annotate uniqprimer-0.5.0/stdout @ 3:3249d78ecfc2 draft

Uploaded
author dereeper
date Mon, 03 Jan 2022 09:56:55 +0000
parents
children
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rev   line source
3
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
1 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
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2 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
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3 # reading input file "nucmer_alignments.ntref" of length 4831747
3249d78ecfc2 Uploaded
dereeper
parents:
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4 # construct suffix tree for sequence of length 4831747
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parents:
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5 # (maximum reference length is 536870908)
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dereeper
parents:
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6 # (maximum query length is 4294967295)
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parents:
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7 # process 48317 characters per dot
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parents:
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8 #....................................................................................................
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dereeper
parents:
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9 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.55
3249d78ecfc2 Uploaded
dereeper
parents:
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10 # 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
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dereeper
parents:
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11 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpgd6MOr/combined_exlude.ffn"
3249d78ecfc2 Uploaded
dereeper
parents:
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12 # against subject-file "nucmer_alignments.ntref"
3249d78ecfc2 Uploaded
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parents:
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13 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.99
3249d78ecfc2 Uploaded
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parents:
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14 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.48
3249d78ecfc2 Uploaded
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parents:
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15 4: FINISHING DATA
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parents:
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16 5: GENERATING COORDS FILE
3249d78ecfc2 Uploaded
dereeper
parents:
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17 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
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18 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
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19 # reading input file "nucmer_alignments.ntref" of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
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20 # construct suffix tree for sequence of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
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21 # (maximum reference length is 536870908)
3249d78ecfc2 Uploaded
dereeper
parents:
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22 # (maximum query length is 4294967295)
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parents:
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23 # process 52400 characters per dot
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parents:
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24 #....................................................................................................
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parents:
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25 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.58
3249d78ecfc2 Uploaded
dereeper
parents:
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26 # 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
3249d78ecfc2 Uploaded
dereeper
parents:
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27 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpgd6MOr/tempSequences.fasta"
3249d78ecfc2 Uploaded
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parents:
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28 # against subject-file "nucmer_alignments.ntref"
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parents:
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29 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.83
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parents:
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30 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.47
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parents:
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31 4: FINISHING DATA
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parents:
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32 5: GENERATING COORDS FILE
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dereeper
parents:
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33 Pick PCR primers and hybridization oligos
3249d78ecfc2 Uploaded
dereeper
parents:
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34 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
35 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
36 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
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37 *** Finding Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
38 *** Creating Combined Fasta File for Exclude Files ***
3249d78ecfc2 Uploaded
dereeper
parents:
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39 *** Finding Sequences Unique to Target Genome ***
3249d78ecfc2 Uploaded
dereeper
parents:
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40 *** Running nucmer ***
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parents:
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41 *** Running nucmer Complete ***
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parents:
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42 data/PX099A.fa tmpgd6MOr/tempSequences.fasta
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parents:
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43 *** Running nucmer ***
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parents:
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44 *** Running nucmer Complete ***
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parents:
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45 *** Finding Primers ***
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parents:
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46 *** Running EPrimer3 ***
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parents:
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47 *** Running EPrimer3 Complete ***
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parents:
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48 *** Cross Validating Primers ***
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parents:
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49 *** Running PrimerSearch ***
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parents:
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50 *** Running PrimerSearch Complete ***
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parents:
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51 *** Running PrimerSearch ***
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parents:
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52 *** Running PrimerSearch Complete ***
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parents:
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53 *** Running PrimerSearch ***
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parents:
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54 *** Running PrimerSearch Complete ***
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parents:
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55 *** Time Elapsed: 7 minutes, 25 seconds ***
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parents:
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56 *** Output Written to primers.txt ***
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parents:
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57 *** Finished ***
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parents:
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58 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
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59 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
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60 # reading input file "nucmer_alignments.ntref" of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
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61 # construct suffix tree for sequence of length 5240076
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parents:
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62 # (maximum reference length is 536870908)
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parents:
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63 # (maximum query length is 4294967295)
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parents:
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64 # process 52400 characters per dot
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parents:
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65 #....................................................................................................
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parents:
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66 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.94
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dereeper
parents:
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67 # 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
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parents:
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68 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpzf5wS8/combined_exlude.ffn"
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parents:
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69 # against subject-file "nucmer_alignments.ntref"
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parents:
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70 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.48
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parents:
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71 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.87
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parents:
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72 4: FINISHING DATA
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parents:
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73 5: GENERATING COORDS FILE
3249d78ecfc2 Uploaded
dereeper
parents:
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74 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
75 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
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76 # reading input file "nucmer_alignments.ntref" of length 4831747
3249d78ecfc2 Uploaded
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parents:
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77 # construct suffix tree for sequence of length 4831747
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parents:
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78 # (maximum reference length is 536870908)
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parents:
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79 # (maximum query length is 4294967295)
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parents:
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80 # process 48317 characters per dot
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parents:
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81 #....................................................................................................
