start at 2016-04-26 10:24:05 #------------------------------------------------ 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_XMXji6/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. 2016-04-26 10:24:05.327665 jhE4: generating Jackhmmer alignment This may take quite a few minutes! 2016-04-26 11:51:12.994862 jhE0: generating Jackhmmer alignment This may take quite a few minutes! 2016-04-26 11:57:46.965572 jhE10: generating Jackhmmer alignment This may take quite a few minutes! 2016-04-26 12:04:13.780418 jhE40: generating Jackhmmer alignment This may take quite a few minutes! 2016-04-26 12:06:52.895660 hhE4: generating HHblits alignment This may take quite a few minutes! 2016-04-26 12:08:17.447017 hhE0: generating HHblits alignment This may take quite a few minutes! 2016-04-26 12:08:46.155247 hhE10: generating HHblits alignment This may take quite a few minutes! 2016-04-26 12:09:08.571751 hhE40: generating HHblits alignment This may take quite a few minutes! 2016-04-26 12:09:35.345948 jhE4: running PSICOV This may take more than an hour. 2016-04-26 12:09:35.349051 jhE0: running PSICOV This may take more than an hour. 2016-04-26 12:10:16.161156 jhE10: running PSICOV This may take more than an hour. 2016-04-26 12:10:24.694690 jhE40: running PSICOV This may take more than an hour. 2016-04-26 12:10:54.978770 hhE4: running PSICOV This may take more than an hour. 2016-04-26 12:11:11.126282 hhE0: running PSICOV This may take more than an hour. 2016-04-26 12:12:20.637261 hhE10: running PSICOV This may take more than an hour. 2016-04-26 12:12:29.723167 hhE40: running PSICOV This may take more than an hour. 2016-04-26 12:13:55.698390 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_XMXji6/pconsc/sequence.fasta.jhE4.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.jhE4.plmdca 0.01 0.01 0.1 8 workers='8' 2016-04-26 12:21:05.131441 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_XMXji6/pconsc/sequence.fasta.jhE0.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.jhE0.plmdca 0.01 0.01 0.1 8 workers='8' 2016-04-26 12:28:14.296409 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_XMXji6/pconsc/sequence.fasta.jhE10.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.jhE10.plmdca 0.01 0.01 0.1 8 workers='8' 2016-04-26 12:35:22.265436 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_XMXji6/pconsc/sequence.fasta.jhE40.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.jhE40.plmdca 0.01 0.01 0.1 8 workers='8' 2016-04-26 12:42:59.921956 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_XMXji6/pconsc/sequence.fasta.hhE4.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.hhE4.plmdca 0.01 0.01 0.1 8 workers='8' 2016-04-26 12:52:01.434668 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_XMXji6/pconsc/sequence.fasta.hhE0.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.hhE0.plmdca 0.01 0.01 0.1 8 workers='8' 2016-04-26 13:01:34.160678 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_XMXji6/pconsc/sequence.fasta.hhE10.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.hhE10.plmdca 0.01 0.01 0.1 8 workers='8' 2016-04-26 13:10:21.627190 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_XMXji6/pconsc/sequence.fasta.hhE40.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.hhE40.plmdca 0.01 0.01 0.1 8 workers='8' Running PconsC2... 2016-04-26 13:19:32.455441: 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_3731': Permission denied cp: cannot create regular file '/scratch/NetSurfP_3731': 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_3731/file.inp: No such file or directory at /home/ubuntu/pconsc2/share/netsurfp/netsurfp-1.0/scripts/make_prof.pl line 87. 2016-04-26 13:19:33.126812: 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_XMXji6/pconsc/sequence.fasta.jhE4.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.jhE4.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.jhE0.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.jhE0.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.jhE10.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.jhE10.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.jhE40.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.jhE40.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.hhE4.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.hhE4.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.hhE0.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.hhE0.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.hhE10.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.hhE10.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc/sequence.fasta.hhE40.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/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_XMXji6/pconsc/sequence.fasta.fasta Running time for PconsC2 is 11212 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_XMXji6/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_XMXji6/pconsc/sequence.fasta.jhE40.psicov is empty! Running time for PconsC1 is 11 seconds End at 2016-04-26 13:31:07 tar -czf /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc.tar.gz -C /media/local_storage/server/var/www/web_pconsc/release/tmp/r_XMXji6/pconsc ./