Error_fragment_generation – Rosetta Commons

This topic has 6 replies, 4 voices, and was last updated 3 years, 1 month ago by Anonymous.

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February 12, 2016 at 8:11 pm #2377
Anonymous
Hi

I was running makefragments.pl for my short length peptide (sequence length 6), as a pre-requirement for abinito FlexPepDock, and I am getting the error:

Error: expected creation of t001_.200.9mers after running “/path/to/make_fragments.pl/fragment_picker.static.linuxgccrelease @t001__picker_cmd_size9.txt -j 1′!

It was working fine before, but with two abnormalities:

a. It was generating only 3 and 9 mers(no 5 mer): so I corrected the make_fragments.pl, where in “my @fragsizes” definition “5” was missing.

b. Also, it was only giving me out the .cfg, ._ss2 and other similar files but no fragment library. I noticed that “$options{n_frags} = 200;” was muted.

Before changes:
```
my @cleanup_files  = ();

my @fragsizes      = ( 3, 9 );  #4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20 );

my @add_vall_files = ();

my @use_vall_files = ();

my @pdbs_to_vall   = ();

#$options{n_frags}      = 200;

$options{n_candidates} = 1000;
```
After changes:
```
my @cleanup_files  = ();

my @fragsizes      = ( 3, 5, 9 );  #4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20 );

my @add_vall_files = ();

my @use_vall_files = ();

my @pdbs_to_vall   = ();

$options{n_frags}      = 200;

$options{n_candidates} = 1000;
```
Could you please help me out to trobleshoot it.

Thanks

Payal
February 14, 2016 at 11:53 am #11437
Anonymous
Hello Payal,

From what I understand, you have successfully ran fragment picker for the same inputs, but before editing the make_fragments.pl file. The reason you edited it, is because you wanted to set the n_frags option to 200, and the fragsizes option to include 5-mers.

First, you should know that you can specify the command line options -n_frags and -frag_sizes to set those options. For example:
```
make_fragments.pl -frag_sizes 3,5,9 -n_frags 200 my_input.fasta
```
If you are unsure what options are available, use
```
make_fragments.pl -help
```
Second, it seems that fragment_picker app (the Rosetta application which does the actual fragment-picking) fails when producing the 9-mer. This means perhaps that all previous steps completed? Can you see other error messages? Since the 9-mer picking part failed, you should see the output log for the fragment_picker app. Can you attach it, so we can identify what went wrong?

Last but not least – can you specify which version of Rosetta you are trying to run? The make_fragments.pl scripts has gone through some changes over the past year or two.

Hope this helps,

Yuval
February 15, 2016 at 8:35 am #11439
Anonymous
Thanks Yuval

The version is 3.10.

I am hereby attaching the log file, and would try as suggested by you after this. Also, I am attaching a screenshot of the files obtained after.

Thanks

Payal
February 15, 2016 at 11:28 pm #11442
Anonymous
Hi I tried using make_fragments.pl -frag_sizes 3,5,9 -n_frags 200 my_input.fasta, but it still yields the same result.

Thanks

Payal

September 10, 2021 at 8:16 am #16010

Anonymous

Hello members,

I have been trying since many days to run make_fragment.pl. I tried to first run install_dependecies.pl standard uniref90 as default nr always fails to download.

Afterwards when I run the make_fragments.pl script, I encounter lot of errors and warnings as following:





ILENAME: t001_.fasta

Sequence: YPSKPDNPGEDAPAEDLARYYSALRHYINLAARQRY

Running sparks for phi, psi, and solvent accessibility predictions

running psiblast for sequence: t001_.fasta

[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /opt/rosetta_bin_linux_2021.16.61629_bundle/main/tools/fragment_tools/sparks-x/blast-NR/nr.01.

[blastpgp] WARNING: Unable to open nr.46.pin

[blastpgp] WARNING: Unable to open nr.47.pin

[blastpgp] WARNING: Unable to open nr.48.pin

[blastpgp] WARNING: Unable to open nr.49.pin

[blastpgp] WARNING: Unable to open nr.50.pin

[blastpgp] WARNING: Unable to open nr.51.pin

[blastpgp] WARNING: Unable to open nr.52.pin

[blastpgp] WARNING: Unable to open nr.53.pin

[blastpgp] WARNING: Unable to open nr.54.pin

[blastpgp] WARNING: Unable to open nr.55.pin

[blastpgp] WARNING: readdb: wrong version of formatdb was used to make database /opt/rosetta_bin_linux_2021.16.61629_bundle/main/tools/fragment_tools/sparks-x/blast-NR/nr.01.





ERROR: Error reading in FragmentPicker::read_spine_x(): does not match size of query!

ERROR:: Exit from: src/protocols/frag_picker/FragmentPicker.cc line: 1180



[ ERROR ]: Caught exception:





File: src/protocols/frag_picker/FragmentPicker.cc:1180

[ ERROR ] UtilityExitException

ERROR: Error reading in FragmentPicker::read_spine_x(): does not match size of query!





AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.





