MARC::blastxCDS

perl diya.pl -conf conf/genome-annotator-for-ncbi.xml tmp/NZ_ABZT01 -out 007 -set OUTPUTDIR=007 -set MYSEQID=008 -set MYUNIREFD=db/uniref50/uniref50.fasta -set MYRPSD=db/cdd/Cdd -set MYCLUSTERS=db/clusters/PRK_Clusters.bcp -set MYCDD=db/cddid_all.tbl

Do It Yourself Annotator (diya) v. 1.0;
	--help for usage
	--license for copyright information

The diya home directory is '/home/jasperk/Apps/DIYA-master/'
Using '007/' as output directory
--set: the value of the global variable $OUTPUTDIR will be '007'
--set: the value of the global variable $MYSEQID will be '008'
--set: the value of the global variable $MYUNIREFD will be 'db/uniref50/uniref50.fasta'
--set: the value of the global variable $MYRPSD will be 'db/cdd/Cdd'
--set: the value of the global variable $MYCLUSTERS will be 'db/clusters/PRK_Clusters.bcp'
--set: the value of the global variable $MYCDD will be 'db/cddid_all.tbl'
Using 'conf/genome-annotator-for-ncbi.xml'
Reading 'conf/genome-annotator-for-ncbi.xml'
File count is 1
Next input file is 'tmp/NZ_ABZT01'
<mode> for the pipeline is 'serial'
Current <order> is 'assemble_pseudocontig make-single-fa MARC::glimmer3 extractCDS MARC::blastpCDS MARC::rpsblastCDS'

Preparing to run 'assemble_pseudocontig', step count of 1
'assemble_pseudocontig' is a 'script'
'assemble_pseudocontig' is a 'script'
Format of 'tmp/NZ_ABZT01' is 'fasta'
No <inputformat> found for step 'assemble_pseudocontig', no conversion needed
No <inputfrom> found for 'assemble_pseudocontig'
'tmp/NZ_ABZT01' will be used as input file for 'assemble_pseudocontig'
Using '007/' as output directory
'007/NZ_ABZT01' will be used as input file for 'assemble_pseudocontig'
Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'assemble_pseudocontig'
Found <executable> 'diya-assemble_pseudocontig.pl' for 'assemble_pseudocontig' in 'conf/genome-annotator-for-ncbi.xml'
Using '007/' as output directory
Output file name for 'assemble_pseudocontig' is '007/2012_11_16_17_41_11-assemble_pseudocontig.out'
Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'assemble_pseudocontig'
Found <executable> 'diya-assemble_pseudocontig.pl' for 'assemble_pseudocontig' in 'conf/genome-annotator-for-ncbi.xml'
Found <command> '-infile INPUTFILE -scaff MYSCAFF -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID -outdir OUTPUTDIR' for 'assemble_pseudocontig'
Found <command> '-infile INPUTFILE -scaff MYSCAFF -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID -outdir OUTPUTDIR' for 'assemble_pseudocontig'
'assemble_pseudocontig' command before substitution is '/home/jasperk/Apps/DIYA-master/scripts/diya-assemble_pseudocontig.pl -infile INPUTFILE -scaff MYSCAFF -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID -outdir OUTPUTDIR'
'INPUTFILE' will be substituted with '007/NZ_ABZT01'
'OUTPUTFILE' will be substituted with '007/2012_11_16_17_41_11-assemble_pseudocontig.out'
'assemble_pseudocontig' command after parser-specific substitution is '/home/jasperk/Apps/DIYA-master/scripts/diya-assemble_pseudocontig.pl -infile 007/NZ_ABZT01 -scaff MYSCAFF -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID -outdir OUTPUTDIR'
Using '007/' as output directory
'OUTPUTDIR' will be substituted with '007/'
'assemble_pseudocontig' command after global substitution is '/home/jasperk/Apps/DIYA-master/scripts/diya-assemble_pseudocontig.pl -infile 007/NZ_ABZT01 -scaff MYSCAFF -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID -outdir 007/'
'MYCDD' will be substituted with 'db/cddid_all.tbl'
'MYUNIREFD' will be substituted with 'db/uniref50/uniref50.fasta'
'MYSEQID' will be substituted with '008'
'MYCLUSTERS' will be substituted with 'db/clusters/PRK_Clusters.bcp'
'MYRPSD' will be substituted with 'db/cdd/Cdd'
'OUTPUTDIR' will be substituted with '007'
'assemble_pseudocontig' command after variable substitution is '/home/jasperk/Apps/DIYA-master/scripts/diya-assemble_pseudocontig.pl -infile 007/NZ_ABZT01 -scaff MYSCAFF -species MYSPECIES -strain MYSTRAIN -seqid 008 -outdir 007/'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
Scaffold file appears not to exist at MYSCAFF. Carrying on without scaffolding

