./buildali_uniref50_dssp.pl /bmm/www/servers/phyre2/public_html/phyre2_output/56da5616b4559c93/query.fasta /bmm/www/servers/phyre2/public_html/phyre2_output/56da5616b4559c93 $ ./reformat.pl -M first -noss a3m a3m /bmm/www/servers/phyre2/public_html/phyre2_output/56da5616b4559c93/query.fasta /tmp/phyre2/26541/query.in.a3m -> 1 $ ./reformat.pl -r a3m psi /tmp/phyre2/26541/query.in.a3m /tmp/phyre2/26541/query.psi -> 1 ************************************************ Building alignment for /tmp/phyre2/26541/query (FER_CAPAN_1-144) ************************************************ Building alignment for query with PSI-BLAST ... $ /bmm/www/servers/phyre2/bin/blast/blastpgp -I T -s T -b 20000 -v 1 -e 0.001 -d /data/data/blast/uniref50.fasta -i /tmp/phyre2/26541/query.seq &> /tmp/phyre2/26541/query.bla $ ./alignhits.pl -cov 80 -e 0.001 -bl 0.33 -bs 0.67 -best -psi -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.core.psi -> 4 $ ./alignhits.pl -cov 80 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -best -psi -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.psi -> 14 $ ./alignhits.pl -cov 80 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -best -a3m -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.a3m -> 14 Found 14 sequences in PSI-BLAST round 1 (E-value<1E-03, coverage>20%, db=uniref50.fasta) $ /bmm/www/servers/phyre2/bin/blast/blastpgp -I T -s T -b 20000 -v 1 -e 0.001 -d /data/data/blast/uniref50.fasta -i /tmp/phyre2/26541/query.seq -B /tmp/phyre2/26541/query.psi &> /tmp/phyre2/26541/query.bla $ ./alignhits.pl -cov 20 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -a3m -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.tmp -> 633 $ cat /tmp/phyre2/26541/query.tmp >> /tmp/phyre2/26541/query.a3m $ ./alignhits.pl -cov 20 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -psi -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.tmp -> 633 $ cat /tmp/phyre2/26541/query.tmp >> /tmp/phyre2/26541/query.psi Found 633 sequences in PSI-BLAST round 2 (E-value<1E-03, coverage>20%, db=uniref50.fasta) $ /bmm/www/servers/phyre2/bin/blast/blastpgp -I T -s T -b 20000 -v 1 -e 0.001 -d /data/data/blast/uniref50.fasta -i /tmp/phyre2/26541/query.seq -B /tmp/phyre2/26541/query.psi &> /tmp/phyre2/26541/query.bla $ ./alignhits.pl -cov 20 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -a3m -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.tmp -> 782 $ cat /tmp/phyre2/26541/query.tmp >> /tmp/phyre2/26541/query.a3m $ ./alignhits.pl -cov 20 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -psi -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.tmp -> 782 $ cat /tmp/phyre2/26541/query.tmp >> /tmp/phyre2/26541/query.psi Found 782 sequences in PSI-BLAST round 3 (E-value<1E-03, coverage>20%, db=uniref50.fasta) $ /bmm/www/servers/phyre2/bin/blast/blastpgp -I T -s T -b 20000 -v 1 -e 0.001 -d /data/data/blast/uniref50.fasta -i /tmp/phyre2/26541/query.seq -B /tmp/phyre2/26541/query.psi &> /tmp/phyre2/26541/query.bla $ ./alignhits.pl -cov 20 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -a3m -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.tmp -> 774 $ cat /tmp/phyre2/26541/query.tmp >> /tmp/phyre2/26541/query.a3m $ ./alignhits.pl -cov 20 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -psi -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.tmp -> 774 $ cat /tmp/phyre2/26541/query.tmp >> /tmp/phyre2/26541/query.psi Found 774 sequences in PSI-BLAST round 4 (E-value<1E-03, coverage>20%, db=uniref50.fasta) $ /bmm/www/servers/phyre2/bin/blast/blastpgp -I T -s T -b 20000 -v 1 -e 0.001 -d /data/data/blast/uniref50.fasta -i /tmp/phyre2/26541/query.seq -B /tmp/phyre2/26541/query.psi &> /tmp/phyre2/26541/query.bla $ ./alignhits.pl -cov 20 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -a3m -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.tmp -> 763 $ cat /tmp/phyre2/26541/query.tmp >> /tmp/phyre2/26541/query.a3m $ ./alignhits.pl -cov 20 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -psi -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.tmp -> 763 $ cat /tmp/phyre2/26541/query.tmp >> /tmp/phyre2/26541/query.psi Found 763 sequences in PSI-BLAST round 5 (E-value<1E-03, coverage>20%, db=uniref50.fasta) $ /bmm/www/servers/phyre2/bin/blast/blastpgp -I T -s T -b 20000 -v 1 -e 0.001 -d /data/data/blast/uniref50.fasta -i /tmp/phyre2/26541/query.seq -B /tmp/phyre2/26541/query.psi &> /tmp/phyre2/26541/query.bla $ ./alignhits.pl -cov 20 