start at 2016-03-08 10:09:28 #------------------------------------------------ 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_GmWUs8/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. 2016-03-08 10:09:28.497594 jhE4: generating Jackhmmer alignment This may take quite a few minutes! 2016-03-08 10:24:59.485515 jhE0: generating Jackhmmer alignment This may take quite a few minutes! 2016-03-08 10:32:39.387708 jhE10: generating Jackhmmer alignment This may take quite a few minutes! 2016-03-08 10:40:12.156946 jhE40: generating Jackhmmer alignment This may take quite a few minutes! 2016-03-08 10:47:26.406693 hhE4: generating HHblits alignment This may take quite a few minutes! 2016-03-08 10:49:18.313152 hhE0: generating HHblits alignment This may take quite a few minutes! 2016-03-08 10:50:06.915952 hhE10: generating HHblits alignment This may take quite a few minutes! 2016-03-08 10:50:42.091823 hhE40: generating HHblits alignment This may take quite a few minutes! 2016-03-08 10:51:14.977858 jhE4: running PSICOV This may take more than an hour. 2016-03-08 10:51:15.091053 jhE0: running PSICOV This may take more than an hour. 2016-03-08 11:54:36.677509 jhE10: running PSICOV This may take more than an hour. 2016-03-08 12:17:43.092169 jhE40: running PSICOV This may take more than an hour. 2016-03-08 12:36:43.566080 hhE4: running PSICOV This may take more than an hour. 2016-03-08 12:38:20.508791 hhE0: running PSICOV This may take more than an hour. 2016-03-08 12:59:04.460406 hhE10: running PSICOV This may take more than an hour. 2016-03-08 13:31:39.312463 hhE40: running PSICOV This may take more than an hour. 2016-03-08 13:49:53.028985 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_GmWUs8/pconsc/sequence.fasta.jhE4.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.jhE4.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-08 16:34:08.922807 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_GmWUs8/pconsc/sequence.fasta.jhE0.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.jhE0.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-08 19:41:31.319012 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_GmWUs8/pconsc/sequence.fasta.jhE10.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.jhE10.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-08 21:31:02.482469 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_GmWUs8/pconsc/sequence.fasta.jhE40.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.jhE40.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-08 22:35:57.902900 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_GmWUs8/pconsc/sequence.fasta.hhE4.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.hhE4.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-09 00:18:29.062712 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_GmWUs8/pconsc/sequence.fasta.hhE0.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.hhE0.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-09 02:38:03.139563 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_GmWUs8/pconsc/sequence.fasta.hhE10.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.hhE10.plmdca 0.01 0.01 0.1 8 workers='8' Segmentation fault (core dumped) 2016-03-09 03:58:04.289281 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_GmWUs8/pconsc/sequence.fasta.hhE40.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.hhE40.plmdca 0.01 0.01 0.1 8 workers='8' Segmentation fault (core dumped) Running PconsC2... 2016-03-09 04:58:43.952771: 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_7667': Permission denied cp: cannot create regular file '/scratch/NetSurfP_7667': 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_7667/file.inp: No such file or directory at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/scripts/make_prof.pl line 87. 2016-03-09 04:58:44.616265: 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_GmWUs8/pconsc/sequence.fasta.jhE4.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.jhE4.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.jhE0.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.jhE0.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.jhE10.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.jhE10.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.jhE40.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.jhE40.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.hhE4.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.hhE4.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.hhE0.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.hhE0.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.hhE10.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.hhE10.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc/sequence.fasta.hhE40.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/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_GmWUs8/pconsc/sequence.fasta.fasta Running time for PconsC2 is 69554 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_GmWUs8/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... Running time for PconsC1 is 23 seconds End at 2016-03-09 05:29:05 tar -czf /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc.tar.gz -C /media/local_storage/server/var/www/web_pconsc/release/tmp/r_GmWUs8/pconsc ./