/projects/compbio/experiments/protein-predict/SAM_T02/scripts/log_user servers@predictioncenter.org /projects/compbio/.html/SAM_T02/results/target02-query-1274285010-30210/T0547.a2m target02-query-1274285010-30210 >> /projects/compbio/.html/SAM_T02/log/logfile
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/create_summary_html T0547 http://www.soe.ucsc.edu/projects/compbio/SAM_T02/results/target02-query-1274285010-30210 > summary.html
Name "main::BASEURL" used only once: possible typo at /projects/compbio/experiments/protein-predict/SAM_T02/scripts/create_summary_html line 11.
chgrp protein summary.html
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_section_head_summary_html "Inputs and Multiple Alignments" >> summary.html
if !(/projects/compbio/experiments/protein-predict/SAM_T02/scripts/clean_a2m T0547.raw > T0547.a2m); \
	then echo "<br><H3>" >> summary.html; \
	echo "Error: The submitted sequence was longer than 500 amino acids \
, or else was not an amino acid sequence.  We suggest breaking long protein chains into different domains \
with blast or psiblast and submitting the domains separately.  Alternatively, you can split long \
proteins into overlapping sections of less than 500 amino acids and submit them separately.  Please \
do not submit DNA sequences - our server is not set up to handle them." >> summary.html; \
	echo "</H3><br><br>"  >> summary.html; \
	fi
Reading /projects/compbio/experiments/models.97/scripts2k/sam-t2k.conf
Path: /projects/compbio/experiments/models.97/scripts2k:/projects/compbio/bin/x86_64:/usr/local/bin:/usr/local/gnu/bin:/sbin:/usr/sbin:/bin:/usr/bin
SAM: /projects/compbio/experiments/protein-predict/SAM_T02/scripts/../bin_freeze/sam/checkseq v3.5 (July 15, 2005) compiled 05/31/06_11:54:08
Done with sequence reading


@@@@ rm -f /projects/compbio/tmp/t02rawinput_9947
Error: Raw file is not in the protein alphabet, or is too long
echo Received sequence T0547.a2m
Received sequence T0547.a2m
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_summary_html "Submitted sequence(s)" \
		T0547.a2m >> summary.html
/projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k/target2k -out T0547.t2k \
		-seed T0547.a2m \
		-db /scratch/data/nrp/nr \
		-tmp_dir /tmp \
		-keep_temporary -1 \
		-blast_max_report 2000
Reading /projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k/sam-t2k.conf
Path: /projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k:/projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/sam:/usr/local/bin:/usr/local/gnu/bin:/sbin:/usr/sbin:/bin:/usr/bin


@@@@ chgrp protein /tmp/target2k-bmecluster-0-6.local-9955


@@@@ cp /projects/compbiotmp/target02-query/target02-query-1274285010-30210/T0547.a2m m0.a2m


@@@@ checkseq foo -alphabet protein -db m0.a2m > init.check
SAM: checkseq v3.5 (July 15, 2005) compiled 05/31/06_11:54:08
Done with sequence reading


@@@@ rm -rf /tmp/target2k-bmecluster-0-6.local-9955 < /dev/null
*** Error: /projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k/target2k: m0.a2m has 0 alignment columns
A2M format requires upper-case for aligned residues
make: *** [T0547.t2k.a2m.gz] Error 9
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_section_summary_html >> summary.html
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_section_head_summary_html \
		'<A NAME="secondary-structure"> \
		Secondary Structure Prediction</A> \
		<A HREF="http://www.soe.ucsc.edu/research/compbio/SAM_T02/sam-t02-faq.html#secondary-meaning"> \
		(Explanation of secondary-structure predictions) \
		</A>' \
		 >> summary.html
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_section_summary_html >> summary.html
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_section_head_summary_html "Target model scores" >> summary.html
/usr/bin/gmake TARGET=T0547 T0547.t2k.100-30-dssp-ebghstl.mlib \
	T0547.t2k.100-30-dssp-ebghstl.dist \
	T0547.t2k.100-30-dssp-ebghstl-target-scores.rdb \
	T0547.t2k.100-30-dssp-ebghstl-target-scores.html \
	T0547.t2k.100-30-dssp-ebghstl-target-scores.report
gmake[1]: Entering directory `/projects/compbiotmp/target02-query/target02-query-1274285010-30210'
/projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k/target2k -out T0547.t2k \
		-seed T0547.a2m \
		-db /scratch/data/nrp/nr \
		-tmp_dir /tmp \
		-keep_temporary -1 \
		-blast_max_report 2000
Reading /projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k/sam-t2k.conf
Path: /projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k:/projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/sam:/usr/local/bin:/usr/local/gnu/bin:/sbin:/usr/sbin:/bin:/usr/bin


