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TomHarrop / honeybee-genotype-pipeline

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Split runs out of suffixes for draft genomes #7

Closed TomHarrop closed 4 years ago

TomHarrop commented 4 years ago 
2020-09-11 14:02:33 WARNING  mkdir output/010_genotypes/015_ref/regions ; awk '{printf("%s:1-%d\n",$1,$2);}' output/010_genotypes/015_ref/ref.fasta.fai | split -a 4 -l 1 -d - output/010_genotypes/015_ref/regions/r
split: output file suffixes exhausted

This could be resolved with a higher a but I think I can do this with demuxbyname.sh instead

TomHarrop commented 4 years ago 
demuxbyname.sh \
    in=../GCA_014170235.1_ASM1417023v1_genomic.fna \
    out=%.fasta \
    delimiter=whitespace \
    column=1
TomHarrop commented 4 years ago

This works but i'm not sure it makes sense - just read the regions from the FAI???