-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathplanemo.out
3522 lines (3469 loc) · 357 KB
/
planemo.out
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
git --git-dir /home/fr2424/sib/lecorguille/.planemo/gx_repo fetch >/dev/null 2>&1
cd /tmp/tmpVCld0W; git clone --branch 'dev' '/home/fr2424/sib/lecorguille/.planemo/gx_repo' 'galaxy-dev'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}
Initialized empty Git repository in /tmp/tmpVCld0W/galaxy-dev/.git/
Set COMMON_STARTUP_ARGS to --dev-wheels
Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample
Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample
Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample
Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample
Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample
Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample
Initializing tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample
Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample
Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample
Initializing static/welcome.html from welcome.html.sample
Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv
Requirement already satisfied: pip>=8.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages
Requirement already satisfied: bx-python==0.7.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2))
Requirement already satisfied: MarkupSafe==0.23 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3))
Requirement already satisfied: PyYAML==3.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))
Requirement already satisfied: SQLAlchemy==1.0.15 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))
Requirement already satisfied: mercurial==3.7.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6))
Requirement already satisfied: numpy==1.9.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7))
Requirement already satisfied: pycrypto==2.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))
Requirement already satisfied: Paste==2.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15))
Requirement already satisfied: PasteDeploy==1.5.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16))
Requirement already satisfied: docutils==0.12 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17))
Requirement already satisfied: wchartype==0.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18))
Requirement already satisfied: repoze.lru==0.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19))
Requirement already satisfied: Routes==2.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20))
Requirement already satisfied: WebOb==1.4.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21))
Requirement already satisfied: WebHelpers==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22))
Requirement already satisfied: Mako==1.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23))
Requirement already satisfied: pytz==2015.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24))
Requirement already satisfied: Babel==2.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25))
Requirement already satisfied: Beaker==1.7.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26))
Requirement already satisfied: dictobj==0.3.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27))
Requirement already satisfied: nose==1.3.7 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 28))
Requirement already satisfied: Parsley==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 29))
Requirement already satisfied: six==1.9.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30))
Requirement already satisfied: Whoosh==2.7.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31))
Requirement already satisfied: testfixtures==4.10.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32))
Requirement already satisfied: Cheetah==2.4.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 35))
Requirement already satisfied: Markdown==2.6.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36))
Requirement already satisfied: bioblend==0.7.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 39))
Requirement already satisfied: boto==2.38.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40))
Requirement already satisfied: requests==2.8.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41))
Requirement already satisfied: requests-toolbelt==0.4.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42))
Requirement already satisfied: kombu==3.0.30 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 45))
Requirement already satisfied: amqp==1.4.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46))
Requirement already satisfied: anyjson==0.3.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47))
Requirement already satisfied: psutil==4.1.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 50))
Requirement already satisfied: pulsar-galaxy-lib==0.7.0.dev5 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51))
Requirement already satisfied: sqlalchemy-migrate==0.10.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 54))
Requirement already satisfied: decorator==4.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 55))
Requirement already satisfied: Tempita==0.5.3dev in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 56))
Requirement already satisfied: sqlparse==0.1.16 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57))
Requirement already satisfied: pbr==1.8.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58))
Requirement already satisfied: svgwrite==1.1.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 61))
Requirement already satisfied: pyparsing==2.1.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 62))
Requirement already satisfied: Fabric==1.10.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 65))
Requirement already satisfied: paramiko==1.15.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66))
Requirement already satisfied: ecdsa==0.13 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 67))
Requirement already satisfied: pysam==0.8.4+gx5 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 70))
Requirement already satisfied: PasteScript in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 51))
Requirement already satisfied: nose in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1))
Requirement already satisfied: NoseHTML in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2))
Requirement already satisfied: twill==0.9.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3))
Requirement already satisfied: mock in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
Requirement already satisfied: selenium in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5))
Requirement already satisfied: funcsigs>=1; python_version < "3.3" in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
Requirement already satisfied: pbr>=0.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
Requirement already satisfied: six>=1.9 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
Testing using galaxy_root /tmp/tmpVCld0W/galaxy-dev
Testing tools with command [cd /tmp/tmpVCld0W/galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /projet/fr2424/sib/lecorguille/script/git/w4m/ipo/galaxy/ipo/tool_test_output.html --xunit_report_file /tmp/tmpVCld0W/xunit.xml --structured_data_report_file /projet/fr2424/sib/lecorguille/script/git/w4m/ipo/galaxy/ipo/tool_test_output.json functional.test_toolbox]
Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv
Requirement already satisfied: pip>=8.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages
Requirement already satisfied: bx-python==0.7.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2))
Requirement already satisfied: MarkupSafe==0.23 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3))
Requirement already satisfied: PyYAML==3.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))
Requirement already satisfied: SQLAlchemy==1.0.15 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))
Requirement already satisfied: mercurial==3.7.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 6))
