hhdb: /data3/data/hhsuite/uniprot20_2013_03/uniprot20_2013_03 hmmerdb: /data3/data/blastdb/uniref90.fasta start at Mon Jun 30 16:20:38 CEST 2014 #------------------------------------------------ Running PconsC2... /home/ubuntu/pconsc2/PconsC2//run_pconsc.py -c 8 --p_psi 1 --p_plm 1 /data3/data/hhsuite/uniprot20_2013_03/uniprot20_2013_03 /data3/data/blastdb/uniref90.fasta /home/ubuntu/web_pconsc/release/tmp/20009/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. 2014-06-30 16:20:41.418972 jhE4: generating Jackhmmer alignment This may take quite a few minutes! 2014-06-30 16:25:07.482560 jhE0: generating Jackhmmer alignment This may take quite a few minutes! 2014-06-30 16:28:36.262449 jhE10: generating Jackhmmer alignment This may take quite a few minutes! 2014-06-30 16:32:09.066930 jhE40: generating Jackhmmer alignment This may take quite a few minutes! 2014-06-30 16:35:37.156777 hhE4: generating HHblits alignment This may take quite a few minutes! 2014-06-30 16:36:45.978530 hhE0: generating HHblits alignment This may take quite a few minutes! 2014-06-30 16:37:11.387579 hhE10: generating HHblits alignment This may take quite a few minutes! 2014-06-30 16:37:36.303524 hhE40: generating HHblits alignment This may take quite a few minutes! /home/ubuntu/pconsc2/PconsC2/dependencies/bin/jackhmmer --cpu 8 -N 5 -E 1e-4 -A /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE4.ali /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.fasta /data3/data/blastdb/uniref90.fasta /home/ubuntu/pconsc2/PconsC2/scripts/reformat.pl sto a3m /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE4.ali /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE4.a3m rm /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE4.ali /home/ubuntu/pconsc2/PconsC2/dependencies/bin/jackhmmer --cpu 8 -N 5 -E 1 -A /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE0.ali /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.fasta /data3/data/blastdb/uniref90.fasta /home/ubuntu/pconsc2/PconsC2/scripts/reformat.pl sto a3m /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE0.ali /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE0.a3m rm /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE0.ali /home/ubuntu/pconsc2/PconsC2/dependencies/bin/jackhmmer --cpu 8 -N 5 -E 1e-10 -A /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE10.ali /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.fasta /data3/data/blastdb/uniref90.fasta /home/ubuntu/pconsc2/PconsC2/scripts/reformat.pl sto a3m /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE10.ali /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE10.a3m rm /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE10.ali /home/ubuntu/pconsc2/PconsC2/dependencies/bin/jackhmmer --cpu 8 -N 5 -E 1e-40 -A /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE40.ali /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.fasta /data3/data/blastdb/uniref90.fasta /home/ubuntu/pconsc2/PconsC2/scripts/reformat.pl sto a3m /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE40.ali /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE40.a3m rm /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE40.ali /home/ubuntu/pconsc2/PconsC2/dependencies/hhblits/hhsuite-2.0.16-linux-x86_64/bin/hhblits -all -oa3m /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE4.a3m -e 1e-4 -cpu 8 -i /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.fasta -d /data3/data/hhsuite/uniprot20_2013_03/uniprot20_2013_03 /home/ubuntu/pconsc2/PconsC2/dependencies/hhblits/hhsuite-2.0.16-linux-x86_64/bin/hhblits -all -oa3m /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE0.a3m -e 1 -cpu 8 -i /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.fasta -d /data3/data/hhsuite/uniprot20_2013_03/uniprot20_2013_03 /home/ubuntu/pconsc2/PconsC2/dependencies/hhblits/hhsuite-2.0.16-linux-x86_64/bin/hhblits -all -oa3m /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE10.a3m -e 1e-10 -cpu 8 -i /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.fasta -d /data3/data/hhsuite/uniprot20_2013_03/uniprot20_2013_03 /home/ubuntu/pconsc2/PconsC2/dependencies/hhblits/hhsuite-2.0.16-linux-x86_64/bin/hhblits -all -oa3m /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE40.a3m -e 1e-40 -cpu 8 -i /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.fasta -d /data3/data/hhsuite/uniprot20_2013_03/uniprot20_2013_03 2014-06-30 16:38:02.872990 jhE4: running PSICOV This may take more than an hour. 2014-06-30 16:38:33.280725 jhE0: running PSICOV This may take more than an hour. 2014-06-30 16:39:02.920312 jhE10: running PSICOV This may take more than an hour. 2014-06-30 16:39:33.511423 jhE40: running PSICOV This may take more than an hour. 2014-06-30 16:39:44.296737 hhE4: running PSICOV This may take more than an hour. 2014-06-30 16:40:04.745009 hhE0: running PSICOV This may take more than an hour. 2014-06-30 16:40:23.873091 hhE10: running PSICOV This may take more than an hour. 2014-06-30 16:40:42.008674 hhE40: running PSICOV This may take more than an hour. /home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE4.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE4.jones /home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE0.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE0.jones /home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE10.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE10.jones /home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE40.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE40.jones /home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE4.