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0xTCG / biser

A fast tool for detecting and decomposing segmental duplications in genome assemblies

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biser long run time .

ASBioinfo opened this issue · comments

commented

Hi,
Thanks for your tool,
I experienced a long runtime (10 Days) with 2TB ram and 96 core system on cattle genome(~3 GB).
The below steps are performed accordingly to hardmask the genome:-

  1. Repeatmask used on raw FASTA file with soft masking.
  2. Trf finder is also used on raw FASTA file and output coordinates are saved in bed format.
  3. bedtools maskfasta used on Repeatmasker output file and Trf bed file as input for final hard-masking of the genome

Then hardmask fasta file is analyzed with biser , with the below command:

biser -T TEMP -t 80 -o output.txt --keep-contigs --no-decomposition --max-error=20 --max-edit-error=10 ./ref.masked.fasta

Please suggest if any changes are required .

Thank You

commented

I am aware of this issue; #19 will have a fix soon.

commented

Please try v1.4--- the issue should be fixed now.