@@@@ chgrp protein /tmp/target2k-bmecluster-0-6.local-9979


@@@@ cp /projects/compbiotmp/target02-query/target02-query-1274285010-30210/T0547.a2m m0.a2m


@@@@ checkseq foo -alphabet protein -db m0.a2m > init.check
SAM: checkseq v3.5 (July 15, 2005) compiled 05/31/06_11:54:08
Done with sequence reading


@@@@ rm -rf /tmp/target2k-bmecluster-0-6.local-9979 < /dev/null
*** Error: /projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k/target2k: m0.a2m has 0 alignment columns
A2M format requires upper-case for aligned residues
gmake[1]: *** [T0547.t2k.a2m.gz] Error 9
gmake[1]: Target `T0547.t2k.100-30-dssp-ebghstl.mlib' not remade because of errors.
gmake[1]: Target `T0547.t2k.100-30-dssp-ebghstl.dist' not remade because of errors.
gmake[1]: Target `T0547.t2k.100-30-dssp-ebghstl-target-scores.rdb' not remade because of errors.
gmake[1]: Target `T0547.t2k.100-30-dssp-ebghstl-target-scores.html' not remade because of errors.
gmake[1]: Target `T0547.t2k.100-30-dssp-ebghstl-target-scores.report' not remade because of errors.
gmake[1]: Leaving directory `/projects/compbiotmp/target02-query/target02-query-1274285010-30210'
make: *** [T0547.t2k.100-30-dssp-ebghstl.target-scores] Error 2
/usr/bin/gmake TARGET=T0547 T0547.t2k.100-30-stride-ebghtl.mlib \
	T0547.t2k.100-30-stride-ebghtl.dist \
	T0547.t2k.100-30-stride-ebghtl-target-scores.rdb \
	T0547.t2k.100-30-stride-ebghtl-target-scores.html \
	T0547.t2k.100-30-stride-ebghtl-target-scores.report
gmake[1]: Entering directory `/projects/compbiotmp/target02-query/target02-query-1274285010-30210'
/projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k/target2k -out T0547.t2k \
		-seed T0547.a2m \
		-db /scratch/data/nrp/nr \
		-tmp_dir /tmp \
		-keep_temporary -1 \
		-blast_max_report 2000
Reading /projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k/sam-t2k.conf
Path: /projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k:/projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/sam:/usr/local/bin:/usr/local/gnu/bin:/sbin:/usr/sbin:/bin:/usr/bin


@@@@ chgrp protein /tmp/target2k-bmecluster-0-6.local-9996


@@@@ cp /projects/compbiotmp/target02-query/target02-query-1274285010-30210/T0547.a2m m0.a2m


@@@@ checkseq foo -alphabet protein -db m0.a2m > init.check
SAM: checkseq v3.5 (July 15, 2005) compiled 05/31/06_11:54:08
Done with sequence reading


@@@@ rm -rf /tmp/target2k-bmecluster-0-6.local-9996 < /dev/null
*** Error: /projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k/target2k: m0.a2m has 0 alignment columns
A2M format requires upper-case for aligned residues
gmake[1]: *** [T0547.t2k.a2m.gz] Error 9
gmake[1]: Target `T0547.t2k.100-30-stride-ebghtl.mlib' not remade because of errors.
gmake[1]: Target `T0547.t2k.100-30-stride-ebghtl.dist' not remade because of errors.
gmake[1]: Target `T0547.t2k.100-30-stride-ebghtl-target-scores.rdb' not remade because of errors.
gmake[1]: Target `T0547.t2k.100-30-stride-ebghtl-target-scores.html' not remade because of errors.
gmake[1]: Target `T0547.t2k.100-30-stride-ebghtl-target-scores.report' not remade because of errors.
gmake[1]: Leaving directory `/projects/compbiotmp/target02-query/target02-query-1274285010-30210'
make: *** [T0547.t2k.100-30-stride-ebghtl.target-scores] Error 2
/usr/bin/gmake TARGET=T0547 T0547.t2k.100-30-str.mlib \
	T0547.t2k.100-30-str.dist \
	T0547.t2k.100-30-str-target-scores.rdb \
	T0547.t2k.100-30-str-target-scores.html \
	T0547.t2k.100-30-str-target-scores.report
gmake[1]: Entering directory `/projects/compbiotmp/target02-query/target02-query-1274285010-30210'
/projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k/target2k -out T0547.t2k \
		-seed T0547.a2m \
		-db /scratch/data/nrp/nr \
		-tmp_dir /tmp \
		-keep_temporary -1 \
		-blast_max_report 2000
Reading /projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k/sam-t2k.conf
Path: /projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k:/projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/sam:/usr/local/bin:/usr/local/gnu/bin:/sbin:/usr/sbin:/bin:/usr/bin


