Dear ModPipe community
I managed to install modpipe in our system, but I'm struggling to test
it. If I try to run the demo sequence using mode 0010 (providing the
missing databases in the configuration file) I get the following error:
$ ../main/ModPipe.pl --conf_file modpipe.conf --sequence_id
97e075794f588a59e8a0fb8a945814b1MLGIKIKP --hits_mode 0010
--score_by_tsvmod OFF
MPLib::MPModules::GetProfile__M> Found profile for sequence
MPLib::MPModules::GetProfile__M> Seqid :
97e075794f588a59e8a0fb8a945814b1MLGIKIKP
MPLib::MPModules::GetProfile__M> Profile:
/nfs/[...]/modpipe-2.2.0/demo//data/97e/97e075794f588a59e8a0fb8a945814b1MLGIKIKP/sequence/97e075794f588a59e8a0fb8a945814b1MLGIKIKP-uniprot90.prf
MPLib::MPModules::GetProfile__M> Will use the above profile
MPLib::MPModules::GetProfile__M> PRFUPDATE: OFF
MPLib::MPUtils::CopyXPRFDB__M> No. of structure profiles in database: 39330
*PLLib::Modeller::RunModeller__E> MODELLER failed: exited with value 1**
**HitsPrfPrf.pl__E> MODELLER failed on profile:
97e075794f588a59e8a0fb8a945814b1MLGIKIKP-uniprot90.prf**
**MPLib::MPModules::GetHitsPP__E> Failed to calculate hits (0010):
97e075794f588a59e8a0fb8a945814b1MLGIKIKP**
*MPLib::MPModules::GetHitsPP__E>
/nfs/[...]/modpipe-2.2.0/src/HitsPrfPrf.pl --alignment_basename
97e075794f588a59e8a0fb8a945814b1MLGIKIKP-prfprf-0010
--set_score_statistics ON --output_alidir
97e075794f588a59e8a0fb8a945814b1MLGIKIKP-prfprf-0010-ali --hitfile_name
97e075794f588a59e8a0fb8a945814b1MLGIKIKP-prfprf-0010.hits
--ccmatrix_offset -100 --profile_list
/nfs/[...]/modpipe-2.2.0/dbs/pdb95/db/pdb95_prf.list --pdb_repository
/nfs/[...]/modpipe-2.2.0/demo//db/pdb --target_profile
97e075794f588a59e8a0fb8a945814b1MLGIKIKP-uniprot90.prf --score_type
CCMAT --gap_extend_cost -70 --custom_tag "MODELLER Prf-Prf (0010)"
--profile_pssmdb /nfs/[...]/modpipe-2.2.0/dbs/pdb95/db/pdb95_prf.pssm
--target_code 97e075794f588a59e8a0fb8a945814b1MLGIKIKP --summary_file
97e075794f588a59e8a0fb8a945814b1MLGIKIKP-prfprf-0010.sum --gap_open_cost
-700 --e_value 1
ModPipe.pl__E> Failed to get Prf-Prf hits (0010):
97e075794f588a59e8a0fb8a945814b1MLGIKIKP
When running the modeller command from the tmp directory the following
ABNORMAL TERMINATION error appears:
$ /nfs/[...]/modpipe-2.2.0/ext/mod/bin/modpy.sh /nfs/[...]/bin/python2
97e075794f588a59e8a0fb8a945814b1MLGIKIKP-prfprf.py
MODELLER 9.13, 2014/02/12, r9876
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2014 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux [...]
2.6.32-358.14.1.el6.x86_64 x86_64
Date and time of compilation : 2014/02/11 22:46:42
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2014/06/05 13:57:11
*alloc_p_215E> Dynamic memory allocation failed.**
** Routine, variable, status: ipssm 3**
***** ABNORMAL TERMINATION of Modeller. This is a bug**
** in Modeller. Please report it to the Modeller**
** developers, including any input files necessary**
** to reproduce the problem.*
Directory names and hostname have been redacted.
The configuration file that has been used it's identical as the one
provided in the modpipe website as an example, with the addition of the
XPRF_LIST and XPRF_PSSMDB variables.
Thanks for your help,
Marco
--
Marco Galardini
Postdoctoral Fellow
EMBL-EBI - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, UK
Phone: +44 (0)1223 49 2547
