Segmentation Fault in Fragment picking

[Anonymous]

Hello Everyone

I am trying to generate fragments for a short peptide  (12 residues) to use them further in Flexpepdock. Following are the flag and weight files

Flag file

-in::file::vall /disk/software_sources/rosetta_bin_linux_2018.09.60072_bundle/tools/fragment_tools/vall.apr24.2008.extended.blast.gz

-in::file::fasta seq.fasta

-frags::ss_pred seq.psipred.ss2 predA

-frags::scoring:config weights.wghts

-frags::frag_sizes 3 5 9

-frags::bounded_protocol

-frags::n_candidates            200

-frags::n_frags                 200

# Output 

-out::file::frag_prefix         frags

-frags::describe_fragments      frags.fsc

 

Weights file

# score name priority wght max_allowed extras

SecondarySimilarity 350 1.0 –  predA

RamaScore 400 2.0 –  predA

FragmentCrmsd             0     0.0     –

 

I am getting segmentation fault when I run fragment_picker application.

Following is the stdout

$ /disk/software_sources/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/fragment_picker.static.linuxgccrelease @options

core.init: Rosetta version: rosetta.binary.linux.release-171 r171 2018.09+release.333d996 333d99699777cd6a50d1c1736bacd689f8f1d1df https://www.rosettacommons.org 2018-02-27T09:57:00.705373

core.init: command: /disk/software_sources/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/fragment_picker.static.linuxgccrelease @options

core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=494517936 seed_offset=0 real_seed=494517936

core.init.random: RandomGenerator:init: Normal mode, seed=494517936 RG_type=mt19937

core.init: found database environment variable ROSETTA3_DB: /disk/software_sources/rosetta_bin_linux_2018.09.60072_bundle/main/database

protocols.frag_picker.FragmentPicker: reading a query sequence from: seq.fasta

protocols.frag_picker.FragmentPicker: [ WARNING ] CAUTION: No sequence profile supplied. Profile-dependant options/scoring will not work.

protocols.frag_picker.FragmentPicker: picking fragments for query sequence: IGYCFDCARACMRRGKYIRTCSFERKLCRCSISDIK

protocols.frag_picker.VallProvider: vallChunksFromLibrary

protocols.frag_picker.VallProvider: Reading Vall library from /disk/software_sources/rosetta_bin_linux_2018.09.60072_bundle/tools/fragment_tools/vall.apr24.2008.extended.blast.gz … startline: 1  endline: 0

Segmentation fault (core dumped)

 

Any suggestions as to what might be causing this?

 

Thank you

 

 

[Anonymous]

Dear Ashu4487,

The output indicates that Rosetta died while trying to read the vall file. Your filename vall.apr24.2008.extended.blast.gz indicates that the vall file is compressed. I’m not certain the fragment picker can read a compressed file.

Try uncompressing it with a command like “gzip -d vall.apr24.2008.extended.blast.gz” That should expand the file into a much larger one named “vall.apr24.2008.extended.blast” and you will have to modify your command line to point to that. Let us know if that doesn’t solve your problem.

 

[Anonymous]

Hi

Thanks so much for that.  It seems that was the reason behind segmentation fault.

There were two files vall.apr24.2008.extended.blast.gz and vall.apr24.2008.extended.gz. Decompressing and then passing path for vall.apr24.2008.extended in -in::file::vall did the trick.

Thank you

Best Regards

Ashutosh

 

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