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 ***