Mercurial > repos > dereeper > uniqprimer

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

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author dereeper
date Mon, 03 Jan 2022 09:56:55 +0000
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2:7e0438dad4e9 3:3249d78ecfc2
1 1: PREPARING DATA
2 2,3: RUNNING mummer AND CREATING CLUSTERS
3 # reading input file "nucmer_alignments.ntref" of length 4831747
4 # construct suffix tree for sequence of length 4831747
5 # (maximum reference length is 536870908)
6 # (maximum query length is 4294967295)
7 # process 48317 characters per dot
8 #....................................................................................................
9 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.55
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
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"
12 # against subject-file "nucmer_alignments.ntref"
13 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.99
14 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.48
15 4: FINISHING DATA
16 5: GENERATING COORDS FILE
17 1: PREPARING DATA
18 2,3: RUNNING mummer AND CREATING CLUSTERS
19 # reading input file "nucmer_alignments.ntref" of length 5240076
20 # construct suffix tree for sequence of length 5240076
21 # (maximum reference length is 536870908)
22 # (maximum query length is 4294967295)
23 # process 52400 characters per dot
24 #....................................................................................................
25 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.58
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
27 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpgd6MOr/tempSequences.fasta"
28 # against subject-file "nucmer_alignments.ntref"
29 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.83
30 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.47
31 4: FINISHING DATA
32 5: GENERATING COORDS FILE
33 Pick PCR primers and hybridization oligos
34 Search DNA sequences for matches with primer pairs
35 Search DNA sequences for matches with primer pairs
36 Search DNA sequences for matches with primer pairs
37 *** Finding Primers ***
38 *** Creating Combined Fasta File for Exclude Files ***
39 *** Finding Sequences Unique to Target Genome ***
40 *** Running nucmer ***
41 *** Running nucmer Complete ***
42 data/PX099A.fa tmpgd6MOr/tempSequences.fasta
43 *** Running nucmer ***
44 *** Running nucmer Complete ***
45 *** Finding Primers ***
46 *** Running EPrimer3 ***
47 *** Running EPrimer3 Complete ***
48 *** Cross Validating Primers ***
49 *** Running PrimerSearch ***
50 *** Running PrimerSearch Complete ***
51 *** Running PrimerSearch ***
52 *** Running PrimerSearch Complete ***
53 *** Running PrimerSearch ***
54 *** Running PrimerSearch Complete ***
55 *** Time Elapsed: 7 minutes, 25 seconds ***
56 *** Output Written to primers.txt ***
57 *** Finished ***
58 1: PREPARING DATA
59 2,3: RUNNING mummer AND CREATING CLUSTERS
60 # reading input file "nucmer_alignments.ntref" of length 5240076
61 # construct suffix tree for sequence of length 5240076
62 # (maximum reference length is 536870908)
63 # (maximum query length is 4294967295)
64 # process 52400 characters per dot
65 #....................................................................................................
66 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.94
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
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"
69 # against subject-file "nucmer_alignments.ntref"
70 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.48
71 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.87
72 4: FINISHING DATA
73 5: GENERATING COORDS FILE
74 1: PREPARING DATA
75 2,3: RUNNING mummer AND CREATING CLUSTERS
76 # reading input file "nucmer_alignments.ntref" of length 4831747
77 # construct suffix tree for sequence of length 4831747
78 # (maximum reference length is 536870908)
79 # (maximum query length is 4294967295)
80 # process 48317 characters per dot
81 #....................................................................................................
82 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.87
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
84 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpzf5wS8/tempSequences.fasta"
85 # against subject-file "nucmer_alignments.ntref"
86 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.98
87 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.85
88 4: FINISHING DATA
89 5: GENERATING COORDS FILE
90 Pick PCR primers and hybridization oligos
91 Search DNA sequences for matches with primer pairs
92 Search DNA sequences for matches with primer pairs
93 Search DNA sequences for matches with primer pairs
94 *** Finding Primers ***
95 *** Creating Combined Fasta File for Exclude Files ***
96 *** Finding Sequences Unique to Target Genome ***
97 *** Running nucmer ***
98 *** Running nucmer Complete ***
99 data/Xoc_BLS256.fasta tmpzf5wS8/tempSequences.fasta
100 *** Running nucmer ***
101 *** Running nucmer Complete ***
102 *** Finding Primers ***
103 *** Running EPrimer3 ***
104 *** Running EPrimer3 Complete ***
105 *** Cross Validating Primers ***
106 *** Running PrimerSearch ***
107 *** Running PrimerSearch Complete ***
108 *** Running PrimerSearch ***
109 *** Running PrimerSearch Complete ***
110 *** Running PrimerSearch ***
111 *** Running PrimerSearch Complete ***
112 *** Time Elapsed: 6 minutes, 16 seconds ***
113 *** Output Written to primers.txt ***
114 *** Finished ***
115 1: PREPARING DATA
116 2,3: RUNNING mummer AND CREATING CLUSTERS
117 # reading input file "nucmer_alignments.ntref" of length 5240076
118 # construct suffix tree for sequence of length 5240076
119 # (maximum reference length is 536870908)
120 # (maximum query length is 4294967295)
121 # process 52400 characters per dot
122 #....................................................................................................