Total size of pseudocontig = 13930
Contigs tiled  = 0
Total length of tiled contigs =
Untiled contigs = 1
Total length of untiled contigs = 13930
Number of excluded contigs =
Total length of excluded contigs = 0

Preparing to run 'make-single-fa', step count of 2
'make-single-fa' is a 'script'
'make-single-fa' is a 'script'
Format of 'tmp/NZ_ABZT01' is 'fasta'
No <inputformat> found for step 'make-single-fa', no conversion needed
No <inputfrom> found for 'make-single-fa'
'tmp/NZ_ABZT01' will be used as input file for 'make-single-fa'
Using '007/' as output directory
'007/NZ_ABZT01' will be used as input file for 'make-single-fa'
Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'make-single-fa'
Found <executable> 'make-single-fa.pl' for 'make-single-fa' in 'conf/genome-annotator-for-ncbi.xml'
Using '007/' as output directory
Output file name for 'make-single-fa' is '007/2012_11_16_17_41_12-make-single-fa.out'
Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'make-single-fa'
Found <executable> 'make-single-fa.pl' for 'make-single-fa' in 'conf/genome-annotator-for-ncbi.xml'
Found <command> 'MYSEQID.gbk OUTPUTDIR' for 'make-single-fa'
Found <command> 'MYSEQID.gbk OUTPUTDIR' for 'make-single-fa'
'make-single-fa' command before substitution is '/home/jasperk/Apps/DIYA-master/scripts/make-single-fa.pl MYSEQID.gbk OUTPUTDIR'
'INPUTFILE' will be substituted with '007/NZ_ABZT01'
'OUTPUTFILE' will be substituted with '007/2012_11_16_17_41_12-make-single-fa.out'
'make-single-fa' command after parser-specific substitution is '/home/jasperk/Apps/DIYA-master/scripts/make-single-fa.pl MYSEQID.gbk OUTPUTDIR'
Using '007/' as output directory
'OUTPUTDIR' will be substituted with '007/'
'make-single-fa' command after global substitution is '/home/jasperk/Apps/DIYA-master/scripts/make-single-fa.pl MYSEQID.gbk 007/'
'MYCDD' will be substituted with 'db/cddid_all.tbl'
'MYUNIREFD' will be substituted with 'db/uniref50/uniref50.fasta'
'MYSEQID' will be substituted with '008'
'MYCLUSTERS' will be substituted with 'db/clusters/PRK_Clusters.bcp'
'MYRPSD' will be substituted with 'db/cdd/Cdd'
'OUTPUTDIR' will be substituted with '007'
'make-single-fa' command after variable substitution is '/home/jasperk/Apps/DIYA-master/scripts/make-single-fa.pl 008.gbk 007/'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'

Preparing to run 'MARC::glimmer3', step count of 3
'MARC::glimmer3' is a 'parser'
Loaded module 'diya::MARC::glimmer3'
'MARC::glimmer3' is a 'parser'
No <inputformat> for 'MARC::glimmer3'
Format of 'tmp/NZ_ABZT01' is 'fasta'
No <inputformat> found for step 'MARC::glimmer3', no conversion needed
No <inputfrom> found for 'MARC::glimmer3'
'tmp/NZ_ABZT01' will be used as input file for 'MARC::glimmer3'
Using '007/' as output directory
'007/NZ_ABZT01' will be used as input file for 'MARC::glimmer3'
Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'MARC::glimmer3'
Found <executable> 'g3-from-scratch2.csh' for 'MARC::glimmer3' in 'conf/genome-annotator-for-ncbi.xml'
Using '007/' as output directory
Output file name for 'MARC::glimmer3' is '007/2012_11_16_17_41_12-MARC::glimmer3.out'
Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'MARC::glimmer3'
Found <executable> 'g3-from-scratch2.csh' for 'MARC::glimmer3' in 'conf/genome-annotator-for-ncbi.xml'
Found <command> 'MYSEQID.fa MYSEQID OUTPUTDIR' for 'MARC::glimmer3'
Found <command> 'MYSEQID.fa MYSEQID OUTPUTDIR' for 'MARC::glimmer3'
'MARC::glimmer3' command before substitution is '/home/jasperk/Apps/DIYA-master/scripts/g3-from-scratch2.csh MYSEQID.fa MYSEQID OUTPUTDIR'
'INPUTFILE' will be substituted with '007/NZ_ABZT01'
'OUTPUTFILE' will be substituted with '007/2012_11_16_17_41_12-MARC::glimmer3.out'
'MARC::glimmer3' command after parser-specific substitution is '/home/jasperk/Apps/DIYA-master/scripts/g3-from-scratch2.csh MYSEQID.fa MYSEQID OUTPUTDIR'
Using '007/' as output directory
'OUTPUTDIR' will be substituted with '007/'
'MARC::glimmer3' command after global substitution is '/home/jasperk/Apps/DIYA-master/scripts/g3-from-scratch2.csh MYSEQID.fa MYSEQID 007/'
'MYCDD' will be substituted with 'db/cddid_all.tbl'
'MYUNIREFD' will be substituted with 'db/uniref50/uniref50.fasta'
'MYSEQID' will be substituted with '008'
'MYCLUSTERS' will be substituted with 'db/clusters/PRK_Clusters.bcp'
'MYRPSD' will be substituted with 'db/cdd/Cdd'
'OUTPUTDIR' will be substituted with '007'
'MARC::glimmer3' command after variable substitution is '/home/jasperk/Apps/DIYA-master/scripts/g3-from-scratch2.csh 008.fa 008 007/'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
Starting at Fri Nov 16 17:41:12 2012

