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marcelauliano / MitoHiFi

Find, circularise and annotate mitogenome from PacBio assemblies
MIT License
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plant genome with raw HIFI reads #14

Closed m-jahani closed 10 months ago

m-jahani commented 2 years ago

Hi,

Thanks for the excellent tool.

I am trying to run mitohifi with raw reads of a plant genome using the following command:

mitohifi_v2.1.py -r Kalea.merged.ccs.contaminationfree.fasta -f MT361980.1.fasta -g MT361980.1.gb -t 40 -o 1 1>MITOHIFI1.LOG 2> MITOHIFI2.LOG

there were some genes from the reference genome not being recognized by mitofinder, so I modified mitohifi_v2.py code at lines 236 and 286 to include the --new-genes parameter at the mitofinder execution code. (base on https://github.com/marcelauliano/MitoHiFi/issues/11). However, motifhifi could not generate final_mitogenome.fasta and final_mitogenome.gb.

Attached are the log files and a list of files in the result directory.

Any idea what can cause the problem?

Thanks, Mojtaba

lift_files.txt MITOHIFI1.LOG MITOHIFI2.LOG ptg000009l.annotation_MitoFinder.log hifiasm.log ptg000009l_RC.annotation_MitoFinder.log

m-jahani commented 2 years ago

Can you please answer my question? :) Thanks

marcelauliano commented 2 years ago

Hi m-jahani! Can you have a look at the new release v2.2 ? Let me know what you can get with it =)