Missing [Seq_ID]_final_genes_NT.fasta file in final results

[pedrogribeiro]

Dear Rémi,

These are rather general question but I think this is still the best channel to ask them since you were very helpful with a previous inquiry of mine.
I used the following array script to run Mitofinder with Megahit. I had done it before with a very similar script and in the end I got a [Seq_ID]_final_genes_NT.fasta file containing all genes found. Nonetheless, this time I am only getting .gb and .fasta files for the contigs. Is there any particular reason why this might be happening?
Also, do you have any recommendations about how to do a "scaffolding" with the assembled contigs? For some samples there is only a single contig of around 15500bp (which is expected for my species), but some times there are up to 6 contigs.

The script is as follows:

#!/bin/bash

#PBS -N mitofinder_ARRAY_SPopGen_2023
#PBS -l select=1:ncpus=8:mem=50gb:scratch_local=300gb
#PBS -l walltime=47:59:00
#PBS -o /storage/brno2/home/pedroribeiro/Projects/Spicauda_PopGen/PBS/out/^array_index^_mitofinder_ARRAY_SPopGen.txt
#PBS -e /storage/brno2/home/pedroribeiro/Projects/Spicauda_PopGen/PBS/err/^array_index^_mitofinder_ARRAY_SPopGen.txt
#PBS -J 1-88

#clean scratch after the end
trap 'clean_scratch' TERM EXIT

# go to scratch directory
cd $SCRATCHDIR || exit 1

export TMPDIR=$SCRATCHDIR

source /storage/brno2/home/pedroribeiro/.bashrc

forward=`sed -n -e "$PBS_ARRAY_INDEX p" /storage/brno2/home/pedroribeiro/Projects/Spicauda_PopGen/raw_reads/forward.list`
reverse=`sed -n -e "$PBS_ARRAY_INDEX p" /storage/brno2/home/pedroribeiro/Projects/Spicauda_PopGen/raw_reads/reverse.list`
seqid=`sed -n -e "$PBS_ARRAY_INDEX p" /storage/brno2/home/pedroribeiro/Projects/Spicauda_PopGen/raw_reads/seqid.list`

cp /storage/brno2/home/pedroribeiro/Projects/Spicauda_PopGen/raw_reads/$forward.fastq $SCRATCHDIR
cp /storage/brno2/home/pedroribeiro/Projects/Spicauda_PopGen/raw_reads/$reverse.fastq $SCRATCHDIR

singularity run -B $SCRATCHDIR  /storage/brno2/home/pedroribeiro/software/mitofinder_latest.sif \
 --megahit -j $seqid.mitogenome \
 -1 /storage/brno2/home/pedroribeiro/Projects/Spicauda_PopGen/raw_reads/$forward.fastq \
 -2 /storage/brno2/home/pedroribeiro/Projects/Spicauda_PopGen/raw_reads/$reverse.fastq \
 -r /storage/brno2/home/pedroribeiro/Projects/Spicauda_PopGen/mito_reference/mito_reference.gb \
 -o 5 \
 -p 8 \
 -m 50

cp -r *.mitogenome* /storage/brno2/home/pedroribeiro/Projects/Spicauda_PopGen/out_mitogenes_for_iqtree/

Thank you very much!

All the best,

Pedro Ribeiro

[RemiAllio]

Hi Pedro,

I am using MitoFinder on my side for a current project and I get the [SeqID]_final_genes_NT.fasta file as expected.
I don't know what's going on on your side. Hopefully we will find something!
Otherwise it's quite easy to generate this file.

Did you check the geneChecker_error.log and geneChecker.log files?

Let me know if you find something in these logs 🙂
Best,
Rémi

[pedrogribeiro]

Hi!

I see!

The geneChecker_error.log is empty and I checked geneChecker.log which says:

Organism type specified: 5
alignCutOff: 30.0
coveCutOff: 7
Checking protein-coding genes, tRNAs and rRNAs from reference with organismType=5...
Formatting database for blast...
Formatting database for blast...
rrnL
rrnS
Features found: 14
Total features: 15

Running tRNA annotation with mitfi
Total features found after mitfi:  37

Could not import Image or ImageDraw library, no image of result being created.

Otherwise, could you point me in some direction to generate the [SeqID]_final_genes_NT.fasta file? All of the .gb files from the assembled contigs are being normally copied to my output directory.

Many thanks!

Best,

Pedro