SDTMPI [error in line 179]

[Alison Lima]

Dear Brejnev:

I hope everything is fine with you! Some time ago I got in touch and your recommendations on SDT were very helpful for my research group. Once again, I would like to count on you...

I have a large dataset (about 3,000 sequences of 400 nt each) and would like to use SDTMPI, but when I test it, I get the following warning:

##################################################################
alison@beagle:~/Desktop/SDTMPI_Linux64$ mpiexec -n 2 python SDTMPI_Linux64.py test.fas muscle
Total pairs 45         :        proc  0     aligning pairs   0  -  45
Total pairs 45         :        proc  0     aligning pairs   0  -  45
Traceback (most recent call last):
  File "SDTMPI_Linux64.py", line 179, in <module>
    os.remove(name_in)    #removing the alignment input file
OSError: [Errno 2] No such file or directory: '/home/alison/Desktop/SDTMPI_Linux64/bin/0__1.fas'
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[16513,1],1]
  Exit code:    1
--------------------------------------------------------------------------

##################################################################

In fact, there is no a file named 0__1.fas in the bin directory (the files within the directory are 0__1algn.fas, 0__2algn.fas, 0__2.fas, clustalw2, muscle3.8.31_i86linux64 and neighbor)

What should I do to solve this problem?

Once again, thank you for your attention

Prof Alison T M Lima

Federal University of Uberlandia

[Brejnev Muhire]

Have you changed the mode of muscle3.8.31_i86linux64 to execulable?

eg. chmod +x muscle3.8.31_i86linux64

Similar should also be done to other programs within the same folders.

[Alison Lima]

Yes, I have! But I get the same warning...

[Brejnev Muhire]

Hi Alison,

There seem to be a strange problem.

would you want to comment the line

os.remove(name_in)    #removing the alignment input file

as 

#os.remove(name_in)    #removing the alignment input file

and rerun the program. we shall see where the problem comes from. In this case it will not remove the fasta files of pairs of sequences whithin the bin/ directory. but it should show another error possibly.