Sequence file = 007//008.fa
Excluded regions file = none
Circular genome = true
Initial minimum gene length = 90 bp
Determine optimal min gene length to maximize number of genes
Maximum overlap bases = 30
Start codons = atg,gtg,ttg
Stop codons = taa,tag,tga
Sequence length = 13930
Final minimum gene length = 286
Number of genes = 10
Total bases = 4965
Starting at Fri Nov 16 17:41:12 2012

Sequence file = 007//008.fa
Number of sequences = 1
ICM model file = 007//008.icm
Excluded regions file = none
List of orfs file = none
Input is NOT separate orfs
Independent (non-coding) scores are used
Circular genome = false
Truncated orfs = false
Minimum gene length = 110 bp
Maximum overlap bases = 50
Threshold score = 30
Use first start codon = false
Start codons = atg,gtg,ttg
Start probs = 0.600,0.300,0.100
Stop codons = taa,tag,tga
GC percentage = 40.9%
Ignore score on orfs longer than 572
Analyzing Sequence #1
Start Find_Orfs
Start Score_Orfs
Start Process_Events
Start Trace_Back
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
Step 1 of 4:  Finding long orfs for training
Step 2 of 4:  Extracting training sequences
Step 3 of 4:  Building ICM
Step 4 of 4:  Running Glimmer3
/usr/bin/tigr-glimmer glimmer3 -l -o50 -g110 -t30 007//008.fa 007//008.icm 007//008
Finished with g3-from-scratch

Created 'diya::MARC::glimmer3' object
Parsing 007/008.predict
Using '007/' as output directory
Sequence is 007/008.gbk
007/2012_11_16_17_41_12-MARC::glimmer3.outFound output file '007/2012_11_16_17_41_12-MARC::glimmer3.out' for 'MARC::glimmer3'
Preparing to run 'extractCDS', step count of 4
'extractCDS' is a 'script'
'extractCDS' is a 'script'
Format of 'tmp/NZ_ABZT01' is 'fasta'
No <inputformat> found for step 'extractCDS', no conversion needed
Found <inputfrom> 'MARC::glimmer3' for 'extractCDS'
Output file from 'MARC::glimmer3' will be used as input file for 'extractCDS'
Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'extractCDS'
Found <executable> 'extractCDS.pl' for 'extractCDS' in 'conf/genome-annotator-for-ncbi.xml'
Using '007/' as output directory
Output file name for 'extractCDS' is '007/2012_11_16_17_41_12-extractCDS.out'
Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'extractCDS'
Found <executable> 'extractCDS.pl' for 'extractCDS' in 'conf/genome-annotator-for-ncbi.xml'
Found <command> 'INPUTFILE OUTPUTFILE OUTPUTDIR' for 'extractCDS'
Found <command> 'INPUTFILE OUTPUTFILE OUTPUTDIR' for 'extractCDS'
'extractCDS' command before substitution is '/home/jasperk/Apps/DIYA-master/scripts/extractCDS.pl INPUTFILE OUTPUTFILE OUTPUTDIR'
'INPUTFILE' will be substituted with '007/2012_11_16_17_41_12-MARC::glimmer3.out'
'OUTPUTFILE' will be substituted with '007/2012_11_16_17_41_12-extractCDS.out'
'extractCDS' command after parser-specific substitution is '/home/jasperk/Apps/DIYA-master/scripts/extractCDS.pl 007/2012_11_16_17_41_12-MARC::glimmer3.out 007/2012_11_16_17_41_12-extractCDS.out OUTPUTDIR'
Using '007/' as output directory
'OUTPUTDIR' will be substituted with '007/'
'extractCDS' command after global substitution is '/home/jasperk/Apps/DIYA-master/scripts/extractCDS.pl 007/2012_11_16_17_41_12-MARC::glimmer3.out 007/2012_11_16_17_41_12-extractCDS.out 007/'
'MYCDD' will be substituted with 'db/cddid_all.tbl'
'MYUNIREFD' will be substituted with 'db/uniref50/uniref50.fasta'
'MYSEQID' will be substituted with '008'
'MYCLUSTERS' will be substituted with 'db/clusters/PRK_Clusters.bcp'
'MYRPSD' will be substituted with 'db/cdd/Cdd'
'OUTPUTDIR' will be substituted with '007'
'extractCDS' command after variable substitution is '/home/jasperk/Apps/DIYA-master/scripts/extractCDS.pl 007/2012_11_16_17_41_12-MARC::glimmer3.out 007/2012_11_16_17_41_12-extractCDS.out 007/'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'

