Problem in the sequence concatenation stage

[lcdallagnol]

Dear Mun,

I'm using MithoPhast and I'm encountering a recurring problem. I have tried to change several parameters, but I still can't solve it.

Problem encountered:

[ 3 ] sequences extracted for gene COX1
[ 3 ] sequences extracted for gene ND1
[ 3 ] sequences extracted for gene COX2
[ 3 ] sequences extracted for gene COX2
[ 3 ] sequences extracted for gene CYTB
[ 3 ] sequences extracted for gene ND5
[ 3 ] sequences extracted for gene COX3
[ 3 ] sequences extracted for gene ND1
[ 3 ] sequences extracted for gene CYTB
[ 3 ] sequences extracted for gene ND4
[ 2 ] sequences extracted for gene rrnS
[ 3 ] sequences extracted for gene ND2
[ 3 ] sequences extracted for gene ND4
[ 3 ] sequences extracted for gene ND3
[ 2 ] sequences extracted for gene rrnL
[ 3 ] sequences extracted for gene ATP6
[ 3 ] sequences extracted for gene ATP6
[ 3 ] sequences extracted for gene COX3
[ 3 ] sequences extracted for gene ND4L
[ 3 ] sequences extracted for gene ND2
[ 3 ] sequences extracted for gene ND3
[ 3 ] sequences extracted for gene ATP8
[ 3 ] sequences extracted for gene ATP8
[ 3 ] sequences extracted for gene ND5
[ 3 ] sequences extracted for gene ND6
[ 3 ] sequences extracted for gene COX1
[ 3 ] sequences extracted for gene ND4L
[ 3 ] sequences extracted for gene ND6

Extracted sequences can be found in analysis_out/results/3.sequences

PHYLOGENETIC ANALYSIS

Mode: custom
Characters: nt
Command: /media/inlab2/dados3/Lilian_Dallagnol/MitoPhast/MitoPhAST-master/V3.0/bin/build_trees.pl -in analysis_out/results/3.sequences -out analysis_out/work/phylogenetics -mito_gcode 5 -mode custom -pcg ATP6, -chars nt -bb on -bbrep 1000 -alrt on -alrtrep 1000 -cpu 1 -interactive on

Save run configurations: OK
Check genes: OK
Check characters: OK
Check files: OK

Check taxa: OK
Aligning sequences...done.
Concatenating sequences...
An error has occurred during concatenation, run terminated
cp: não foi possível obter estado de 'analysis_out/work/phylogenetics/2.buildtree/.tre': Arquivo ou diretório inexistente
cp: não foi possível obter estado de 'analysis_out/work/phylogenetics/2.buildtree/.fasta': Arquivo ou diretório inexistente
cp: não foi possível obter estado de 'analysis_out/work/phylogenetics/2.buildtree/*.phy': Arquivo ou diretório inexistente

Alignment and tree files can be found in analysis_out/results/4.trees

Error: Pipeline terminated - tree building step failed

I would be very happy if you could help me.

Yours sincerely,

Lilian.