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RemiAllio / MitoFinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
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Error while annotating assembled mitochondrion #11

Closed kimnegrette3 closed 3 years ago

kimnegrette3 commented 4 years ago

Hi! I have an assembled mitochondrion from a microalgae (Scenedesmaceae). I was trying to annotate it with this command line:

mitofinder -j Sdimorphus -a mt_Sdim_flye_consensus.fasta -r mitochondrions_sphaeropleales_refseq.gb -o 22

But I got this error:

Traceback (most recent call last): File "/home/kim/MitoFinder/mitofinder", line 635, in geneOut=open("ref_"+name+"_database.fasta",'a') IOError: [Errno 2] No such file or directory: 'ref_hypotheticalreversetranscriptase/maturase_database.fasta'

I guess it has something to do with the reference file? I downloaded a genbank file directly from NCBI using "mitochondrion" AND "sphaeropleales" search terms and filtering by RefSeq and sequence length, as described here.

I appreciate any suggestions.

Thank you very much!

RemiAllio commented 4 years ago

Hi!

Thank you for your comment.

It seems that in your reference, there is at least one gene name with a "/" inside. In this precise case that is : "hypothetical reverse transcriptase/maturase"

To avoid this issue, you just need to remove/replace the "/" in the gene name (in the genbank file). Sorry for the inconvenience. Your issue will be taken into account for the next version of MitoFinder.

Thank you, Cheers, Rémi

kimnegrette3 commented 4 years ago

Thank you for your prompt answer. That solved the problem! Many thanks, and best regards!

RemiAllio commented 3 years ago

Hi!

This bug has been taken into account for the new version of MitoFinder (v1.4)

Thanks again! Rémi