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0xTCG / biser

A fast tool for detecting and decomposing segmental duplications in genome assemblies
MIT License
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ERROR: BISER failed (-9): #26

Closed dorachu625 closed 10 months ago

dorachu625 commented 1 year ago

Hi，when I ran BISER v1.4 on one genome, it failed with an error "ERROR: BISER failed (-9)". How to solve this problem? Thank you so much.
Command is as follows: biser -o new.sd -t 20 --gc-heap 1G --keep-contigs genome.fa

file genome.fa is soft-maskered and indexed with samtools.

inumanag commented 1 year ago

Hi @dorachu625

One way is to add --gc-heap to the run and lower the number of threads (see #29 for details). Try -t 2 and --gc-heap 10G.

Which genome you are analyzing? Some genomes---especially ones that are not filtered---are tricky. I suggest doing RepMasker first with the complete uncurated dfam before running BISER on contig genomes (note: RepMasker might take from a day to weeks to complete depending on the genome). This will tremendously speed up BISER and improve the quality of calls.

shokrof commented 9 months ago

I am trying to run BISER on Bos Taurus masked genome from this link (https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/bosTau9.fa.masked.gz) and I am getting -9 error. I have tried setting --gc-heap to 2,10,200,400GB, also I tried to decrease the number of threads to 2. I am running on an HPC cluster running on Linux.