Question: [ Mustang ] Problem with Server
gravatar for ReWeeda
4.1 years ago by
University of Bologna
ReWeeda70 wrote:

Good Morning,

working on a personal project I've recently obtained the accession to a server in order to run Multiple Structural Alignment process on it instead of using my pc that I require for studying (I'm a student).

So, I use MUSTANG to compute the multiple structural alignment over a set of PDB files.

I run mustang with the following command on a Screen form the directory where I've got all the PDB file (Edited and so with just one chain) and the file that list path and pdb id :

mustang -f ListPdbMust21.txt -F ‘fasta’ -r ‘ON’ 2> Output_Error.txt ; echo ‘Must END’ | mail -s ‘PROJECT NOTIFICATION’

Checking the process on the screen the parsing procedure seems to be concluded fine and the computation of the pairwise alignment too. Redirecting the stderr to the Output_Error.txt didn't produce anything.

In spite of this no output files are produced by mustang.

Now I'm quite confused.. Do I miss something about how mustang works on server? There is nothing about it on the mustang manual.

mustang server • 1.1k views
ADD COMMENTlink written 4.1 years ago by ReWeeda70

Is there a file called 'core' in the directory where you ran MUSTANG? I find that it crashes on some inputs after the pairwise alignments, but before producing any output.

ADD REPLYlink written 4.1 years ago by gearoid200

No, nothing called ''core''

ADD REPLYlink written 4.1 years ago by ReWeeda70

Have you tried other inputs? You could just check if it produces an alignment of two chains only, it shouldn't take too long.

I can't see anything wrong with your parameters or anything. If MUSTANG produces an alignment for a different set of files, then it could just be that it's crashing on the original input data.

ADD REPLYlink written 4.1 years ago by gearoid200

I've run mustang over 2 structures and I've also tried specifying directly through the command path and structures.

In both case everything was completed fine and correctly.

I'm not able to explain why, I've applied the same procedure.

ADD REPLYlink written 4.1 years ago by ReWeeda70
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