Preparing to run 'MARC::blastpCDS', step count of 5
'MARC::blastpCDS' is a 'parser'
Loaded module 'diya::MARC::blastpCDS'
'MARC::blastpCDS' is a 'parser'
No <inputformat> for 'MARC::blastpCDS'
Format of 'tmp/NZ_ABZT01' is 'fasta'
No <inputformat> found for step 'MARC::blastpCDS', no conversion needed
Found <inputfrom> 'extractCDS' for 'MARC::blastpCDS'
Output file from 'extractCDS' will be used as input file for 'MARC::blastpCDS'
Found <home> '/usr/bin/' for 'MARC::blastpCDS'
Found <executable> 'blastall' for 'MARC::blastpCDS' in 'conf/genome-annotator-for-ncbi.xml'
Using '007/' as output directory
Output file name for 'MARC::blastpCDS' is '007/2012_11_16_17_41_12-MARC::blastpCDS.out'
Found <home> '/usr/bin/' for 'MARC::blastpCDS'
Found <executable> 'blastall' for 'MARC::blastpCDS' in 'conf/genome-annotator-for-ncbi.xml'
Found <command> '-i INPUTFILE -p blastx -d MYUNIREFD -o OUTPUTFILE -e .001 -v 1 -b 1 -a 8' for 'MARC::blastpCDS'
Found <command> '-i INPUTFILE -p blastx -d MYUNIREFD -o OUTPUTFILE -e .001 -v 1 -b 1 -a 8' for 'MARC::blastpCDS'
'MARC::blastpCDS' command before substitution is '/usr/bin/blastall -i INPUTFILE -p blastx -d MYUNIREFD -o OUTPUTFILE -e .001 -v 1 -b 1 -a 8'
'INPUTFILE' will be substituted with '007/2012_11_16_17_41_12-extractCDS.out'
'OUTPUTFILE' will be substituted with '007/2012_11_16_17_41_12-MARC::blastpCDS.out'
'MARC::blastpCDS' command after parser-specific substitution is '/usr/bin/blastall -i 007/2012_11_16_17_41_12-extractCDS.out -p blastx -d MYUNIREFD -o 007/2012_11_16_17_41_12-MARC::blastpCDS.out -e .001 -v 1 -b 1 -a 8'
Using '007/' as output directory
'OUTPUTDIR' will be substituted with '007/'
'MARC::blastpCDS' command after global substitution is '/usr/bin/blastall -i 007/2012_11_16_17_41_12-extractCDS.out -p blastx -d MYUNIREFD -o 007/2012_11_16_17_41_12-MARC::blastpCDS.out -e .001 -v 1 -b 1 -a 8'
'MYCDD' will be substituted with 'db/cddid_all.tbl'
'MYUNIREFD' will be substituted with 'db/uniref50/uniref50.fasta'
'MYSEQID' will be substituted with '008'
'MYCLUSTERS' will be substituted with 'db/clusters/PRK_Clusters.bcp'
'MYRPSD' will be substituted with 'db/cdd/Cdd'
'OUTPUTDIR' will be substituted with '007'
'MARC::blastpCDS' command after variable substitution is '/usr/bin/blastall -i 007/2012_11_16_17_41_12-extractCDS.out -p blastx -d db/uniref50/uniref50.fasta -o 007/2012_11_16_17_41_12-MARC::blastpCDS.out -e .001 -v 1 -b 1 -a 8'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'

