Mercurial > repos > dereeper > uniqprimer
diff uniqprimer-0.5.0/stdout @ 3:3249d78ecfc2 draft
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author | dereeper |
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date | Mon, 03 Jan 2022 09:56:55 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/uniqprimer-0.5.0/stdout Mon Jan 03 09:56:55 2022 +0000 @@ -0,0 +1,504 @@ +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 4831747 +# construct suffix tree for sequence of length 4831747 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 48317 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.55 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpgd6MOr/combined_exlude.ffn" of length 4941439 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpgd6MOr/combined_exlude.ffn" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.99 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.48 +4: FINISHING DATA +5: GENERATING COORDS FILE +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 5240076 +# construct suffix tree for sequence of length 5240076 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 52400 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.58 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpgd6MOr/tempSequences.fasta" of length 366574 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpgd6MOr/tempSequences.fasta" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.83 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.47 +4: FINISHING DATA +5: GENERATING COORDS FILE +Pick PCR primers and hybridization oligos +Search DNA sequences for matches with primer pairs +Search DNA sequences for matches with primer pairs +Search DNA sequences for matches with primer pairs +*** Finding Primers *** +*** Creating Combined Fasta File for Exclude Files *** +*** Finding Sequences Unique to Target Genome *** +*** Running nucmer *** +*** Running nucmer Complete *** +data/PX099A.fa tmpgd6MOr/tempSequences.fasta +*** Running nucmer *** +*** Running nucmer Complete *** +*** Finding Primers *** +*** Running EPrimer3 *** +*** Running EPrimer3 Complete *** +*** Cross Validating Primers *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Time Elapsed: 7 minutes, 25 seconds *** +*** Output Written to primers.txt *** +*** Finished *** +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 5240076 +# construct suffix tree for sequence of length 5240076 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 52400 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.94 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpzf5wS8/combined_exlude.ffn" of length 4941439 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpzf5wS8/combined_exlude.ffn" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.48 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.87 +4: FINISHING DATA +5: GENERATING COORDS FILE +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 4831747 +# construct suffix tree for sequence of length 4831747 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 48317 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.87 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpzf5wS8/tempSequences.fasta" of length 161807 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpzf5wS8/tempSequences.fasta" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.98 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.85 +4: FINISHING DATA +5: GENERATING COORDS FILE +Pick PCR primers and hybridization oligos +Search DNA sequences for matches with primer pairs +Search DNA sequences for matches with primer pairs +Search DNA sequences for matches with primer pairs +*** Finding Primers *** +*** Creating Combined Fasta File for Exclude Files *** +*** Finding Sequences Unique to Target Genome *** +*** Running nucmer *** +*** Running nucmer Complete *** +data/Xoc_BLS256.fasta tmpzf5wS8/tempSequences.fasta +*** Running nucmer *** +*** Running nucmer Complete *** +*** Finding Primers *** +*** Running EPrimer3 *** +*** Running EPrimer3 Complete *** +*** Cross Validating Primers *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Time Elapsed: 6 minutes, 16 seconds *** +*** Output Written to primers.txt *** +*** Finished *** +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 5240076 +# construct suffix tree for sequence of length 5240076 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 52400 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.15 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpbX8CHe/combined_exlude.ffn" of length 4941439 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpbX8CHe/combined_exlude.ffn" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.63 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.87 +4: FINISHING DATA +5: GENERATING COORDS FILE +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 4831747 +# construct suffix tree for sequence of length 4831747 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 48317 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.83 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpbX8CHe/tempSequences.fasta" of length 161807 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpbX8CHe/tempSequences.fasta" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.04 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.85 +4: FINISHING DATA +5: GENERATING COORDS FILE +Pick PCR primers and hybridization oligos +*** Finding Primers *** +*** Creating Combined Fasta File for Exclude Files *** +*** Finding Sequences Unique to Target Genome *** +*** Running nucmer *** +*** Running nucmer Complete *** +data/Xoc_BLS256.fasta tmpbX8CHe/tempSequences.fasta +*** Running nucmer *** +*** Running nucmer Complete *** +*** Finding Primers *** +*** Running EPrimer3 *** +*** Running EPrimer3 Complete *** +*** Time Elapsed: 5 minutes, 0 seconds *** +*** Output Written to primers.txt *** +*** Removing temporary directory *** +*** Finished *** +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 4831747 +# construct suffix tree for sequence of length 4831747 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 48317 