123 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.15
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
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"
126 # against subject-file "nucmer_alignments.ntref"
127 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.63
128 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.87
129 4: FINISHING DATA
130 5: GENERATING COORDS FILE
131 1: PREPARING DATA
132 2,3: RUNNING mummer AND CREATING CLUSTERS
133 # reading input file "nucmer_alignments.ntref" of length 4831747
134 # construct suffix tree for sequence of length 4831747
135 # (maximum reference length is 536870908)
136 # (maximum query length is 4294967295)
137 # process 48317 characters per dot
138 #....................................................................................................
139 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.83
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
141 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpbX8CHe/tempSequences.fasta"
142 # against subject-file "nucmer_alignments.ntref"
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
145 4: FINISHING DATA
146 5: GENERATING COORDS FILE
147 Pick PCR primers and hybridization oligos
148 *** Finding Primers ***
149 *** Creating Combined Fasta File for Exclude Files ***
150 *** Finding Sequences Unique to Target Genome ***
151 *** Running nucmer ***
152 *** Running nucmer Complete ***
153 data/Xoc_BLS256.fasta tmpbX8CHe/tempSequences.fasta
154 *** Running nucmer ***
155 *** Running nucmer Complete ***
156 *** Finding Primers ***
157 *** Running EPrimer3 ***
158 *** Running EPrimer3 Complete ***
159 *** Time Elapsed: 5 minutes, 0 seconds ***
160 *** Output Written to primers.txt ***
161 *** Removing temporary directory ***
162 *** Finished ***
163 1: PREPARING DATA
164 2,3: RUNNING mummer AND CREATING CLUSTERS
165 # reading input file "nucmer_alignments.ntref" of length 4831747
166 # construct suffix tree for sequence of length 4831747
167 # (maximum reference length is 536870908)
168 # (maximum query length is 4294967295)
169 # process 48317 characters per dot
170 #....................................................................................................
171 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.79
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
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"
174 # against subject-file "nucmer_alignments.ntref"
175 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.55
176 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.48
177 4: FINISHING DATA
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
183 # (maximum reference length is 536870908)
184 # (maximum query length is 4294967295)
185 # process 52400 characters per dot
186 #....................................................................................................
187 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.91
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
189 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpuVRdjW/tempSequences.fasta"
190 # against subject-file "nucmer_alignments.ntref"
191 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.18
192 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.47
193 4: FINISHING DATA
194 5: GENERATING COORDS FILE
195 Pick PCR primers and hybridization oligos
196 *** Finding Primers ***
197 *** Creating Combined Fasta File for Exclude Files ***
198 *** Finding Sequences Unique to Target Genome ***
199 *** Running nucmer ***
200 *** Running nucmer Complete ***
201 data/PX099A.fa tmpuVRdjW/tempSequences.fasta
202 *** Running nucmer ***
203 *** Running nucmer Complete ***
204 *** Finding Primers ***
205 *** Running EPrimer3 ***
206 *** Running EPrimer3 Complete ***
207 *** Time Elapsed: 3 minutes, 16 seconds ***
208 *** Output Written to primers.txt ***
209 *** Removing temporary directory ***
210 *** Finished ***
211 1: PREPARING DATA
212 2,3: RUNNING mummer AND CREATING CLUSTERS
213 # reading input file "nucmer_alignments.ntref" of length 4831747
214 # construct suffix tree for sequence of length 4831747
215 # (maximum reference length is 536870908)
216 # (maximum query length is 4294967295)
217 # process 48317 characters per dot
218 #....................................................................................................
