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
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:
If you are unsure what options are available, use
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
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
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
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
command directly?
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.
Thanks
Payal
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:
I will be thankful to all of you if you could help me run this script.
Kind regards
Mustafa