start at 2016-04-13 10:50:18 #------------------------------------------------ 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_o7ligQ/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. 2016-04-13 10:50:18.941067 jhE4: generating Jackhmmer alignment This may take quite a few minutes! 2016-04-13 11:02:31.576587 jhE0: generating Jackhmmer alignment This may take quite a few minutes! 2016-04-13 11:06:52.072578 jhE10: generating Jackhmmer alignment This may take quite a few minutes! 2016-04-13 11:12:35.859122 jhE40: generating Jackhmmer alignment This may take quite a few minutes! 2016-04-13 11:19:48.285018 hhE4: generating HHblits alignment This may take quite a few minutes! 2016-04-13 11:21:06.241454 hhE0: generating HHblits alignment This may take quite a few minutes! 2016-04-13 11:21:27.986094 hhE10: generating HHblits alignment This may take quite a few minutes! 2016-04-13 11:21:43.555268 hhE40: generating HHblits alignment This may take quite a few minutes! 2016-04-13 11:22:01.690918 jhE4: running PSICOV This may take more than an hour. 2016-04-13 11:22:01.696183 jhE0: running PSICOV This may take more than an hour. 2016-04-13 11:22:07.819076 jhE10: running PSICOV This may take more than an hour. 2016-04-13 11:22:08.418748 jhE40: running PSICOV This may take more than an hour. 2016-04-13 11:22:15.893756 hhE4: running PSICOV This may take more than an hour. 2016-04-13 11:22:15.945419 hhE0: running PSICOV This may take more than an hour. 2016-04-13 11:22:20.263286 hhE10: running PSICOV This may take more than an hour. 2016-04-13 11:22:20.473307 hhE40: running PSICOV This may take more than an hour. 2016-04-13 11:22:26.174065 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_o7ligQ/pconsc/sequence.fasta.jhE4.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.jhE4.plmdca 0.01 0.01 0.1 8 workers='8' Segmentation fault (core dumped) 2016-04-13 11:26:33.317971 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_o7ligQ/pconsc/sequence.fasta.jhE0.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.jhE0.plmdca 0.01 0.01 0.1 8 workers='8' 2016-04-13 11:30:14.338746 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_o7ligQ/pconsc/sequence.fasta.jhE10.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.jhE10.plmdca 0.01 0.01 0.1 8 workers='8' 2016-04-13 11:34:08.195191 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_o7ligQ/pconsc/sequence.fasta.jhE40.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.jhE40.plmdca 0.01 0.01 0.1 8 workers='8' 2016-04-13 11:37:07.058520 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_o7ligQ/pconsc/sequence.fasta.hhE4.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.hhE4.plmdca 0.01 0.01 0.1 8 workers='8' 2016-04-13 11:41:10.138962 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_o7ligQ/pconsc/sequence.fasta.hhE0.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.hhE0.plmdca 0.01 0.01 0.1 8 workers='8' 2016-04-13 11:45:10.091943 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_o7ligQ/pconsc/sequence.fasta.hhE10.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.hhE10.plmdca 0.01 0.01 0.1 8 workers='8' 2016-04-13 11:49:17.540605 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_o7ligQ/pconsc/sequence.fasta.hhE40.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.hhE40.plmdca 0.01 0.01 0.1 8 workers='8' Segmentation fault (core dumped) Running PconsC2... 2016-04-13 11:52:59.283384: 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_14435': Permission denied cp: cannot create regular file '/scratch/NetSurfP_14435': 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_14435/file.inp: No such file or directory at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/scripts/make_prof.pl line 87. 2016-04-13 11:52:59.823742: 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_o7ligQ/pconsc/sequence.fasta.jhE4.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.jhE4.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.jhE0.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.jhE0.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.jhE10.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.jhE10.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.jhE40.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.jhE40.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.hhE4.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.hhE4.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.hhE0.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.hhE0.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.hhE10.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.hhE10.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc/sequence.fasta.hhE40.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/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_o7ligQ/pconsc/sequence.fasta.fasta Running time for PconsC2 is 4150 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_o7ligQ/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 5 seconds End at 2016-04-13 11:59:33 tar -czf /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc.tar.gz -C /media/local_storage/server/var/www/web_pconsc/release/tmp/r_o7ligQ/pconsc ./