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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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An error in halMergeChroms #1168

Open zhangqing970 opened 1 year ago

zhangqing970 commented 1 year ago

Hi, I was run the cactus by split genome into multiple chromosomes, now i want to merge the HAL file, when i run halMergeChroms, i got this error:

terminate called after throwing an instance of 'hal_exception' what(): Duplicate sequence name found: Anc01.Anc01refChr0 /var/spool/slurm/d/job9356440/slurm_script: line 9: 8590 Aborted (core dumped) halMergeChroms Cactus_Chr01.hal,Cactus_Chr02.hal,Cactus_Chr03.hal,Cactus_Chr04.hal,Cactus_Chr05.hal,Cactus_Chr06.hal,Cactus_Chr07.hal,Cactus_Chr08.hal,Cactus_Chr09.hal,Cactus_Chr10.hal,Cactus_Chr11.hal,Cactus_Chr12.hal,Cactus_Chr13.hal,Cactus_Chr14.hal,Cactus_Chr15.hal Cactus.hal

Can you give me advise on how to fix this error ?

glennhickey commented 1 year ago

halMergeChroms only runs on star trees (ie those used in pangenome alignments). It does not work with Progressive Cactus alignments.

zhangqing970 commented 1 year ago

halMergeChroms only runs on star trees (ie those used in pangenome alignments). It does not work with Progressive Cactus alignments.

Is there any way to merge the HALs ? because the multiple genome alignment is too time cost.