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