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NameError: name 'featureName' is not defined #50

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madhubioinfo opened this issue Jul 31, 2023 · 3 comments
Open

NameError: name 'featureName' is not defined #50

madhubioinfo opened this issue Jul 31, 2023 · 3 comments

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@madhubioinfo
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This is the command I have used to run for fungal genomes

singularity run mitofinder_v1.4.1.sif -j A5_mito -s A5_HiFi_reads.fastq -r Rhizophagus_irregularis_DAOM197198_mtDNA.gb -o 1 -p 5 -m 10

I am getting following error
Command line: /opt/MitoFinder/mitofinder -j A5_mito -s A5_HiFi_reads.fastq -r Rhizophagus_irregularis_DAOM197198_mtDNA.gb -o 1 -p 5 -m 10

Now running MitoFinder ...

Start time : 2023-07-31 16:01:30

Job name = A5_mito

Creating Output directory : /home/eniac/A5_mito
All results will be written here

Program folders:
MEGAHIT = /opt/MitoFinder/megahit/
MetaSPAdes folder = /opt/MitoFinder/metaspades/bin/
IDBA-UD folder = /opt/MitoFinder/idba/bin/
Blast folder = /opt/MitoFinder/blast/bin/
ARWEN folder = /opt/MitoFinder/arwen/
MiTFi folder = /opt/MitoFinder/mitfi/
tRNAscan-SE folder = /opt/MitoFinder/trnascanSE/tRNAscan-SE-2.0/

Traceback (most recent call last):
File "/opt/MitoFinder/mitofinder", line 574, in
featureName = ''.join(featureName.split())
NameError: name 'featureName' is not defined

@RemiAllio
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Owner

Hi,

Please, could you send me the file Rhizophagus_irregularis_DAOM197198_mtDNA.gb?
It seems that something is wrong with this file...

Thank you,
Rémi

@madhubioinfo
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madhubioinfo commented Aug 2, 2023

Rhizophagus_irregularis_DAOM197198_mtDNA.zip
Hi,
Please find the attached file

@RemiAllio
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Owner

Hi,

Unfortunately, this file needs some edits to be usable by MitoFinder.
I can make these edits but otherwise, the easiest way to use MitoFinder on your sample might be to use this reference instead.

Also, since you are using HiFi reads, I would recommend to perform the assembly before using MitoFinder (with a dedicated software) and give the assembly to MitoFinder using the -aoption.

Let me know if it helps,
Best,
Rémi

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