Mitochondrial contigs were detected after blast, but no results were written in to <Sample_ID>_mitfi_Final_Results folder

[Menglinhsy]

Hi Remi,

Recently, we found mitochondrial contigs were detected according to the blast results (IDXX_blast_ouT.txt), but no results were written into folder _mitfi_Final_Results.

We assumed that it was probably because of some threshold settings. So is there any way to change the settings, or is there any other reasons?

Here i attached one example.

73.txt

73.zip

Best wishes, Menglin

[RemiAllio]

Hi Menglin,

Could you please send me all the files generated by MitoFinder (log file + output directory)? I am just wondering if MitoFinder finished the job.

If so, there are several options to deal with threshold setting:

-e BLASTEVAL, --blast-eval BLASTEVAL
                        e-value of blast program used for contig
                        identification and annotation. Default = 0.00001
--blast-identity-nucl BLASTIDENTITYNUCL
                        Nucleotide identity percentage for a hit to be
                        retained. Default = 50
--blast-identity-prot BLASTIDENTITYPROT
                        Amino acid identity percentage for a hit to be
                        retained. Default = 40
--blast-size ALIGNCUTOFF
                        Percentage of overlap in blast best hit to be
                        retained. Default = 30

Tell me if it helps, Cheers, Rémi

[Menglinhsy]

Hi, Remi,

Thanks for your reply and suggestions, I will try that.

but which .py file should I go and change these parameters?

here is all the output.

73.zip

Best, Menglin

[RemiAllio]

Hi Menglin,

Thank you for the files. Indeed, MitoFinder didn't find mitochondrial contigs given the threshold used. There is also a threshold for the size of the contig to be considered. By default, contigs smaller than 1000 bp are not considered. You can change this threshold using the following argument:

--contig-size-min CONTIGSIZEMIN
                        Minimum size of a contig to be considered. Default =
                        1000

To change the parameters you need to specify them in the command line. For example:

mitofinder -j 73 -a 73.fasta -r sequence.gb -o 5 -p 10  --blast-eval 0.00001 --blast-identity-nucl 50 --blast-identity-prot 40 --blast-size 30 --contig-size-min 300

I hope this helps. Best, Rémi

[RemiAllio]

Hi Menglin,

Did my previous message help you? Can I close this issue?

Best, Rémi

[Menglinhsy]

Hi, Remi,

Sorry for the late reply. it works!

Thanks a lot!

Best, Menglin

[RemiAllio]

Hi,

Great! I am happy we found the solution :-)

Best, Rémi