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -a3m -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.tmp -> 761 $ cat /tmp/phyre2/26541/query.tmp >> /tmp/phyre2/26541/query.a3m $ ./alignhits.pl -cov 20 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -psi -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.tmp -> 761 $ cat /tmp/phyre2/26541/query.tmp >> /tmp/phyre2/26541/query.psi Found 761 sequences in PSI-BLAST round 6 (E-value<1E-03, coverage>20%, db=uniref50.fasta) $ /bmm/www/servers/phyre2/bin/blast/blastpgp -I T -s T -b 20000 -v 1 -e 0.001 -d /data/data/blast/uniref50.fasta -i /tmp/phyre2/26541/query.seq -B /tmp/phyre2/26541/query.psi &> /tmp/phyre2/26541/query.bla $ ./alignhits.pl -cov 20 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -a3m -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.tmp -> 764 $ cat /tmp/phyre2/26541/query.tmp >> /tmp/phyre2/26541/query.a3m $ ./alignhits.pl -cov 20 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -psi -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.tmp -> 764 $ cat /tmp/phyre2/26541/query.tmp >> /tmp/phyre2/26541/query.psi Found 764 sequences in PSI-BLAST round 7 (E-value<1E-03, coverage>20%, db=uniref50.fasta) $ /bmm/www/servers/phyre2/bin/blast/blastpgp -I T -s T -b 20000 -v 1 -e 0.001 -d /data/data/blast/uniref50.fasta -i /tmp/phyre2/26541/query.seq -B /tmp/phyre2/26541/query.psi &> /tmp/phyre2/26541/query.bla $ ./alignhits.pl -cov 20 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -a3m -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.tmp -> 762 Found 762 sequences in PSI-BLAST round 8 (E-value<1E-03, coverage>20%, db=uniref50.fasta) $ cat /tmp/phyre2/26541/query.tmp >> /tmp/phyre2/26541/query.a3m $ ./alignhits.pl -cov 20 -e 0.001 -bl 0 -bs 0.167 -bg 20 -B /tmp/phyre2/26541/query.core.psi -psi -q /tmp/phyre2/26541/query.seq /tmp/phyre2/26541/query.bla /tmp/phyre2/26541/query.tmp -> 762 $ cat /tmp/phyre2/26541/query.tmp >> /tmp/phyre2/26541/query.psi $ ./hhfilter -M a3m -id 90 -cov 20 -diff 0 -i /tmp/phyre2/26541/query.a3m -o /tmp/phyre2/26541/query.fil Input file = /tmp/phyre2/26541/query.a3m Output file = /tmp/phyre2/26541/query.fil Read /tmp/phyre2/26541/query.a3m with 5253 sequences Alignment in /tmp/phyre2/26541/query.a3m contains 144 match states 891 out of 5253 sequences passed filter (20% min coverage, 90% max pairwise sequence identity) $ ./reformat.pl -r a3m psi /tmp/phyre2/26541/query.fil /tmp/phyre2/26541/query.psi -> 891 Read DSSP state sequence Searching DSSP state assignments... name=FER_CAPAN_1-144 range= WARNING: Cannot open /bmm/data/dssp//FER_CAPAN_1-144.dssp: No such file or directory WARNING Cannot open /pdbFER_CAPAN_1-144.ent: No such file or directory Predicting secondary structure with PSIPRED ... $ /bmm/www/servers/phyre2/bin/blast/blastpgp -I T -s T -b 1 -j 1 -h 0.001 -d /bmm/www/servers/phyre/public_html/Version_1.1/data/dummydb -i /tmp/phyre2/26541/query.seq -B /tmp/phyre2/26541/query.psi -C /tmp/phyre2/26541/query.chk &> /tmp/phyre2/26541/query.bla $ /bmm/www/servers/phyre2/bin/psipred25/bin/psipred /tmp/phyre2/26541/query.mtx /bmm/www/servers/phyre2/bin/psipred25/data/weights.dat /bmm/www/servers/phyre2/bin/psipred25/data/weights.dat2 /bmm/www/servers/phyre2/bin/psipred25/data/weights.dat3 /bmm/www/servers/phyre2/bin/psipred25/data/weights.dat4 > /tmp/phyre2/26541/query.ss $ /bmm/www/servers/phyre2/bin/psipred25/bin/psipass2 /bmm/www/servers/phyre2/bin/psipred25/data/weights_p2.dat 1 0.98 1.09 /tmp/phyre2/26541/query.ss2 /tmp/phyre2/26541/query.ss > /tmp/phyre2/26541/query.horiz $ cat /tmp/phyre2/26541/query.a3m /tmp/phyre2/26541/query.in.a3m /tmp/phyre2/26541/query.fil > /tmp/phyre2/26541/query.tmp.a3m $ ./hhfilter -M a3m -id 90 -cov 20 -diff 0 -i /tmp/phyre2/26541/query.tmp.a3m -o /bmm/www/servers/phyre2/public_html/phyre2_output/56da5616b4559c93/query.a3m Input file = /tmp/phyre2/26541/query.tmp.a3m Output file = /bmm/www/servers/phyre2/public_html/phyre2_output/56da5616b4559c93/query.a3m Read /tmp/phyre2/26541/query.tmp.a3m with 894 sequences Alignment in /tmp/phyre2/26541/query.tmp.a3m contains 144 match states 891 out of 892 sequences passed filter (20% min coverage, 90% max pairwise sequence identity) Written alignment with 891 sequences to /bmm/www/servers/phyre2/public_html/phyre2_output/56da5616b4559c93/query.a3m Finished buildali.pl /bmm/www/servers/phyre2/public_html/phyre2_output/56da5616b4559c93/query.fasta /bmm/www/servers/phyre2/public_html/phyre2_output/56da5616b4559c93