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parents:
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82 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.87
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dereeper
parents:
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83 # 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
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dereeper
parents:
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84 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpzf5wS8/tempSequences.fasta"
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parents:
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85 # against subject-file "nucmer_alignments.ntref"
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parents:
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86 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.98
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parents:
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87 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.85
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parents:
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88 4: FINISHING DATA
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dereeper
parents:
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89 5: GENERATING COORDS FILE
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dereeper
parents:
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90 Pick PCR primers and hybridization oligos
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
91 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
92 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
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93 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
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94 *** Finding Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
95 *** Creating Combined Fasta File for Exclude Files ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
96 *** Finding Sequences Unique to Target Genome ***
3249d78ecfc2 Uploaded
dereeper
parents:
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97 *** Running nucmer ***
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parents:
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98 *** Running nucmer Complete ***
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dereeper
parents:
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99 data/Xoc_BLS256.fasta tmpzf5wS8/tempSequences.fasta
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dereeper
parents:
diff changeset
100 *** Running nucmer ***
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dereeper
parents:
diff changeset
101 *** Running nucmer Complete ***
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parents:
diff changeset
102 *** Finding Primers ***
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parents:
diff changeset
103 *** Running EPrimer3 ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
104 *** Running EPrimer3 Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
105 *** Cross Validating Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
106 *** Running PrimerSearch ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
107 *** Running PrimerSearch Complete ***
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dereeper
parents:
diff changeset
108 *** Running PrimerSearch ***
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dereeper
parents:
diff changeset
109 *** Running PrimerSearch Complete ***
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parents:
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110 *** Running PrimerSearch ***
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parents:
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111 *** Running PrimerSearch Complete ***
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parents:
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112 *** Time Elapsed: 6 minutes, 16 seconds ***
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parents:
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113 *** Output Written to primers.txt ***
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parents:
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114 *** Finished ***
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parents:
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115 1: PREPARING DATA
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parents:
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116 2,3: RUNNING mummer AND CREATING CLUSTERS
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parents:
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117 # reading input file "nucmer_alignments.ntref" of length 5240076
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parents:
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118 # construct suffix tree for sequence of length 5240076
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parents:
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119 # (maximum reference length is 536870908)
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parents:
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120 # (maximum query length is 4294967295)
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parents:
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121 # process 52400 characters per dot
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parents:
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122 #....................................................................................................
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parents:
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123 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.15
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parents:
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124 # 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
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parents:
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125 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpbX8CHe/combined_exlude.ffn"
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parents:
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126 # against subject-file "nucmer_alignments.ntref"
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parents:
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127 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.63
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parents:
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128 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.87
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parents:
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129 4: FINISHING DATA
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parents:
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130 5: GENERATING COORDS FILE
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parents:
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131 1: PREPARING DATA
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parents:
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132 2,3: RUNNING mummer AND CREATING CLUSTERS
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parents:
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133 # reading input file "nucmer_alignments.ntref" of length 4831747
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parents:
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134 # construct suffix tree for sequence of length 4831747
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parents:
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135 # (maximum reference length is 536870908)
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parents:
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136 # (maximum query length is 4294967295)
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parents:
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137 # process 48317 characters per dot
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parents:
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138 #....................................................................................................
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parents:
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139 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.83
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parents:
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140 # 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
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parents:
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141 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpbX8CHe/tempSequences.fasta"
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parents:
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142 # against subject-file "nucmer_alignments.ntref"
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parents:
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143 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.04
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parents:
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144 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.85
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parents:
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145 4: FINISHING DATA
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parents:
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146 5: GENERATING COORDS FILE
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dereeper
parents:
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147 Pick PCR primers and hybridization oligos
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dereeper
parents:
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148 *** Finding Primers ***
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dereeper
parents:
diff changeset
149 *** Creating Combined Fasta File for Exclude Files ***
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dereeper
parents:
diff changeset
150 *** Finding Sequences Unique to Target Genome ***
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dereeper
parents:
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151 *** Running nucmer ***
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parents:
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152 *** Running nucmer Complete ***
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parents:
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153 data/Xoc_BLS256.fasta tmpbX8CHe/tempSequences.fasta
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parents:
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154 *** Running nucmer ***
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parents:
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155 *** Running nucmer Complete ***
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parents:
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156 *** Finding Primers ***
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parents:
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157 *** Running EPrimer3 ***
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parents:
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158 *** Running EPrimer3 Complete ***
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parents:
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159 *** Time Elapsed: 5 minutes, 0 seconds ***
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parents:
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160 *** Output Written to primers.txt ***
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parents:
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161 *** Removing temporary directory ***
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parents:
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162 *** Finished ***
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parents:
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163 1: PREPARING DATA
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parents:
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164 2,3: RUNNING mummer AND CREATING CLUSTERS
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parents:
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165 # reading input file "nucmer_alignments.ntref" of length 4831747
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parents:
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166 # construct suffix tree for sequence of length 4831747
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parents:
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167 # (maximum reference length is 536870908)
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parents:
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168 # (maximum query length is 4294967295)
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parents:
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169 # process 48317 characters per dot
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parents:
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170 #....................................................................................................
