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