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tangerzhang / ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
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threads and time #186

Open Rhia15 opened 1 month ago

Rhia15 commented 1 month ago

Hi, I was wondering how long allhic should take to run? I am currently running the pruning step on an autotetraploid and it is still running after 4 days, I was just wondering if this is normal or if I should be doing something else? :)

Thank you for any advice!

This is the command I put in: ./ALLHiC_prune -i /gpfs01/home/mbars7/COFF001/hetero_hifi_hic/Allele.ctg.table -t 96 -b /gpfs01/home/mbars7/COFF001/HiC_aligned.bam -r /gpfs01/home/mbars7/COFF001/COFF001.fastq.gz

Rhia15 commented 1 month ago

Sorry I just wanted to add to this, would separating homologous groups to reduce scaffolding complexity decrease the run time of the pruning step?

Thank you!