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parents:
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171 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.79
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parents:
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172 # 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
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parents:
diff changeset
173 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpuVRdjW/combined_exlude.ffn"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
174 # against subject-file "nucmer_alignments.ntref"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
175 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.55
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
176 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.48
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
177 4: FINISHING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
178 5: GENERATING COORDS FILE
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
179 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
180 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
181 # reading input file "nucmer_alignments.ntref" of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
182 # construct suffix tree for sequence of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
183 # (maximum reference length is 536870908)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
184 # (maximum query length is 4294967295)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
185 # process 52400 characters per dot
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
186 #....................................................................................................
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
187 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.91
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
188 # 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
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
189 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpuVRdjW/tempSequences.fasta"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
190 # against subject-file "nucmer_alignments.ntref"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
191 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.18
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
192 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.47
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
193 4: FINISHING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
194 5: GENERATING COORDS FILE
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
195 Pick PCR primers and hybridization oligos
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
196 *** Finding Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
197 *** Creating Combined Fasta File for Exclude Files ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
198 *** Finding Sequences Unique to Target Genome ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
199 *** Running nucmer ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
200 *** Running nucmer Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
201 data/PX099A.fa tmpuVRdjW/tempSequences.fasta
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
202 *** Running nucmer ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
203 *** Running nucmer Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
204 *** Finding Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
205 *** Running EPrimer3 ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
206 *** Running EPrimer3 Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
207 *** Time Elapsed: 3 minutes, 16 seconds ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
208 *** Output Written to primers.txt ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
209 *** Removing temporary directory ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
210 *** Finished ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
211 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
212 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
213 # reading input file "nucmer_alignments.ntref" of length 4831747
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
214 # construct suffix tree for sequence of length 4831747
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
215 # (maximum reference length is 536870908)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
216 # (maximum query length is 4294967295)
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dereeper
parents:
diff changeset
217 # process 48317 characters per dot
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dereeper
parents:
diff changeset
218 #....................................................................................................
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dereeper
parents:
diff changeset
219 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.91
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dereeper
parents:
diff changeset
220 # 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
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
221 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpLVmpjS/combined_exlude.ffn"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
222 # against subject-file "nucmer_alignments.ntref"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
223 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.93
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
224 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.48
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
225 4: FINISHING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
226 5: GENERATING COORDS FILE
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
227 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
228 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
229 # reading input file "nucmer_alignments.ntref" of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
230 # construct suffix tree for sequence of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
231 # (maximum reference length is 536870908)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
232 # (maximum query length is 4294967295)
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dereeper
parents:
diff changeset
233 # process 52400 characters per dot
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
234 #....................................................................................................
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
235 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.39
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
236 # 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
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
237 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpLVmpjS/tempSequences.fasta"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
238 # against subject-file "nucmer_alignments.ntref"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
239 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.73
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
240 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.47
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
241 4: FINISHING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
242 5: GENERATING COORDS FILE
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
243 Pick PCR primers and hybridization oligos
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
244 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
245 *** Finding Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
246 *** Creating Combined Fasta File for Exclude Files ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
247 *** Finding Sequences Unique to Target Genome ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
248 *** Running nucmer ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
249 *** Running nucmer Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
250 data/PX099A.fa tmpLVmpjS/tempSequences.fasta
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
251 *** Running nucmer ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
252 *** Running nucmer Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
253 *** Finding Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
254 *** Running EPrimer3 ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
255 *** Running EPrimer3 Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
256 *** Cross Validating Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
257 *** Running PrimerSearch ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
258 *** Running PrimerSearch Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
259 *** Time Elapsed: 5 minutes, 26 seconds ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
260 *** Output Written to primers.txt ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
261 *** Removing temporary directory ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
262 *** Finished ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
263 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
264 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
265 # reading input file "nucmer_alignments.ntref" of length 4831747
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
266 # construct suffix tree for sequence of length 4831747
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
267 # (maximum reference length is 536870908)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
268 # (maximum query length is 4294967295)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
269 # process 48317 characters per dot
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
270 #....................................................................................................
