start at Fri Jun 27 11:10:08 CEST 2014
/home/ubuntu/pconsc2/PconsC2//run_pconsc.py -c 8 /data3/data/hhsuite/uniprot20_2013_03/uniprot20_2013_03 /data3/data/blastdb/uniref90.fasta /home/ubuntu/web_pconsc/release/tmp/20002/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.
2014-06-27 11:10:17.623700 jhE4: generating Jackhmmer alignment
This may take quite a few minutes!
 2014-06-27 12:52:36.140172 jhE0: generating Jackhmmer alignment
This may take quite a few minutes!
 2014-06-27 14:35:46.977191 jhE10: generating Jackhmmer alignment
This may take quite a few minutes!
 2014-06-27 14:44:46.489345 jhE40: generating Jackhmmer alignment
This may take quite a few minutes!
 2014-06-27 14:46:35.556249 hhE4: generating HHblits alignment
This may take quite a few minutes!
 2014-06-27 14:54:00.558962 hhE0: generating HHblits alignment
This may take quite a few minutes!
 2014-06-27 14:54:29.138752 hhE10: generating HHblits alignment
This may take quite a few minutes!
 2014-06-27 14:54:54.597253 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/20002/pconsc/sequence.fasta.jhE4.ali /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.fasta /data3/data/blastdb/uniref90.fasta
/home/ubuntu/pconsc2/PconsC2/scripts/reformat.pl sto a3m /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE4.ali /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE4.a3m
rm /home/ubuntu/web_pconsc/release/tmp/20002/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/20002/pconsc/sequence.fasta.jhE0.ali /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.fasta /data3/data/blastdb/uniref90.fasta
/home/ubuntu/pconsc2/PconsC2/scripts/reformat.pl sto a3m /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE0.ali /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE0.a3m
rm /home/ubuntu/web_pconsc/release/tmp/20002/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/20002/pconsc/sequence.fasta.jhE10.ali /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.fasta /data3/data/blastdb/uniref90.fasta
/home/ubuntu/pconsc2/PconsC2/scripts/reformat.pl sto a3m /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE10.ali /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE10.a3m
rm /home/ubuntu/web_pconsc/release/tmp/20002/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/20002/pconsc/sequence.fasta.jhE40.ali /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.fasta /data3/data/blastdb/uniref90.fasta
/home/ubuntu/pconsc2/PconsC2/scripts/reformat.pl sto a3m /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE40.ali /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE40.a3m
rm /home/ubuntu/web_pconsc/release/tmp/20002/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/20002/pconsc/sequence.fasta.hhE4.a3m -e 1e-4 -cpu 8 -i /home/ubuntu/web_pconsc/release/tmp/20002/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/20002/pconsc/sequence.fasta.hhE0.a3m -e 1 -cpu 8 -i /home/ubuntu/web_pconsc/release/tmp/20002/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/20002/pconsc/sequence.fasta.hhE10.a3m -e 1e-10 -cpu 8 -i /home/ubuntu/web_pconsc/release/tmp/20002/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/20002/pconsc/sequence.fasta.hhE40.a3m -e 1e-40 -cpu 8 -i /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.fasta -d /data3/data/hhsuite/uniprot20_2013_03/uniprot20_2013_03
2014-06-27 14:55:15.913899 jhE40: running PSICOV
This may take more than an hour.
2014-06-27 14:55:15.914195 hhE40: running PSICOV
This may take more than an hour.
2014-06-27 14:55:15.915031 jhE10: running PSICOV
This may take more than an hour.
2014-06-27 14:55:15.934314 jhE0: running PSICOV
This may take more than an hour.
2014-06-27 14:55:15.969688 hhE10: running PSICOV
This may take more than an hour.
2014-06-27 14:55:16.030597 jhE4: running PSICOV
This may take more than an hour.
2014-06-27 14:55:16.051720 hhE4: running PSICOV
This may take more than an hour.
2014-06-27 14:55:16.057828 hhE0: running PSICOV
This may take more than an hour.
*** Bad alignment file!
*** Sorry - failed to find suitable value for rho (0 < rho < 1)!
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE40.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE40.jones
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE40.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE40.jones
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE10.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE10.jones
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE10.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE10.jones
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE4.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE4.jones
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE0.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE0.jones
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE0.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE0.jones
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToJones.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE4.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/psicov/Version1/psicov -o /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE4.jones
2014-06-27 14:56:14.482217 jhE40: running plmDCA
This may take more than an hour.
2014-06-27 14:56:14.500667 jhE10: running plmDCA
This may take more than an hour.