219 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.91
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
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"
222 # against subject-file "nucmer_alignments.ntref"
223 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.93
224 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.48
225 4: FINISHING DATA
226 5: GENERATING COORDS FILE
227 1: PREPARING DATA
228 2,3: RUNNING mummer AND CREATING CLUSTERS
229 # reading input file "nucmer_alignments.ntref" of length 5240076
230 # construct suffix tree for sequence of length 5240076
231 # (maximum reference length is 536870908)
232 # (maximum query length is 4294967295)
233 # process 52400 characters per dot
234 #....................................................................................................
235 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.39
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
237 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpLVmpjS/tempSequences.fasta"
238 # against subject-file "nucmer_alignments.ntref"
239 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.73
240 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.47
241 4: FINISHING DATA
242 5: GENERATING COORDS FILE
243 Pick PCR primers and hybridization oligos
244 Search DNA sequences for matches with primer pairs
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
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 #....................................................................................................
271 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.29
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
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"
274 # against subject-file "nucmer_alignments.ntref"
275 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 6.73
276 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.48
277 4: FINISHING DATA
278 5: GENERATING COORDS FILE
279 1: PREPARING DATA
280 2,3: RUNNING mummer AND CREATING CLUSTERS
281 # reading input file "nucmer_alignments.ntref" of length 5240076
282 # construct suffix tree for sequence of length 5240076
283 # (maximum reference length is 536870908)
284 # (maximum query length is 4294967295)
285 # process 52400 characters per dot
286 #....................................................................................................
287 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.27
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
289 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmppJaqDI/tempSequences.fasta"
290 # against subject-file "nucmer_alignments.ntref"
291 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.60
292 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.47
293 4: FINISHING DATA
294 5: GENERATING COORDS FILE
295 Pick PCR primers and hybridization oligos
296 Search DNA sequences for matches with primer pairs
297 Search DNA sequences for matches with primer pairs
298 Search DNA sequences for matches with primer pairs
299 *** Finding Primers ***
300 *** Creating Combined Fasta File for Exclude Files ***
301 *** Finding Sequences Unique to Target Genome ***
302 *** Running nucmer ***
303 *** Running nucmer Complete ***
304 data/PX099A.fa tmppJaqDI/tempSequences.fasta
305 *** Running nucmer ***
306 *** Running nucmer Complete ***
307 *** Finding Primers ***
308 *** Running EPrimer3 ***
309 *** Running EPrimer3 Complete ***
310 *** Cross Validating Primers ***
311 *** Running PrimerSearch ***
312 *** Running PrimerSearch Complete ***
313 *** Running PrimerSearch ***
314 *** Running PrimerSearch Complete ***
315 *** Running PrimerSearch ***
316 *** Running PrimerSearch Complete ***
317 *** Time Elapsed: 8 minutes, 28 seconds ***
318 *** Output Written to primers.txt ***
319 *** Finished ***
320 Traceback (most recent call last):
321 File "./uniqprimer.py", line 18, in <module>
322 from primertools import *
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>
324 import fastaparser
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>
326 from Bio import SeqIO
327 ImportError: No module named Bio
328 1: PREPARING DATA
329 2,3: RUNNING mummer AND CREATING CLUSTERS
330 # reading input file "nucmer_alignments.ntref" of length 5240076
331 # construct suffix tree for sequence of length 5240076
332 # (maximum reference length is 536870908)
333 # (maximum query length is 4294967295)
334 # process 52400 characters per dot
335 #....................................................................................................
336 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.11
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
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"
339 # against subject-file "nucmer_alignments.ntref"
340 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 5.92
341 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.87
342 4: FINISHING DATA
343 5: GENERATING COORDS FILE
344 1: PREPARING DATA
345 2,3: RUNNING mummer AND CREATING CLUSTERS
346 # reading input file "nucmer_alignments.ntref" of length 4831747
347 # construct suffix tree for sequence of length 4831747
348 # (maximum reference length is 536870908)
349 # (maximum query length is 4294967295)
350 # process 48317 characters per dot
351 #....................................................................................................