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
271 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.29
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
272 # 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
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
273 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmppJaqDI/combined_exlude.ffn"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
274 # against subject-file "nucmer_alignments.ntref"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
275 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 6.73
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
276 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.48
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
277 4: FINISHING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
278 5: GENERATING COORDS FILE
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
279 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
280 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
281 # reading input file "nucmer_alignments.ntref" of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
282 # construct suffix tree for sequence of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
283 # (maximum reference length is 536870908)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
284 # (maximum query length is 4294967295)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
285 # process 52400 characters per dot
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
286 #....................................................................................................
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
287 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.27
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
288 # 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
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
289 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmppJaqDI/tempSequences.fasta"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
290 # against subject-file "nucmer_alignments.ntref"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
291 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.60
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
292 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.47
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
293 4: FINISHING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
294 5: GENERATING COORDS FILE
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
295 Pick PCR primers and hybridization oligos
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
296 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
297 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
298 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
299 *** Finding Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
300 *** Creating Combined Fasta File for Exclude Files ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
301 *** Finding Sequences Unique to Target Genome ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
302 *** Running nucmer ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
303 *** Running nucmer Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
304 data/PX099A.fa tmppJaqDI/tempSequences.fasta
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
305 *** Running nucmer ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
306 *** Running nucmer Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
307 *** Finding Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
308 *** Running EPrimer3 ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
309 *** Running EPrimer3 Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
310 *** Cross Validating Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
311 *** Running PrimerSearch ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
312 *** Running PrimerSearch Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
313 *** Running PrimerSearch ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
314 *** Running PrimerSearch Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
315 *** Running PrimerSearch ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
316 *** Running PrimerSearch Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
317 *** Time Elapsed: 8 minutes, 28 seconds ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
318 *** Output Written to primers.txt ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
319 *** Finished ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
320 Traceback (most recent call last):
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
321 File "./uniqprimer.py", line 18, in <module>
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
322 from primertools import *
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
323 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>
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
324 import fastaparser
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
325 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>
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
326 from Bio import SeqIO
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
327 ImportError: No module named Bio
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
328 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
329 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
330 # reading input file "nucmer_alignments.ntref" of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
331 # construct suffix tree for sequence of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
332 # (maximum reference length is 536870908)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
333 # (maximum query length is 4294967295)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
334 # process 52400 characters per dot
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
335 #....................................................................................................
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
336 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.11
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
337 # 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
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
338 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpFv9Owj/combined_exlude.ffn"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
339 # against subject-file "nucmer_alignments.ntref"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
340 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.92
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
341 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.87
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
342 4: FINISHING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
343 5: GENERATING COORDS FILE
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
344 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
345 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
346 # reading input file "nucmer_alignments.ntref" of length 4831747
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
347 # construct suffix tree for sequence of length 4831747
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
348 # (maximum reference length is 536870908)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
349 # (maximum query length is 4294967295)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
350 # process 48317 characters per dot
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
351 #....................................................................................................
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
352 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.58
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
353 # 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
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
354 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpFv9Owj/tempSequences.fasta"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
355 # against subject-file "nucmer_alignments.ntref"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
356 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.77
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
357 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.85
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
358 4: FINISHING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
359 5: GENERATING COORDS FILE
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
360 Pick PCR primers and hybridization oligos
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
361 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
362 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
363 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
364 *** Finding Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
365 *** Creating Combined Fasta File for Exclude Files ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
366 *** Finding Sequences Unique to Target Genome ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
367 *** Running nucmer ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
368 *** Running nucmer Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
369 data/Xoc_BLS256.fasta tmpFv9Owj/tempSequences.fasta
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
370 *** Running nucmer ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
371 *** Running nucmer Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
372 *** Finding Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
373 *** Running EPrimer3 ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
374 *** Running EPrimer3 Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
375 *** Cross Validating Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
376 *** Running PrimerSearch ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
377 *** Running PrimerSearch Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
378 *** Running PrimerSearch ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
379 *** Running PrimerSearch Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
380 *** Running PrimerSearch ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
381 *** Running PrimerSearch Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
382 *** Time Elapsed: 7 minutes, 2 seconds ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
383 *** Output Written to primers.txt ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
384 *** Finished ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
385 Traceback (most recent call last):
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
386 File "./uniqprimer.py", line 18, in <module>
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
387 from primertools import *
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
388 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>
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
389 import fastaparser
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
390 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>
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
391 from Bio import SeqIO
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
392 ImportError: No module named Bio
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
393 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
394 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
395 # reading input file "nucmer_alignments.ntref" of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
396 # construct suffix tree for sequence of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
397 # (maximum reference length is 536870908)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
398 # (maximum query length is 4294967295)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
399 # process 52400 characters per dot
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
400 #....................................................................................................
