"gene not recognized"

[quattrinia]

Hi Remi,

I am having more trouble with gene name errors in v 1.4 than 1.2. Clearly. the gene COX2 is in the ref list. Any ideas? I could use --new genes or --ignore but wondering if I am missing something.
Thanks!
Andrea

ERROR: Gene named "COX2" in the reference file(s) are not recognized by MitoFinder
This gene is not a standard mitochondrial gene (use --ignore or --new-genes options) or please change it to one of the following gene names:
COX1; COX2; COX3; CYTB; ND1; ND2; ND3; ND4; ND4L; ND5; ND6; ATP8; ATP6; rrnL; rrnS

[RemiAllio]

Hi Andrea,

I am very sorry to hear that you have more trouble using the v1.4 than the v1.2...

This error is surprising, I honestly don't know what is happening here.
Could you share the reference file with me to see if I can reproduce the error and find out from where it came?

Thank you!
Best,
Rémi

[quattrinia]

Yea it is quite odd! Here is the file
Thanks for the help~
Andrea
antipath.ref.gb.txt

[RemiAllio]

Thank you for the file.
Using the singularity image of the version 1.4.1 I could not reproduce the error.
I only find the HEG gene not recognized by MitoFinder.

Did you try to use the singularity image to avoid any installation issue?
Best,
Rémi

[quattrinia]

Interesting. I am trying to get singularity installed...I dont have root permissions. And, I am on the go installation step right now and had some difficulties there. I will update you when I make some progress
Thanks!
Andrea

[Surbhigrewal]

Hi Remi,

I'm having a similar issue. I get the following in the scaffold_xxx.annotation_MitoFinder.log file. It does this for all potential mito contigs and stalls while making the scaffold_xxx.annotation folder and does not complete the annotation process. I am using the --new-genes setting but the scaffold_xxx.annotation_MitoFinder_mitfi_Final_Results folder doesn't populate with the required files. See attached zip file for one of these folders.
Are you able to point to what is it that might be stalling the pipeline. I cannot install singularity on my work mac so would really appreciate any help.
...
Gene named "rps4" in the reference file is not recognized by MitoFinder.
MitoFinder will try to annotate it.

WARNING: COX2 is not in the reference file. MitoFinder will not annotate this gene.
WARNING: ND1 is not in the reference file. MitoFinder will not annotate this gene.
WARNING: ND2 is not in the reference file. MitoFinder will not annotate this gene.
WARNING: ND5 is not in the reference file. MitoFinder will not annotate this gene.
WARNING: rrnL is not in the reference file. MitoFinder will not annotate this gene.
WARNING: rrnS is not in the reference file. MitoFinder will not annotate this gene.
Formatting database for mitochondrial contigs identification...
Running mitochondrial contigs identification step...

MitoFinder found a single mitochondrial contig
Checking resulting contig for circularization...

Evidences of circularization could not be found, but everyother step was successful

Creating summary statistics for the mtDNA contig
...

scaffold_679.annotation.zip

[RemiAllio]

Hi,

Since you are working on Mac, could you please confirm that you have followed all the installation steps described here?

Then, could you please share the geneChecker_error.log and geneChecker.log files?

Thanks,
Rémi