Finished running command: /opt/rosetta_bin_linux_2021.16.61629_bundle/main/tools/fragment_tools/../../../main/source/bin/fragment_picker.default.linuxgccrelease @t001__picker_cmd_size3.txt -j 0

Output: core.init: Checking for fconfig files in pwd and ./rosetta/flags

core.init: Rosetta version: rosetta.binary.linux.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:52:25.363712

core.init: command: /opt/rosetta_bin_linux_2021.16.61629_bundle/main/tools/fragment_tools/../../../main/source/bin/fragment_picker.default.linuxgccrelease @t001__picker_cmd_size3.txt -j 0

basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1961974647 seed_offset=0 real_seed=1961974647

basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1961974647 RG_type=mt19937

protocols.frag_picker.FragmentPicker: reading a query profile from: t001_.checkpoint

protocols.frag_picker.FragmentPicker: picking fragments for query profile: YPSKPDNPGEDAPAEDLARYYSALRHYINLAARQRY

protocols.frag_picker.FragmentPicker: reading a query sequence from: t001_.fasta

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



Error: expected creation of t001_.200.3mers after running '/opt/rosetta_bin_linux_2021.16.61629_bundle/main/tools/fragment_tools/../../../main/source/bin/fragment_picker.default.linuxgccrelease @t001__picker_cmd_size3.txt -j 0'!

I will be thankful to all of you if you could help me run this script.

Kind regards

Mustafa

February 24, 2016 at 4:47 pm #11456
Anonymous
From your included log file, it looks like there might be issues with making the PSSM for the protein. What is your peptide like, and do you get anything when you BLAST it (e.g. using http://blast.ncbi.nlm.nih.gov/Blast.cgi)?

Also, what output do you get if you run the
```
/home/lyna/rosetta_workshop/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/static/fragment_picker.static.linuxgccrelease @pep00_picker_cmd_size9.txt -j 1
```
command directly?

February 24, 2016 at 6:35 pm #11458

Anonymous



core.init: Rosetta version exported  from http://www.rosettacommons.org

core.init: command: /home/lyna/rosetta_workshop/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/static/fragment_picker.static.linuxgccrelease @pep00_picker_cmd_size9.txt -j 1

core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-15295745 seed_offset=0 real_seed=-15295745

core.init.random: RandomGenerator:init: Normal mode, seed=-15295745 RG_type=mt19937

protocols.frag_picker.FragmentPicker: reading a query profile from: pep00.checkpoint

protocols.frag_picker.FragmentPicker: picking fragments for query profile: PLFAAR

protocols.frag_picker.FragmentPicker: reading a query sequence from: pep00.fasta

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

protocols.frag_picker.VallProvider: vallChunksFromLibrary

protocols.frag_picker.VallProvider: Reading Vall library from /shared/home/lyna/rosetta_workshop/rosetta/tools/fragment_tools/vall.jul19.2011 ... startline: 1  endline: 0

protocols.frag_picker.VallProvider: ... done.  Read 4126307 lines.  Time elapsed: 72 seconds.

protocols.frag_picker.VallProvider: Total chunks: 25463

protocols.frag_picker.VallProvider: Largest chunk: 1264 aa

core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set.  Created 42632 residue types

core.chemical.ResidueTypeSet: Total time to initialize 1.49 seconds.

protocols.frag_picker.FragmentPicker: Will pick fragments of size:9

protocols.frag_picker.FragmentPicker: Creating fragment scoring scheme

protocols.frag_picker.scores.ProfileScoreL1: Profile scoring method is: L1

protocols.frag_picker.scores.ProfileScoreL1: Created cache for fraglen: 9

protocols.frag_picker.scores.ProfileScoreStructL1: Profile scoring method is: L1

protocols.frag_picker.scores.ProfileScoreStructL1: Created cache for fraglen: 9

basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts

basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts

basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts

basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_F.counts

basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts

basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_F.counts

basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts

basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts

basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts

basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts

basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts

basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts

protocols.frag_picker.FragmentPicker: Picking 200 fragments based on 1000 candidates

protocols.frag_picker.FragmentPicker: Creating fragment scoring scheme for the selection step

protocols.frag_picker.FragmentPicker: Collector for fragment size: 9 set to: BoundedCollector

protocols.frag_picker.FragmentPicker: Fragment scoring scheme used:

id    fragment score method name   weight

1                 ProfileScoreL1    1

2            SecondarySimilarity    1

3           SolventAccessibility  1.5

4                      RamaScore  0.8

5                            Phi    1

6                            Psi  0.6

7           ProfileScoreStructL1    4



protocols.frag_picker.FragmentPicker:

fragment_picker: After setup; size of a query is: 6

fragment_picker: Picking candidates

fragment_picker: Running bounded protocol

protocols.frag_picker.FragmentPicker: pick fragments using bounded protocol...

protocols.frag_picker.FragmentPicker: Picking candidates...

Segmentation fault

Thanks for the response. Attached above is what I got after running the provided command directly.

My peptide is a 6-residues long peptide (PLFAAR)-which is also a part of the protein PDB Id 3JAV (http://www.rcsb.org/pdb/results/results.do?qrid=37D144BC&tabtoshow=Current). I obtained this by doing a sequence motif advance search on RCSB. I also did a BLAST for the same, but did not yield relevant results.