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Generate structural fragments

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Generate structural fragments
#1

Hello everyone,when I run "/rosetta/fragments/nnmake/make_fragments.pl -nopsipred -nosam -nojufo -noprof -verbose trhl2.fasta",I got the error follow:
[root@localhost input]# /rosetta/fragments/nnmake/make_fragments.pl -nopsipred -nosam -nojufo -noprof -verbose trhl2.fasta
Run options:
be verbose.
don't run psipred.
don't run prof.
don't run jufo.
don't run sam.
FILENAME: trhl2.fasta
no id specified. parse filename instead.
INTERMEDIATE: trhl2.fasta
ID: trhl CHAIN: 2
Warning: can't find executable file /work/chu/src/shareware/psipred/bin/psipred!
Warning: can't find executable file /work/chu/src/shareware/psipred/bin/psipass2!
Warning: can't find executable file /rosetta/fragments/chemshift/pCHEMSHIFT.gnu!
Warning: can't find executable file /work/chu/src/shareware/jufo/molecule.exe!
Warning: can't find executable file /sam/bin/target99!
Warning: can't find executable file /sam/bin/uniqueseq!
Warning: can't find executable file /sam/sam.predict-2nd/!
Warning: can't find executable file /sam/sam.predict-2nd/predict-2nd!
Sequence: MFIVWLWVGFAMAASVVADRSKLPPACDSMIYCHGPLLNTVQMAGLYNDSKTFVDMKIKMSPNITLEHFYDMMSRTDSNPTKADIQEFVNQNFDPEGSEFEDWRPSDWKHNPGFLAKIKDPLLHKWASALNDLWLDLGRKMKEAVKESPDLYSIIYVEHPFIVPGGRFREFYYWDSYWIIKGLLLSEMRTTAKGMVNNLLSIVDRYGFIPNGGRIYYLMRSQPPLLIPMVQLLMEDTDDLEYLREHIHTLDKEFDYWMTNHTIEVNHEGKKLKMAMYMDNSQGPRPESYKEDVDCARHFDTTEKKEELYAELKAAAESGWDFSSRWFILNGTNKGNLTNLKVRSIIPVDLNAILCWNAQLMMEYHTRLQNEEKASYYRRIHDDFMEAIEELLWHEDVGVWLDYSLESSRRRDYFYPSNLSPLWAGSYDKARKDYFVNRVVNYLDKVKMDIFEGGIPTTFEHTGEQWDYPNAWPPLQYIVIMGLANTGHPEAMRYATELATKWVRSNFEVWKQKAAMLEKYDATILGGLGGGGEYVVQTGFGWSNGVVMSLLNRYGDVISAADNFGTAAESGAVYGAGVGAGGVVTALLVVLASLAAGTLGLMVYKRRKDYAGFCNGEVDKLISKKPYTELKSLNGASNQKQR
cmd is: /blast/bin/blastpgp -t T -i trhl2.fasta -F F -j2 -o trhl2.blast -d /blast/db/nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C trhl2.check -Q trhl2.pssm
[blastpgp] WARNING: a standard checkpoint file should have extension ".chk".

cmd is: /blast/bin/blastpgp -t T -i trhl2.fasta -F F -j2 -o trhl2.blast -d /blast/db/nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C trhl2.check -Q trhl2.pssm
[blastpgp] WARNING: a standard checkpoint file should have extension ".chk".

checkpoint psi-blast failed!

Post Situation: 
Tue, 2011-05-10 20:18
kingljy

You will need to use at least two secondary structure predictions for fragment generation to make sense, but that's not the problem here. It seems that blast is failing. Try running the blast command directly to get a better idea of what's going on. That is, type

/blast/bin/blastpgp -t T -i trhl2.fasta -F F -j2 -o trhl2.blast -d /blast/db/nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C trhl2.check -Q trhl2.pssm

If this fails, check the paths for the blastpgp executable and the nr database and update make_fragments.pl as necessary.

Tue, 2011-05-24 10:48
weitzner

I'm running the same script on Ubuntu and ran into the same error. I found that the make_fragment.pl script was looking for checkpoint files with a .check extension rather than a .chk extension... I'm not sure what the difference is between them or even if the make_fragments.pl script included in the Rosetta 3.4 release is correct. Has anyone run make_fragments.pl successfully recently? If so, what tools did you install, how much customization was necessary to get it running?

Wed, 2012-06-06 11:54
pepfolder