V3 does not analyze nt datasets

[AntonioBaeza]

Hello. This is part of the message provided by the program. I have tried many thinks but nothing appears to work when I want to analyze nt. The aa analysis runs properly. Your comments will be appreciated.

Gene ID successfully identified all missing genes for all samples.
[ 78 ] sequences extracted for gene ATP6
[ 78 ] sequences extracted for gene ATP8
[ 78 ] sequences extracted for gene COX1
[ 78 ] sequences extracted for gene COX2
[ 78 ] sequences extracted for gene COX3
[ 78 ] sequences extracted for gene CYTB
[ 78 ] sequences extracted for gene ND1
[ 78 ] sequences extracted for gene ND2
[ 78 ] sequences extracted for gene ND3
[ 78 ] sequences extracted for gene ND4
[ 78 ] sequences extracted for gene ND4L
[ 78 ] sequences extracted for gene ND5
[ 78 ] sequences extracted for gene ND6
[ 78 ] sequences extracted for gene ATP6
[ 78 ] sequences extracted for gene ATP8
[ 78 ] sequences extracted for gene COX1
[ 78 ] sequences extracted for gene COX2
[ 78 ] sequences extracted for gene COX3
[ 78 ] sequences extracted for gene CYTB
[ 78 ] sequences extracted for gene ND1
[ 78 ] sequences extracted for gene ND2
[ 78 ] sequences extracted for gene ND3
[ 78 ] sequences extracted for gene ND4
[ 78 ] sequences extracted for gene ND4L
[ 78 ] sequences extracted for gene ND5
[ 78 ] sequences extracted for gene ND6
[ 78 ] sequences extracted for gene rrnL
[ 78 ] sequences extracted for gene rrnS

Extracted sequences can be found in Lontra_out3/results/3.sequences

PHYLOGENETIC ANALYSIS

Mode: pcg
Characters: nt
Command: /home/ant/MitoPhAST-master/V3.0/bin/build_trees.pl -in Lontra_out3/results/3.sequences -out Lontra_out3/work/phylogenetics -mito_gcode 2 -mode pcg -chars nt -bb on -bbrep 1000 -alrt on -alrtrep 1000 -cpu 13 -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: cannot stat 'Lontra_out3/work/phylogenetics/2.buildtree/.tre': No such file or directory
cp: cannot stat 'Lontra_out3/work/phylogenetics/2.buildtree/.fasta': No such file or directory
cp: cannot stat 'Lontra_out3/work/phylogenetics/2.buildtree/*.phy': No such file or directory

Alignment and tree files can be found in Lontra_out3/results/4.trees

Error: Pipeline terminated - tree building step failed

[lcdallagnol]

Hello, how are you?
Were you able to solve this problem?
The same thing is happening to me.
If you can help me, I really appreciate it.

Yours sincerely,
Lilian.

[AntonioBaeza]

Hi lcdallagnol. I was not able. I am not using this software anymore. The software is not being maintained and there is no communication from the developers. Some colleagues are considering this software deprecated at this point in time.

[lcdallagnol]

Hello, Antonio!
I thank you very much for your quick feedback.
I'm trying to solve it, but I'm not succeeding.
Which software are you using now?

[AntonioBaeza]

Doing the analysis manually plus a couple of modest scripts
how many species are you working with?

[lcdallagnol]

I'm analyzing 56 sequences.

[AntonioBaeza]

write me to my email [email protected] with details if you wish

[lcdallagnol]

Perfect!
Thank you very much.