rosetta_2013wk52: make_fragments.pl failed

[Anonymous]

Hi there,
Here goes a cut&paste of the rosetta_2013wk52 make_fragments.pl output.
This is a kind of low priority since Rosetta-3.5 make_fragments is running just fine.
Also, I could not be able to complete fragment_picker with the extra option boost.
Best

###############
cmd is: /home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/psipred/bin/psipass2 /home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/psipred/data/weights_p2.dat 1 1.0 1.0 psipred_ss2 psipred_ss > psipred_horiz
psipred file ok.
Command: /home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/../../main/source/bin/fragment_picker.default.linuxgccrelease @query_picker_cmd_size3.txt -j 8

ERROR: Error reading in FragmentPicker::read_spine_x(): does not match size of query!
ERROR:: Exit from: src/protocols/frag_picker/FragmentPicker.cc line: 1239
Finished running command: /home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/../../main/source/bin/fragment_picker.default.linuxgccrelease @query_picker_cmd_size3.txt -j 8
Output: core.init: Rosetta version unknown from unknown
core.init: command: /home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/../../main/source/bin/fragment_picker.default.linuxgccrelease @query_picker_cmd_size3.txt -j 8
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=83764020 seed_offset=0 real_seed=83764020
core.init.random: RandomGenerator:init: Normal mode, seed=83764020 RG_type=mt19937
protocols.frag_picker.FragmentPicker: reading a query profile from: query.checkpoint
protocols.frag_picker.FragmentPicker: picking fragments for query profile: EMVFGKDALLGPRRPRPHKIWKKKYIKLIVVGDSGLGKTTLIKSLISIPGERLQVHDGSYTPTEQFRRDPESLSSTVSWRDEEDRVIWVYKIQDTPGYGDELDVFRNLKMVQDYIESQNRKWLELEQARDRKEDLAEIEDPRVDLCIFCIPPHRLRPIDLKYMFELGKHVPVVPVVTKADTMTIREANTYRTEVANRIANPMVPGIHDKINIFKFERDTLERAGVQDHATPHPPFLVIASNDISEELAAAEPPLFWPERRYPWGTAEAFNKEHSDLLAVRALLMKEALEEISKTKRARYEAWRRTTLG
protocols.frag_picker.FragmentPicker: reading a query sequence from: query.fasta
protocols.frag_picker.FragmentPicker: picking fragments for query sequence: EMVFGKDALLGPRRPRPHKIWKKKYIKLIVVGDSGLGKTTLIKSLISIPGERLQVHDGSYTPTEQFRRDPESLSSTVSWRDEEDRVIWVYKIQDTPGYGDELDVFRNLKMVQDYIESQNRKWLELEQARDRKEDLAEIEDPRVDLCIFCIPPHRLRPIDLKYMFELGKHVPVVPVVTKADTMTIREANTYRTEVANRIANPMVPGIHDKINIFKFERDTLERAGVQDHATPHPPFLVIASNDISEELAAAEPPLFWPERRYPWGTAEAFNKEHSDLLAVRALLMKEALEEISKTKRARYEAWRRTTLG
caught exception

[ERROR] EXCN_utility_exit has been thrown from: src/protocols/frag_picker/FragmentPicker.cc line: 1239
ERROR: Error reading in FragmentPicker::read_spine_x(): does not match size of query!

[Anonymous]

It looks like something might be off with your “sparks” runs. When you run make_fragments.pl, it should output a “name.phipsi” file in the working directory. How does that file compare between the Rosetta3.5 and the rosetta_2013wk52 runs for the same protein?

If they’re different, if you replace the wk52 file with the 3.5 file and manually run the “/home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/../../main/source/bin/fragment_picker.default.linuxgccrelease @query_picker_cmd_size3.txt -j 8” command, does it still give you the same error?

[Anonymous]

You are right. The file.phipsi from Rosetawk52 has the header only. Copying that one from rosetta-3.5 to rosettawk52 directory solve the problem. I’ll try to figure out is going on with the sparks run. Thanks.

[Anonymous]

I couldn’t be able to figure out whats going wrong with the script buildinp_mat.pl from sparks. Actually, I barely can read Perl.
It seems a quote problem. It is intriguing that this is the same script from Rosetta-3.5 sparks, which is working just fine. Any help is appreciated.
Thanks in advance.

######################## SCREEN OUTPUT #########################
Running sparks for phi, psi, and solvent accessibility predictions
running psiblast for sequence: t001_.fasta
Unquoted string “a” may clash with future reserved word at /home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/sparks-x/SPINE-X/bin/buildinp_mat.pl line 64.
Unquoted string “z” may clash with future reserved word at /home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/sparks-x/SPINE-X/bin/buildinp_mat.pl line 64.
Name “main::inpfetfl” used only once: possible typo at /home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/sparks-x/SPINE-X/bin/buildinp_mat.pl line 11.
At line 180 of file phipsi_ss0.f
Fortran runtime error: Bad real number in item 1 of list input
Aborting: Can’t run first SS0 predictor
Error in file: t001_.fasta.phipsi
Traceback (most recent call last):
File “/home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/sparks-x/bin/buildinp.py”, line 255, in run1
buildinp(fphipsiss, fmat, finp)
File “/home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/sparks-x/bin/buildinp.py”, line 238, in buildinp
seq1, ssec1, phipsi1, Fphipsi = rdphipsi(fphipsiss)
File “/home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/sparks-x/bin/buildinp.py”, line 9, in rdphipsi
for line in file(fn):
IOError: [Errno 2] No such file or directory: ‘t001_.fasta.phipsi’
sparks failed!

[Anonymous]

From what I can tell (I don’t have much experience with Sparks), it’s likely there’s an issue with the PSSM file that’s being used. Is there a difference between the two PSSMs that are coming out of the psiblast runs?

[Anonymous]

Dear rmoretti,
Thanks for your replay. The problem has been solved downgrading from Perl-5.14.4 to Perl-5.12.5.
Best.

P.S.: Just by chance. In some rosetta apps I’ve seen a warning like “old frag file format…”. Is there any difference/improvement between frag files from rosetta-3.5 and rosetta52wk?

[Anonymous]

Not that I’m aware of, at least not format-wise. If there’s been improvements it’s been in things like improved valls, better incorporation of secondary structure prediction, different quota schemes, etc.

I think the message you’re referring to is actually “rosetta++ fileformat detected! Calling legacy reader”, so the “old” file format is older than Rosetta3.5. I’m not quite sure what benefits the “new” format has, but the old format certainly works, so it’s not a big deal if that’s what your fragment files are in.

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