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.79 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpuVRdjW/combined_exlude.ffn" of length 4941439 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpuVRdjW/combined_exlude.ffn" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.55 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.48 +4: FINISHING DATA +5: GENERATING COORDS FILE +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 5240076 +# construct suffix tree for sequence of length 5240076 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 52400 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.91 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpuVRdjW/tempSequences.fasta" of length 366574 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpuVRdjW/tempSequences.fasta" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.18 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.47 +4: FINISHING DATA +5: GENERATING COORDS FILE +Pick PCR primers and hybridization oligos +*** Finding Primers *** +*** Creating Combined Fasta File for Exclude Files *** +*** Finding Sequences Unique to Target Genome *** +*** Running nucmer *** +*** Running nucmer Complete *** +data/PX099A.fa tmpuVRdjW/tempSequences.fasta +*** Running nucmer *** +*** Running nucmer Complete *** +*** Finding Primers *** +*** Running EPrimer3 *** +*** Running EPrimer3 Complete *** +*** Time Elapsed: 3 minutes, 16 seconds *** +*** Output Written to primers.txt *** +*** Removing temporary directory *** +*** Finished *** +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 4831747 +# construct suffix tree for sequence of length 4831747 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 48317 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.91 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpLVmpjS/combined_exlude.ffn" of length 4941439 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpLVmpjS/combined_exlude.ffn" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.93 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.48 +4: FINISHING DATA +5: GENERATING COORDS FILE +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 5240076 +# construct suffix tree for sequence of length 5240076 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 52400 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.39 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpLVmpjS/tempSequences.fasta" of length 366574 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpLVmpjS/tempSequences.fasta" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.73 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.47 +4: FINISHING DATA +5: GENERATING COORDS FILE +Pick PCR primers and hybridization oligos +Search DNA sequences for matches with primer pairs +*** Finding Primers *** +*** Creating Combined Fasta File for Exclude Files *** +*** Finding Sequences Unique to Target Genome *** +*** Running nucmer *** +*** Running nucmer Complete *** +data/PX099A.fa tmpLVmpjS/tempSequences.fasta +*** Running nucmer *** +*** Running nucmer Complete *** +*** Finding Primers *** +*** Running EPrimer3 *** +*** Running EPrimer3 Complete *** +*** Cross Validating Primers *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Time Elapsed: 5 minutes, 26 seconds *** +*** Output Written to primers.txt *** +*** Removing temporary directory *** +*** Finished *** +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 4831747 +# construct suffix tree for sequence of length 4831747 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 48317 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.29 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmppJaqDI/combined_exlude.ffn" of length 4941439 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmppJaqDI/combined_exlude.ffn" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 6.73 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.48 +4: FINISHING DATA +5: GENERATING COORDS FILE +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 5240076 +# construct suffix tree for sequence of length 5240076 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 52400 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.27 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmppJaqDI/tempSequences.fasta" of length 366574 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmppJaqDI/tempSequences.fasta" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.60 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.47 +4: FINISHING DATA +5: GENERATING COORDS FILE +Pick PCR primers and hybridization oligos +Search DNA sequences for matches with primer pairs +Search DNA sequences for matches with primer pairs +Search DNA sequences for matches with primer pairs +*** Finding Primers *** +*** Creating Combined Fasta File for Exclude Files *** +*** Finding Sequences Unique to Target Genome *** +*** Running nucmer *** +*** Running nucmer Complete *** +data/PX099A.fa tmppJaqDI/tempSequences.fasta +*** Running nucmer *** +*** Running nucmer Complete *** +*** Finding Primers *** +*** Running EPrimer3 *** +*** Running EPrimer3 Complete *** +*** Cross Validating Primers *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Time Elapsed: 8 minutes, 28 seconds *** +*** Output Written to primers.txt *** +*** Finished *** +Traceback (most recent call last): + File "./uniqprimer.py", line 18, in <module> + from primertools import * + File "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/primertools/excludefilemanager.py", line 7, in <module> + import fastaparser + File "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/primertools/fastaparser.py", line 14, in <module> + from Bio import SeqIO +ImportError: No module named Bio +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 5240076 +# construct suffix tree for sequence of length 5240076 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 52400 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.11 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpFv9Owj/combined_exlude.ffn" of length 4941439 