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE4.jones /home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE0.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE0.jones /home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE10.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE10.jones /home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE40.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE40.jones 2014-06-30 16:41:07.169168 jhE4: running plmDCA This may take more than an hour. OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". 2014-06-30 16:45:51.448727 jhE0: running plmDCA This may take more than an hour. OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". 2014-06-30 16:50:23.180658 jhE10: running plmDCA This may take more than an hour. OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". 2014-06-30 16:54:55.597795 jhE40: running plmDCA This may take more than an hour. OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". 2014-06-30 16:58:55.633329 hhE4: running plmDCA This may take more than an hour. OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". 2014-06-30 17:03:39.719058 hhE0: running plmDCA This may take more than an hour. OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". 2014-06-30 17:08:23.891859 hhE10: running plmDCA This may take more than an hour. OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". 2014-06-30 17:12:49.933915 hhE40: running plmDCA This may take more than an hour. OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors. OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled". /home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE4.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE4.trimmed /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE4.plmdca 0.01 0.01 0.1 8 /home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE0.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE0.trimmed /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE0.plmdca 0.01 0.01 0.1 8 /home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE10.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE10.trimmed /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE10.plmdca 0.01 0.01 0.1 8 /home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE40.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE40.trimmed /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE40.plmdca 0.01 0.01 0.1 8 /home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE4.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE4.trimmed /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE4.plmdca 0.01 0.01 0.1 8 /home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE0.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE0.trimmed /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE0.plmdca 0.01 0.01 0.1 8 /home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE10.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE10.trimmed /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE10.plmdca 0.01 0.01 0.1 8 /home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE40.a3m /home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE40.trimmed /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE40.plmdca 0.01 0.01 0.1 8 Running PconsC2... 2014-06-30 17:17:26.521205: 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. 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()?) [blastpgp] WARNING: Unable to open nr70.pin [blastpgp] WARNING: Unable to open nr70.pin 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. 2014-06-30 17:17:35.135357: running Psipred This may take quite a few minutes! Predicting... Parsing NetSurfP Parsing PSIPRED Parsing PSSM Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE4.psicov Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE4.plmdca Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE0.psicov Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE0.plmdca Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE10.psicov Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE10.plmdca Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE40.psicov Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE40.plmdca Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE4.psicov Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE4.plmdca Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE0.psicov Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE0.plmdca Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE10.psicov Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE10.plmdca Parsing /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.hhE40.psicov Parsing /home/ubuntu/web_pconsc/release/tmp/20009/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/netsurfp/netsurfp-1.0/netsurfp -i /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta -a /home/ubuntu/pconsc2/PconsC2/dependencies/psipred/psipred3.5/runpsipred /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.fasta Running time for PconsC2 is 4456 seconds #------------------------------------------------ Running PconsC1... /home/ubuntu/pconsc2/PconsC2//run_pconsc.py -c 8 --p_psi 1 --p_plm 1 --pconsc1 /data3/data/hhsuite/uniprot20_2013_03/uniprot20_2013_03 /data3/data/blastdb/uniref90.fasta /home/ubuntu/web_pconsc/release/tmp/20009/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... /home/ubuntu/web_pconsc/release/tmp/20009/pconsc/sequence.fasta.jhE40.psicov is empty! Running time for PconsC1 is 8 seconds End at Mon Jun 30 17:35:03 CEST 2014 tar -czf /home/ubuntu/web_pconsc/release/tmp/20009/pconsc.tar.gz -C /home/ubuntu/web_pconsc/release/tmp/20009/pconsc ./