_data/INVITE_DATA/160-INVITE-WGS/angsd/results/LC_WGS/ohana/global/combined.subsetted.k2.q.matrix, /storage/Anurag/INVITE/pub_data/INVITE_DATA/160-INVITE-WGS/angsd/results/LC_WGS/ohana/global/combined.subsetted.k2.f.matrix, /storage/Anurag/INVITE/pub_data/INVITE_DATA/160-INVITE-WGS/angsd/results/LC_WGS/ohana/global/combined.subsetted.k2.done log: /storage/Anurag/INVITE/pub_data/INVITE_DATA/160-INVITE-WGS/angsd/results/LC_WGS/ohana/global/combined.subsetted.k2.log (check log file(s) for error details) conda-env: /storage/Anurag/INVITE/pub_data/INVITE_DATA/160-INVITE-WGS/angsd/results/LCWGS/.snakemake/conda/e1c50c2dcf2ca5a14ed7db05c034bb17 shell:

     qpas /storage/Anurag/INVITE/pub_data/INVITE_DATA/160-INVITE-WGS/angsd/results/LC_WGS/ohana/global/combined.subsetted.lgm          -k 2          -qo /storage/Anurag/INVITE/pub_data/INVITE_DATA/160-INVITE-WGS/angsd/results/LC_WGS/ohana/global/combined.subsetted.k2.q.matrix          -fo /storage/Anurag/INVITE/pub_data/INVITE_DATA/160-INVITE-WGS/angsd/results/LC_WGS/ohana/global/combined.subsetted.k2.f.matrix          -mi 50 &> /storage/Anurag/INVITE/pub_data/INVITE_DATA/160-INVITE-WGS/angsd/results/LC_WGS/ohana/global/combined.subsetted.k2.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

The log file "combined.subsetted.k2.log" : error reading likelihood genotype matrix '/storage/Anurag/INVITE/pub_data/INVITE_DATA/160-INVITE-WGS/angsd/results/LC_WGS/ohana/global/combined.subsetted.lgm': failed to parse matrix size

The "combined.subsetted.lgm" only has "0 0"

Looking forward to your response.

Best regards, Anurag

nicolas931010 commented 1 month ago

Hi Anurag,

Yeah that doesn't sound right. Does the beagle formatted GL file (/storage/Anurag/INVITE/pub_data/INVITE_DATA/160-INVITE-WGS/angsd/results/LC_WGS/angsd/snp_calling_global/combined.subsetted.beagle) seem to be correct and not empty? And did the global PCA work ok? Lastly, did the get_ohana_input_global rule generate some error messages (e.g. check the file inslurm-logs/get_ohana_input_global/?

Best, Nicolas