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpFv9Owj/combined_exlude.ffn" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.92 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.87 +4: FINISHING DATA +5: GENERATING COORDS FILE +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 4831747 +# construct suffix tree for sequence of length 4831747 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 48317 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.58 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpFv9Owj/tempSequences.fasta" of length 161807 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpFv9Owj/tempSequences.fasta" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.77 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.85 +4: FINISHING DATA +5: GENERATING COORDS FILE +Pick PCR primers and hybridization oligos +Search DNA sequences for matches with primer pairs +Search DNA sequences for matches with primer pairs +Search DNA sequences for matches with primer pairs +*** Finding Primers *** +*** Creating Combined Fasta File for Exclude Files *** +*** Finding Sequences Unique to Target Genome *** +*** Running nucmer *** +*** Running nucmer Complete *** +data/Xoc_BLS256.fasta tmpFv9Owj/tempSequences.fasta +*** Running nucmer *** +*** Running nucmer Complete *** +*** Finding Primers *** +*** Running EPrimer3 *** +*** Running EPrimer3 Complete *** +*** Cross Validating Primers *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Time Elapsed: 7 minutes, 2 seconds *** +*** Output Written to primers.txt *** +*** Finished *** +Traceback (most recent call last): + File "./uniqprimer.py", line 18, in <module> + from primertools import * + File "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/primertools/excludefilemanager.py", line 7, in <module> + import fastaparser + File "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/primertools/fastaparser.py", line 14, in <module> + from Bio import SeqIO +ImportError: No module named Bio +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 5240076 +# construct suffix tree for sequence of length 5240076 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 52400 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.00 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpPHilD4/combined_exlude.ffn" of length 9773186 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpPHilD4/combined_exlude.ffn" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.99 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 14.56 +4: FINISHING DATA +5: GENERATING COORDS FILE +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 4831747 +# construct suffix tree for sequence of length 4831747 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 48317 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.91 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpPHilD4/tempSequences.fasta" of length 169503 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpPHilD4/tempSequences.fasta" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.07 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.86 +4: FINISHING DATA +5: GENERATING COORDS FILE +Pick PCR primers and hybridization oligos +Search DNA sequences for matches with primer pairs +Search DNA sequences for matches with primer pairs +Search DNA sequences for matches with primer pairs +*** Finding Primers *** +*** Creating Combined Fasta File for Exclude Files *** +*** Finding Sequences Unique to Target Genome *** +*** Running nucmer *** +*** Running nucmer Complete *** +data/Xoc_BLS256.fasta tmpPHilD4/tempSequences.fasta +*** Running nucmer *** +*** Running nucmer Complete *** +*** Finding Primers *** +*** Running EPrimer3 *** +*** Running EPrimer3 Complete *** +*** Cross Validating Primers *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +Failure: No unique primers exist for this combination +*** Finished *** +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 5240076 +# construct suffix tree for sequence of length 5240076 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 52400 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.13 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpz0OJOq/combined_exlude.ffn" of length 9773186 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpz0OJOq/combined_exlude.ffn" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 6.27 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 14.56 +4: FINISHING DATA +5: GENERATING COORDS FILE +1: PREPARING DATA +2,3: RUNNING mummer AND CREATING CLUSTERS +# reading input file "nucmer_alignments.ntref" of length 4831747 +# construct suffix tree for sequence of length 4831747 +# (maximum reference length is 536870908) +# (maximum query length is 4294967295) +# process 48317 characters per dot +#.................................................................................................... +# CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.24 +# reading input file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpz0OJOq/tempSequences.fasta" of length 169503 +# matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpz0OJOq/tempSequences.fasta" +# against subject-file "nucmer_alignments.ntref" +# COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.33 +# SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.86 +4: FINISHING DATA +5: GENERATING COORDS FILE +Pick PCR primers and hybridization oligos +Search DNA sequences for matches with primer pairs +Search DNA sequences for matches with primer pairs +Search DNA sequences for matches with primer pairs +*** Finding Primers *** +*** Creating Combined Fasta File for Exclude Files *** +*** Finding Sequences Unique to Target Genome *** +*** Running nucmer *** +*** Running nucmer Complete *** +data/Xoc_BLS256.fasta tmpz0OJOq/tempSequences.fasta +*** Running nucmer *** +*** Running nucmer Complete *** +*** Finding Primers *** +*** Running EPrimer3 *** +*** Running EPrimer3 Complete *** +*** Cross Validating Primers *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +*** Running PrimerSearch *** +*** Running PrimerSearch Complete *** +Failure: No unique primers exist for this combination +*** Finished ***