2014-06-27 14:56:14.507791 hhE40: running plmDCA
This may take more than an hour.
2014-06-27 14:56:14.533906 jhE4: running plmDCA
This may take more than an hour.
2014-06-27 14:56:14.551238 jhE0: running plmDCA
This may take more than an hour.
2014-06-27 14:56:14.562333 hhE10: running plmDCA
This may take more than an hour.
2014-06-27 14:56:14.649975 hhE4: running plmDCA
This may take more than an hour.
2014-06-27 14:56:14.672885 hhE0: running plmDCA
This may take more than an hour.
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE40.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE40.trimmed /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE40.plmdca 0.01 0.01 0.1 1
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE40.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE40.trimmed /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE40.plmdca 0.01 0.01 0.1 1
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE10.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE10.trimmed /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE10.plmdca 0.01 0.01 0.1 1
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE10.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE10.trimmed /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE10.plmdca 0.01 0.01 0.1 1
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE4.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE4.trimmed /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE4.plmdca 0.01 0.01 0.1 1
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE0.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE0.trimmed /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE0.plmdca 0.01 0.01 0.1 1
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE0.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE0.trimmed /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE0.plmdca 0.01 0.01 0.1 1
/home/ubuntu/pconsc2/PconsC2/scripts/a3mToTrimmed.py /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE4.a3m
/home/ubuntu/pconsc2/PconsC2/dependencies/plmDCA/plmdca_standalone/2012/build01/bin/plmdca /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE4.trimmed /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE4.plmdca 0.01 0.01 0.1 1
Running PconsC2...
2014-06-27 15:06:00.601148: 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.
2014-06-27 15:06:09.347141: running Psipred
This may take quite a few minutes!
Predicting...
Parsing NetSurfP
Parsing PSIPRED
Parsing PSSM
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE4.psicov
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE4.plmdca
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE0.psicov
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE0.plmdca
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE10.psicov
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE10.plmdca
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE40.psicov
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.jhE40.plmdca
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE4.psicov
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE4.plmdca
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE0.psicov
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE0.plmdca
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE10.psicov
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE10.plmdca
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.hhE40.psicov
Parsing /home/ubuntu/web_pconsc/release/tmp/20002/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/20002/pconsc/sequence.fasta -a
/home/ubuntu/pconsc2/PconsC2/dependencies/psipred/psipred3.5/runpsipred /home/ubuntu/web_pconsc/release/tmp/20002/pconsc/sequence.fasta.fasta
End at Fri Jun 27 15:20:02 CEST 2014
Running time 14993.968./
./sequence.fasta.jhE4.a3m
./sequence.fasta.jhE0.trimmed
./sequence.fasta
./sequence.fasta.hhE10.jones
./sequence.fasta.ss2
./sequence.fasta.jhE4.plmdca
./sequence.fasta.hhE0.psicov
./sequence.fasta.pconsc2.out
./sequence.fasta.jhE0.plmdca
./sequence.fasta.hhE10.psicov
./sequence.fasta.hhE10.plmdca
./sequence.fasta.pconsc2.out.cm.png
./sequence.fasta.fasta
./sequence.fasta.jhE40.psicov
./sequence.fasta.jhE4.trimmed
./sequence.fasta.hhE40.jones
./sequence.fasta.jhE40.a3m
./sequence.fasta.jhE40.jones
./sequence.fasta.bak
./sequence.fasta.jhE0.psicov
./sequence.fasta.hhE4.plmdca
./sequence.fasta.horiz
./sequence.fasta.hhE4.trimmed
./sequence.fasta.jhE10.jones
./sequence.fasta.hhE40.psicov
./sequence.fasta.hhE4.psicov
./sequence.fasta.jhE4.psicov
./sequence.fasta.ss
./sequence.fasta.hhE40.a3m
./sequence.fasta.hhE0.a3m
./sequence.fasta.jhE10.plmdca
./sequence.fasta.hhE4.jones
./sequence.fasta.hhE10.trimmed
./sequence.fasta.hhr
./sequence.fasta.jhE0.a3m
./sequence.fasta.jhE4.jones
./sequence.fasta.jhE40.trimmed
./sequence.fasta.jhE10.trimmed
./sequence.fasta.hhE40.plmdca
./sequence.fasta.jhE10.psicov
./sequence.fasta.hhE40.trimmed
./sequence.fasta.hhE10.a3m
./sequence.fasta.hhE0.plmdca
./sequence.fasta.rsa
./sequence.fasta.jhE0.jones
./sequence.fasta.hhE0.jones
./sequence.fasta.hhE4.a3m
./sequence.fasta.hhE0.trimmed