Problem running make_fragments.pl script

[Anonymous]

Hi ALL,

I am trying to run the make_fragments.pl program to generate fragment files to be used in structure prediction. In it i am using PSI-PRED and PROF as the ss prediction tools. However while executing the script I am getting the following error:

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Sequence: NLYIQWLKDGGPSSGRPPPS
running prof.
cmd is: /md1/anirbang/Software/ROSETTA/rosetta_fragments/nnmake/run_prof.py 1l2y_.fasta ss_blast 1l2y_.prof_rdb
psiblast_file= ss_blast round: 1 nseq: 0 max_e: 0
psiblast_file= ss_blast round: 2 nseq: 0 max_e: 0
/md1/anirbang/Software/Prof/src/Prof tmp0.922131.align fileRdb=tmp0.666513.out sec ascii
bad option tmp0.922131.align
bad option fileRdb=tmp0.666513.out
bad option sec
bad option ascii
file of secondary structure output not found
In automatic mode :
usage is Prof -A -v -d -m 0 -i [filename in fasta format] -b [database name for psiblast] -o [filename for the output]
Or if you want a casp format as output
usage is Prof -c -v -d -m 0 -i [filename in fasta format] -b [database name for psiblast] -o [filename for the output]

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In non-automatic mode :
usage is Prof -A -v -d -m 1 -a [Output from clustalw in aln format] -p [Output profil form psi-blast] -o [filename for the output]
Or if you want a casp format as output
usage is Prof -c -v -d -m 1 -a [Output from clustalw in aln format] -p [Output profil form psi-blast] -o [filename for the output]

file of sequence not found. With option [-m 0] need file of sequence in fasta format.
prof failed: maybe too many sequences?? 1
Traceback (most recent call last):
File “/md1/anirbang/Software/ROSETTA/rosetta_fragments/nnmake/run_prof.py”, line 323, in ?
data = open(tmp_outfile,’r’)
IOError: [Errno 2] No such file or directory: ‘tmp0.666513.out’
cmd is: /md1/anirbang/Software/ROSETTA/rosetta_fragments/nnmake/run_prof.py 1l2y_.fasta ss_blast 1l2y_.prof_rdb
psiblast_file= ss_blast round: 1 nseq: 0 max_e: 0
psiblast_file= ss_blast round: 2 nseq: 0 max_e: 0
/md1/anirbang/Software/Prof/src/Prof tmp0.532689.align fileRdb=tmp0.151388.out sec ascii
bad option tmp0.532689.align
bad option fileRdb=tmp0.151388.out
bad option sec
bad option ascii
file of secondary structure output not found
In automatic mode :
usage is Prof -A -v -d -m 0 -i [filename in fasta format] -b [database name for psiblast] -o [filename for the output]
Or if you want a casp format as output
usage is Prof -c -v -d -m 0 -i [filename in fasta format] -b [database name for psiblast] -o [filename for the output]

---

In non-automatic mode :
usage is Prof -A -v -d -m 1 -a [Output from clustalw in aln format] -p [Output profil form psi-blast] -o [filename for the output]
Or if you want a casp format as output
usage is Prof -c -v -d -m 1 -a [Output from clustalw in aln format] -p [Output profil form psi-blast] -o [filename for the output]

file of sequence not found. With option [-m 0] need file of sequence in fasta format.
prof failed: maybe too many sequences?? 1
Traceback (most recent call last):
File “/md1/anirbang/Software/ROSETTA/rosetta_fragments/nnmake/run_prof.py”, line 323, in ?
data = open(tmp_outfile,’r’)
IOError: [Errno 2] No such file or directory: ‘tmp0.151388.out’
prof failed.

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Can you please tell me what is going wrong here? Why PROF is not running, although the standalone version of PROF is running fine. Any suggestion is welcome. Thanks a lot.

Regards,

Anirban

[Author]

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