352 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.58
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
354 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpFv9Owj/tempSequences.fasta"
355 # against subject-file "nucmer_alignments.ntref"
356 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.77
357 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.85
358 4: FINISHING DATA
359 5: GENERATING COORDS FILE
360 Pick PCR primers and hybridization oligos
361 Search DNA sequences for matches with primer pairs
362 Search DNA sequences for matches with primer pairs
363 Search DNA sequences for matches with primer pairs
364 *** Finding Primers ***
365 *** Creating Combined Fasta File for Exclude Files ***
366 *** Finding Sequences Unique to Target Genome ***
367 *** Running nucmer ***
368 *** Running nucmer Complete ***
369 data/Xoc_BLS256.fasta tmpFv9Owj/tempSequences.fasta
370 *** Running nucmer ***
371 *** Running nucmer Complete ***
372 *** Finding Primers ***
373 *** Running EPrimer3 ***
374 *** Running EPrimer3 Complete ***
375 *** Cross Validating Primers ***
376 *** Running PrimerSearch ***
377 *** Running PrimerSearch Complete ***
378 *** Running PrimerSearch ***
379 *** Running PrimerSearch Complete ***
380 *** Running PrimerSearch ***
381 *** Running PrimerSearch Complete ***
382 *** Time Elapsed: 7 minutes, 2 seconds ***
383 *** Output Written to primers.txt ***
384 *** Finished ***
385 Traceback (most recent call last):
386 File "./uniqprimer.py", line 18, in <module>
387 from primertools import *
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>
389 import fastaparser
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>
391 from Bio import SeqIO
392 ImportError: No module named Bio
393 1: PREPARING DATA
394 2,3: RUNNING mummer AND CREATING CLUSTERS
395 # reading input file "nucmer_alignments.ntref" of length 5240076
396 # construct suffix tree for sequence of length 5240076
397 # (maximum reference length is 536870908)
398 # (maximum query length is 4294967295)
399 # process 52400 characters per dot
400 #....................................................................................................
401 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.00
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
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"
404 # against subject-file "nucmer_alignments.ntref"
405 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 9.99
406 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 14.56
407 4: FINISHING DATA
408 5: GENERATING COORDS FILE
409 1: PREPARING DATA
410 2,3: RUNNING mummer AND CREATING CLUSTERS
411 # reading input file "nucmer_alignments.ntref" of length 4831747
412 # construct suffix tree for sequence of length 4831747
413 # (maximum reference length is 536870908)
414 # (maximum query length is 4294967295)
415 # process 48317 characters per dot
416 #....................................................................................................
417 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.91
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
419 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpPHilD4/tempSequences.fasta"
420 # against subject-file "nucmer_alignments.ntref"
421 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 2.07
422 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.86
423 4: FINISHING DATA
424 5: GENERATING COORDS FILE
425 Pick PCR primers and hybridization oligos
426 Search DNA sequences for matches with primer pairs
427 Search DNA sequences for matches with primer pairs
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 ***
433 *** Running nucmer Complete ***
434 data/Xoc_BLS256.fasta tmpPHilD4/tempSequences.fasta
435 *** Running nucmer ***
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 ***
444 *** Running PrimerSearch Complete ***
445 *** Running PrimerSearch ***
446 *** Running PrimerSearch Complete ***
447 Failure: No unique primers exist for this combination
448 *** Finished ***
449 1: PREPARING DATA
450 2,3: RUNNING mummer AND CREATING CLUSTERS
451 # reading input file "nucmer_alignments.ntref" of length 5240076
452 # construct suffix tree for sequence of length 5240076
453 # (maximum reference length is 536870908)
454 # (maximum query length is 4294967295)
455 # process 52400 characters per dot
456 #....................................................................................................
457 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.13
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
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"
460 # against subject-file "nucmer_alignments.ntref"
461 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 6.27
462 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 14.56
463 4: FINISHING DATA
464 5: GENERATING COORDS FILE
465 1: PREPARING DATA
466 2,3: RUNNING mummer AND CREATING CLUSTERS
467 # reading input file "nucmer_alignments.ntref" of length 4831747
468 # construct suffix tree for sequence of length 4831747
469 # (maximum reference length is 536870908)
470 # (maximum query length is 4294967295)
471 # process 48317 characters per dot
472 #....................................................................................................
473 # CONSTRUCTIONTIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.24
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
475 # matching query-file "/homedir/galaxy/shed_tools/galaxy.southgreen.fr/toolshed/repos/dereeper/uniqprimer/631882b4244e/uniqprimer/uniqprimer-0.5.0/tmpz0OJOq/tempSequences.fasta"
476 # against subject-file "nucmer_alignments.ntref"
477 # COMPLETETIME /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 1.33
478 # SPACE /usr/local/bioinfo/MUMmer/3.23/mummer nucmer_alignments.ntref 4.86
479 4: FINISHING DATA
480 5: GENERATING COORDS FILE
481 Pick PCR primers and hybridization oligos
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
504 *** Finished ***