@@@@ chgrp protein /tmp/target2k-bmecluster-0-6.local-10012


@@@@ cp /projects/compbiotmp/target02-query/target02-query-1274285010-30210/T0547.a2m m0.a2m


@@@@ checkseq foo -alphabet protein -db m0.a2m > init.check
SAM: checkseq v3.5 (July 15, 2005) compiled 05/31/06_11:54:08
Done with sequence reading


@@@@ rm -rf /tmp/target2k-bmecluster-0-6.local-10012 < /dev/null
*** Error: /projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/scripts2k/target2k: m0.a2m has 0 alignment columns
A2M format requires upper-case for aligned residues
gmake[1]: *** [T0547.t2k.a2m.gz] Error 9
gmake[1]: Target `T0547.t2k.100-30-str.mlib' not remade because of errors.
gmake[1]: Target `T0547.t2k.100-30-str.dist' not remade because of errors.
gmake[1]: Target `T0547.t2k.100-30-str-target-scores.rdb' not remade because of errors.
gmake[1]: Target `T0547.t2k.100-30-str-target-scores.html' not remade because of errors.
gmake[1]: Target `T0547.t2k.100-30-str-target-scores.report' not remade because of errors.
gmake[1]: Leaving directory `/projects/compbiotmp/target02-query/target02-query-1274285010-30210'
make: *** [T0547.t2k.100-30-str.target-scores] Error 2
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_section_summary_html >> summary.html
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_section_head_summary_html "Template model scores" >> summary.html
/projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/sam/hmmscore T0547.template-lib \
		-modellibrary /projects/compbio/experiments/models.97/indexes/t2k-w0.5-db.mlib \
		-db_size 17000 \
		-db T0547.a2m -rdb 1 \
		-select_score 4 -Emax 40
SAM: /projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/sam/hmmscore v3.5 (July 15, 2005) compiled 06/01/06_09:03:53
Opening T0547.template-lib.dist-rdb for RDB distance output
/projects/compbio/experiments/models.97/indexes/t2k-w0.5-db.mlib(2):  Reading model 1 (2bcoA.t2k-w0.5.mod)
/projects/compbio/experiments/models.97/pdb/2b/2bcoA/nostruct-align/2bcoA.t2k-w0.5.mod(2):  Reading nostruct-align/2bcoA.t2k-w0.5-db-tmp model number 1 from MODEL --  Model from alignment file /var/tmp/tmp-build-weighted-model-farm03-3121/tmp.a2m
Scoring model 2bcoA.t2k-w0.5.mod (nostruct-align/2bcoA.t2k-w0.5-db-tmp model number 1)
Calculating Distances (. = 1000 sequences)
% Subsequence-submodel (local) (SW = 2)
% Simple scores adjusted by +1.5*ln(seq len) (adjust_score = 2)
% Track 0 FIMs added (geometric mean of match probabilities (6))
% Single Track Model:  2bcoA.t2k-w0.5.mod
Error: No sequences found in database files.

make: *** [T0547.template-lib-scores.rdb] Error 1
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_section_summary_html >> summary.html
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_section_head_summary_html "Top Hits" >> summary.html
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_section_summary_html >> summary.html
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/add_section_head_summary_html "Alignments for Top Hits" >> summary.html
/projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/sam/modelfromalign T0547 \
	-alignfile T0547.a2m \
	-insert /projects/compbio/lib/fssp-trained.regularizer \
                -aweight_bits 0.8 \
                -fimtrans -1 \
        -fimstrength 1 \
        -ins_jump_conf 1 \
        -match_jump_conf 1 \
        -del_jump_conf 1 \
        -binary_output 1 \
        -prior_library /projects/compbio/lib/recode3.20comp \
        -a2mdots 0 \
        -a protein \
        -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \
        -aweight_method 1 \
        -aweight_exponent 10 
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: /projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/sam/modelfromalign v3.5 (July 15, 2005) compiled 05/31/06_11:54:00
Reading alignment file T0547.a2m (0 sequences, 0 columns) as all positions alignment.
No alignment found in alignment file T0547.a2m.
Error: No alignment found from which to create a model.

make: *** [T0547.mod] Error 1
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_section_summary_html >> summary.html
/projects/compbio/experiments/protein-predict/SAM_T02/scripts/end_summary_html >> summary.html
make: Target `default' not remade because of errors.