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
401 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.00
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
402 # 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
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
403 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpPHilD4/combined_exlude.ffn"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
404 # against subject-file "nucmer_alignments.ntref"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
405 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.99
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
406 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 14.56
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
407 4: FINISHING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
408 5: GENERATING COORDS FILE
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
409 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
410 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
411 # reading input file "nucmer_alignments.ntref" of length 4831747
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
412 # construct suffix tree for sequence of length 4831747
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
413 # (maximum reference length is 536870908)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
414 # (maximum query length is 4294967295)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
415 # process 48317 characters per dot
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
416 #....................................................................................................
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
417 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.91
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
418 # 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
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
419 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpPHilD4/tempSequences.fasta"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
420 # against subject-file "nucmer_alignments.ntref"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
421 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.07
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
422 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.86
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
423 4: FINISHING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
424 5: GENERATING COORDS FILE
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
425 Pick PCR primers and hybridization oligos
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
426 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
427 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
428 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
429 *** Finding Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
430 *** Creating Combined Fasta File for Exclude Files ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
431 *** Finding Sequences Unique to Target Genome ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
432 *** Running nucmer ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
433 *** Running nucmer Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
434 data/Xoc_BLS256.fasta tmpPHilD4/tempSequences.fasta
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
435 *** Running nucmer ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
436 *** Running nucmer Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
437 *** Finding Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
438 *** Running EPrimer3 ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
439 *** Running EPrimer3 Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
440 *** Cross Validating Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
441 *** Running PrimerSearch ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
442 *** Running PrimerSearch Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
443 *** Running PrimerSearch ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
444 *** Running PrimerSearch Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
445 *** Running PrimerSearch ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
446 *** Running PrimerSearch Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
447 Failure: No unique primers exist for this combination
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
448 *** Finished ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
449 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
450 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
451 # reading input file "nucmer_alignments.ntref" of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
452 # construct suffix tree for sequence of length 5240076
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
453 # (maximum reference length is 536870908)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
454 # (maximum query length is 4294967295)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
455 # process 52400 characters per dot
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
456 #....................................................................................................
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
457 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.13
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
458 # 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
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
459 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpz0OJOq/combined_exlude.ffn"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
460 # against subject-file "nucmer_alignments.ntref"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
461 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 6.27
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
462 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 14.56
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
463 4: FINISHING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
464 5: GENERATING COORDS FILE
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
465 1: PREPARING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
466 2,3: RUNNING mummer AND CREATING CLUSTERS
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
467 # reading input file "nucmer_alignments.ntref" of length 4831747
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
468 # construct suffix tree for sequence of length 4831747
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
469 # (maximum reference length is 536870908)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
470 # (maximum query length is 4294967295)
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
471 # process 48317 characters per dot
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
472 #....................................................................................................
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
473 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.24
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
474 # 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
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
475 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpz0OJOq/tempSequences.fasta"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
476 # against subject-file "nucmer_alignments.ntref"
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
477 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.33
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
478 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.86
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
479 4: FINISHING DATA
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
480 5: GENERATING COORDS FILE
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
481 Pick PCR primers and hybridization oligos
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
482 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
483 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
484 Search DNA sequences for matches with primer pairs
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
485 *** Finding Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
486 *** Creating Combined Fasta File for Exclude Files ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
487 *** Finding Sequences Unique to Target Genome ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
488 *** Running nucmer ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
489 *** Running nucmer Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
490 data/Xoc_BLS256.fasta tmpz0OJOq/tempSequences.fasta
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
491 *** Running nucmer ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
492 *** Running nucmer Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
493 *** Finding Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
494 *** Running EPrimer3 ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
495 *** Running EPrimer3 Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
496 *** Cross Validating Primers ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
497 *** Running PrimerSearch ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
498 *** Running PrimerSearch Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
499 *** Running PrimerSearch ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
500 *** Running PrimerSearch Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
501 *** Running PrimerSearch ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
502 *** Running PrimerSearch Complete ***
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
503 Failure: No unique primers exist for this combination
3249d78ecfc2 Uploaded
dereeper
parents:
diff changeset
504 *** Finished ***