start at 2016-03-08 10:10:28 #------------------------------------------------ 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_zkX5cz/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 10:10:32.836496 jhE4: generating Jackhmmer alignment This may take quite a few minutes! 2016-03-08 10:23:19.427727 jhE0: generating Jackhmmer alignment This may take quite a few minutes! 2016-03-08 10:31:50.841631 jhE10: generating Jackhmmer alignment This may take quite a few minutes! 2016-03-08 10:38:46.915827 jhE40: generating Jackhmmer alignment This may take quite a few minutes! 2016-03-08 10:45:54.955977 hhE4: generating HHblits alignment This may take quite a few minutes! 2016-03-08 10:47:44.982832 hhE0: generating HHblits alignment This may take quite a few minutes! 2016-03-08 10:48:34.652323 hhE10: generating HHblits alignment This may take quite a few minutes! 2016-03-08 10:49:10.793420 hhE40: generating HHblits alignment This may take quite a few minutes! 2016-03-08 10:49:43.226341 jhE4: running PSICOV This may take more than an hour. 2016-03-08 10:49:43.247023 jhE0: running PSICOV This may take more than an hour. 2016-03-08 11:48:12.993822 jhE10: running PSICOV This may take more than an hour. 2016-03-08 11:49:49.953399 jhE40: running PSICOV This may take more than an hour. 2016-03-08 12:08:45.769838 hhE4: running PSICOV This may take more than an hour. 2016-03-08 12:26:21.011868 hhE0: running PSICOV This may take more than an hour. 2016-03-08 12:28:27.854627 hhE10: running PSICOV This may take more than an hour. 2016-03-08 12:59:35.063967 hhE40: running PSICOV This may take more than an hour. 2016-03-08 13:15:35.969590 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_zkX5cz/pconsc/sequence.fasta.jhE4.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.jhE4.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-08 16:05:52.262851 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_zkX5cz/pconsc/sequence.fasta.jhE0.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.jhE0.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-08 19:18:23.030499 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_zkX5cz/pconsc/sequence.fasta.jhE10.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.jhE10.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-08 21:13:27.443303 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_zkX5cz/pconsc/sequence.fasta.jhE40.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.jhE40.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-08 22:17:14.216837 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_zkX5cz/pconsc/sequence.fasta.hhE4.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.hhE4.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-08 23:56:45.019009 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_zkX5cz/pconsc/sequence.fasta.hhE0.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.hhE0.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-09 02:06:02.778880 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_zkX5cz/pconsc/sequence.fasta.hhE10.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.hhE10.plmdca 0.01 0.01 0.1 8 workers='8' 2016-03-09 03:22:51.408439 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_zkX5cz/pconsc/sequence.fasta.hhE40.trimmed /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.hhE40.plmdca 0.01 0.01 0.1 8 workers='8' Running PconsC2... 2016-03-09 04:22:45.675042: 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_3435': Permission denied cp: cannot create regular file '/scratch/NetSurfP_3435': 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_3435/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 04:22:46.871546: 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_zkX5cz/pconsc/sequence.fasta.jhE4.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.jhE4.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.jhE0.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.jhE0.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.jhE10.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.jhE10.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.jhE40.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.jhE40.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.hhE4.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.hhE4.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.hhE0.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.hhE0.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.hhE10.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.hhE10.plmdca Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc/sequence.fasta.hhE40.psicov Parsing /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/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_zkX5cz/pconsc/sequence.fasta.fasta Running time for PconsC2 is 66954 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_zkX5cz/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 21 seconds End at 2016-03-09 04:46:43 tar -czf /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc.tar.gz -C /media/local_storage/server/var/www/web_pconsc/release/tmp/r_zkX5cz/pconsc ./