Created 'diya::MARC::blastpCDS' object
007/2012_11_16_17_41_12-MARC::blastpCDS.outFound output file '007/2012_11_16_17_41_12-MARC::blastpCDS.out' for 'MARC::blastpCDS'
Indexing '007/2012_11_16_17_41_12-MARC::blastpCDS.out'
007/2012_11_16_17_41_12-MARC::glimmer3.outFound output file '007/2012_11_16_17_41_12-MARC::glimmer3.out' for 'MARC::glimmer3'
Genbank output file is '007/2012_11_16_17_41_12-MARC::blastpCDS.out.gbk'
Preparing to run 'MARC::rpsblastCDS', step count of 6
'MARC::rpsblastCDS' is a 'parser'
Loaded module 'diya::MARC::rpsblastCDS'
'MARC::rpsblastCDS' is a 'parser'
No <inputformat> for 'MARC::rpsblastCDS'
Format of 'tmp/NZ_ABZT01' is 'fasta'
No <inputformat> found for step 'MARC::rpsblastCDS', no conversion needed
Found <inputfrom> 'extractCDS' for 'MARC::rpsblastCDS'
Output file from 'extractCDS' will be used as input file for 'MARC::rpsblastCDS'
Found <home> '/usr/bin/' for 'MARC::rpsblastCDS'
Found <executable> 'rpsblast' for 'MARC::rpsblastCDS' in 'conf/genome-annotator-for-ncbi.xml'
Using '007/' as output directory
Output file name for 'MARC::rpsblastCDS' is '007/2012_11_16_17_42_34-MARC::rpsblastCDS.out'
Found <home> '/usr/bin/' for 'MARC::rpsblastCDS'
Found <executable> 'rpsblast' for 'MARC::rpsblastCDS' in 'conf/genome-annotator-for-ncbi.xml'
Found <command> '-d MYRPSD -i INPUTFILE -o OUTPUTFILE -e .001 -I T -p F -v 1 -b 1 -a 8' for 'MARC::rpsblastCDS'
Found <command> '-d MYRPSD -i INPUTFILE -o OUTPUTFILE -e .001 -I T -p F -v 1 -b 1 -a 8' for 'MARC::rpsblastCDS'
'MARC::rpsblastCDS' command before substitution is '/usr/bin/rpsblast -d MYRPSD -i INPUTFILE -o OUTPUTFILE -e .001 -I T -p F -v 1 -b 1 -a 8'
'INPUTFILE' will be substituted with '007/2012_11_16_17_41_12-extractCDS.out'
'OUTPUTFILE' will be substituted with '007/2012_11_16_17_42_34-MARC::rpsblastCDS.out'
'MARC::rpsblastCDS' command after parser-specific substitution is '/usr/bin/rpsblast -d MYRPSD -i 007/2012_11_16_17_41_12-extractCDS.out -o 007/2012_11_16_17_42_34-MARC::rpsblastCDS.out -e .001 -I T -p F -v 1 -b 1 -a 8'
Using '007/' as output directory
'OUTPUTDIR' will be substituted with '007/'
'MARC::rpsblastCDS' command after global substitution is '/usr/bin/rpsblast -d MYRPSD -i 007/2012_11_16_17_41_12-extractCDS.out -o 007/2012_11_16_17_42_34-MARC::rpsblastCDS.out -e .001 -I T -p F -v 1 -b 1 -a 8'
'MYCDD' will be substituted with 'db/cddid_all.tbl'
'MYUNIREFD' will be substituted with 'db/uniref50/uniref50.fasta'
'MYSEQID' will be substituted with '008'
'MYCLUSTERS' will be substituted with 'db/clusters/PRK_Clusters.bcp'
'MYRPSD' will be substituted with 'db/cdd/Cdd'
'OUTPUTDIR' will be substituted with '007'
'MARC::rpsblastCDS' command after variable substitution is '/usr/bin/rpsblast -d db/cdd/Cdd -i 007/2012_11_16_17_41_12-extractCDS.out -o 007/2012_11_16_17_42_34-MARC::rpsblastCDS.out -e .001 -I T -p F -v 1 -b 1 -a 8'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'

Created 'diya::MARC::rpsblastCDS' object
Cluster map from 'db/clusters/PRK_Clusters.bcp' loaded
CDD map from 'db/cddid_all.tbl' loaded
007/2012_11_16_17_42_34-MARC::rpsblastCDS.outFound output file '007/2012_11_16_17_42_34-MARC::rpsblastCDS.out' for 'MARC::rpsblastCDS'
Indexing '007/2012_11_16_17_42_34-MARC::rpsblastCDS.out'
No output file name for parser 'MARC::blastxCDS' found at /usr/local/share/perl/5.14.2/diya.pm line 1542.