start at 2016-03-14 20:24:57 #------------------------------------------------ Running PconsC2... /home/ubuntu/pconsc2//PconsC2//run_pconsc2_nj1.py -c 8 --p_psi 2 --p_plm 1 /data/hhsuite/uniprot20_2015_06/uniprot20_2015_06 /data/blastdb/uniref90.fasta /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta *********************************************************************** PconsC2 : Improved contact predictions using the recognition of protein like contact patterns. *********************************************************************** If you use PconsC2 for contact prediction, please cite: Skwark M.J., Raimondi D., Michel M.. and Elofsson A. "Improved contact predictions using the recognition of protein like contact patterns." ----------------------------------------------------------------------- Testing dependencies... Dependencies OK. 2016-03-14 20:24:57.935612 jhE4: generating Jackhmmer alignment This may take quite a few minutes! 2016-03-14 20:35:58.080487 jhE0: generating Jackhmmer alignment This may take quite a few minutes! 2016-03-14 20:44:27.679691 jhE10: generating Jackhmmer alignment This may take quite a few minutes! 2016-03-14 20:50:27.732258 jhE40: generating Jackhmmer alignment This may take quite a few minutes! 2016-03-14 20:53:19.569876 hhE4: generating HHblits alignment This may take quite a few minutes! 2016-03-14 20:54:12.397798 hhE0: generating HHblits alignment This may take quite a few minutes! 2016-03-14 20:54:34.754334 hhE10: generating HHblits alignment This may take quite a few minutes! 2016-03-14 20:54:50.849221 hhE40: generating HHblits alignment This may take quite a few minutes! 2016-03-14 20:55:08.465774 jhE4: running PSICOV This may take more than an hour. 2016-03-14 20:55:08.467974 jhE0: running PSICOV This may take more than an hour. 2016-03-14 20:55:20.716653 jhE10: running PSICOV This may take more than an hour. 2016-03-14 20:55:21.041183 jhE40: running PSICOV This may take more than an hour. 2016-03-14 20:55:33.484143 hhE4: running PSICOV This may take more than an hour. 2016-03-14 20:55:34.722170 hhE0: running PSICOV This may take more than an hour. 2016-03-14 20:55:46.295003 hhE10: running PSICOV This may take more than an hour. 2016-03-14 20:55:48.219154 hhE40: running PSICOV This may take more than an hour. 2016-03-14 20:56:01.993171 jhE4: running plmDCA This may take more than an hour. debug: commandline: /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE4.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE4.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-14 20:58:44.966444 jhE0: running plmDCA This may take more than an hour. debug: commandline: /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE0.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE0.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-14 21:01:19.039337 jhE10: running plmDCA This may take more than an hour. debug: commandline: /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE10.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE10.plmdca 0.01 0.01 0.1 8 workers='8' Segmentation fault (core dumped) 2016-03-14 21:03:45.175004 jhE40: running plmDCA This may take more than an hour. debug: commandline: /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE40.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE40.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-14 21:06:09.110854 hhE4: running plmDCA This may take more than an hour. debug: commandline: /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE4.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE4.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-14 21:09:13.191764 hhE0: running plmDCA This may take more than an hour. debug: commandline: /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE0.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE0.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-14 21:12:51.322458 hhE10: running plmDCA This may take more than an hour. debug: commandline: /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE10.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE10.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-14 21:15:47.349696 hhE40: running plmDCA This may take more than an hour. debug: commandline: /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE40.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE40.plmdca 0.01 0.01 0.1 8 workers='8' Running PconsC2... 2016-03-14 21:18:42.721955: running NetSurfP This may take quite a few minutes! defined(%hash) is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/FASTA.pm line 369. (Maybe you should just omit the defined()?) defined(%hash) is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/FASTA.pm line 372. (Maybe you should just omit the defined()?) Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 11. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 11. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 12. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 13. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 14. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 20. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 20. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 22. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 23. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 30. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 36. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 37. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 39. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 42. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 49. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 104. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 105. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 106. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 108. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 108. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 108. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 108. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 110. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 111. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 123. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 124. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 125. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 127. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 127. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 127. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 127. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 148. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/ACT.pm line 154. mkdir: cannot create directory '/scratch/NetSurfP_28747': Permission denied cp: cannot create regular file '/scratch/NetSurfP_28747': Permission denied Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 11. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 11. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 12. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 13. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 14. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 20. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 20. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 22. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 23. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 30. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 36. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 37. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 39. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 42. Using a hash as a reference is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/HOW.pm line 49. defined(%hash) is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/FASTA.pm line 369. (Maybe you should just omit the defined()?) defined(%hash) is deprecated at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/modules/FASTA.pm line 372. (Maybe you should just omit the defined()?) can't open file /scratch/NetSurfP_28747/file.inp: No such file or directory at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/scripts/make_prof.pl line 87. 2016-03-14 21:18:42.913038: running Psipred This may take quite a few minutes! Predicting... Parsing NetSurfP Parsing PSIPRED Parsing PSSM Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE4.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE4.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE0.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE0.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE10.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE10.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE40.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE40.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE4.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE4.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE0.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE0.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE10.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE10.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE40.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE40.plmdca Coalescing data Loading RF 0 Predicting layer 0 Coalescing data Loading RF 1 Predicting layer 1 Loading RF 2 Predicting layer 2 Loading RF 3 Predicting layer 3 Loading RF 4 Predicting layer 4 Loading RF 5 Predicting layer 5 /home/ubuntu/pconsc2/PconsC2/dependencies/psipred/psipred3.5/runpsipred /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.fasta Running time for PconsC2 is 3671 seconds #------------------------------------------------ Running PconsC1... /home/ubuntu/pconsc2//PconsC2//run_pconsc2_nj1.py -c 8 --p_psi 2 --p_plm 1 --pconsc1 /data/hhsuite/uniprot20_2015_06/uniprot20_2015_06 /data/blastdb/uniref90.fasta /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta *********************************************************************** PconsC2 : Improved contact predictions using the recognition of protein like contact patterns. *********************************************************************** If you use PconsC2 for contact prediction, please cite: Skwark M.J., Raimondi D., Michel M.. and Elofsson A. "Improved contact predictions using the recognition of protein like contact patterns." ----------------------------------------------------------------------- Testing dependencies... Dependencies OK. Running PconsC1... Predicting... /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE4.psicov is empty! /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE0.psicov is empty! /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE10.psicov is empty! /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.jhE40.psicov is empty! /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc/sequence.fasta.hhE4.psicov is empty! Running time for PconsC1 is 6 seconds End at 2016-03-14 21:26:14 tar -czf /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc.tar.gz -C /media/local_storage/server/var/www/web_pconsc/release/tmp/r_BjEjIx/pconsc ./