biser long run time .
ASBioinfo opened this issue · comments
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:-
- Repeatmask used on raw FASTA file with soft masking.
- Trf finder is also used on raw FASTA file and output coordinates are saved in bed format.
- 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
I am aware of this issue; #19 will have a fix soon.
Please try v1.4--- the issue should be fixed now.