Requirement already satisfied: numpy==1.9.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7))
Requirement already satisfied: pycrypto==2.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))
Requirement already satisfied: Paste==2.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 15))
Requirement already satisfied: PasteDeploy==1.5.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16))
Requirement already satisfied: docutils==0.12 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17))
Requirement already satisfied: wchartype==0.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18))
Requirement already satisfied: repoze.lru==0.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19))
Requirement already satisfied: Routes==2.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20))
Requirement already satisfied: WebOb==1.4.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21))
Requirement already satisfied: WebHelpers==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22))
Requirement already satisfied: Mako==1.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23))
Requirement already satisfied: pytz==2015.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24))
Requirement already satisfied: Babel==2.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25))
Requirement already satisfied: Beaker==1.7.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26))
Requirement already satisfied: dictobj==0.3.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27))
Requirement already satisfied: nose==1.3.7 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 28))
Requirement already satisfied: Parsley==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 29))
Requirement already satisfied: six==1.9.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30))
Requirement already satisfied: Whoosh==2.7.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31))
Requirement already satisfied: testfixtures==4.10.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 32))
Requirement already satisfied: Cheetah==2.4.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 35))
Requirement already satisfied: Markdown==2.6.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36))
Requirement already satisfied: bioblend==0.7.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 39))
Requirement already satisfied: boto==2.38.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40))
Requirement already satisfied: requests==2.8.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41))
Requirement already satisfied: requests-toolbelt==0.4.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42))
Requirement already satisfied: kombu==3.0.30 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 45))
Requirement already satisfied: amqp==1.4.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46))
Requirement already satisfied: anyjson==0.3.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47))
Requirement already satisfied: psutil==4.1.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 50))
Requirement already satisfied: pulsar-galaxy-lib==0.7.0.dev5 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51))
Requirement already satisfied: sqlalchemy-migrate==0.10.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 54))
Requirement already satisfied: decorator==4.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 55))
Requirement already satisfied: Tempita==0.5.3dev in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 56))
Requirement already satisfied: sqlparse==0.1.16 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57))
Requirement already satisfied: pbr==1.8.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58))
Requirement already satisfied: svgwrite==1.1.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 61))
Requirement already satisfied: pyparsing==2.1.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 62))
Requirement already satisfied: Fabric==1.10.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 65))
Requirement already satisfied: paramiko==1.15.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66))
Requirement already satisfied: ecdsa==0.13 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 67))
Requirement already satisfied: pysam==0.8.4+gx5 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 70))
Requirement already satisfied: PasteScript in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 51))
Requirement already satisfied: nose in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1))
Requirement already satisfied: NoseHTML in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2))
Requirement already satisfied: twill==0.9.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3))
Requirement already satisfied: mock in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
Requirement already satisfied: selenium in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5))
Requirement already satisfied: funcsigs>=1; python_version < "3.3" in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
Requirement already satisfied: pbr>=0.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
Requirement already satisfied: six>=1.9 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4))
Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv
DEBUG:galaxy.app:python path is: /tmp/tmpVCld0W/galaxy-dev/scripts, /tmp/tmpVCld0W/galaxy-dev/lib, /tmp/tmpVCld0W/galaxy-dev/lib, /tmp/tmpVCld0W/galaxy-dev/test, /tmp/tmpVCld0W/galaxy-dev, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python27.zip, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/plat-linux2, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-old, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-dynload, /opt/6.x/python-2.7.2/lib/python2.7, /opt/6.x/python-2.7.2/lib/python2.7/plat-linux2, /opt/6.x/python-2.7.2/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages
INFO:galaxy.config:Logging at '10' level to 'stdout'
galaxy.queue_worker INFO 2017-01-12 16:13:30,782 Initializing main Galaxy Queue Worker on sqlalchemy+sqlite://
tool_shed.tool_shed_registry DEBUG 2017-01-12 16:13:30,836 Loading references to tool sheds from /tmp/tmpVCld0W/tool_sheds_conf.xml
tool_shed.tool_shed_registry DEBUG 2017-01-12 16:13:30,837 Loaded reference to tool shed: Target Shed
galaxy.app DEBUG 2017-01-12 16:13:30,845 Using "galaxy.ini" config file: config/galaxy.ini.sample
migrate.versioning.repository DEBUG 2017-01-12 16:13:30,955 Loading repository lib/galaxy/model/migrate...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,956 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,956 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,957 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,957 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,957 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,957 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,957 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,957 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,957 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,957 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,957 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,957 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,957 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,958 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,958 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,958 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,958 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,958 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,958 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,958 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,958 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,958 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,958 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,958 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,959 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,959 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,959 Loading script lib/galaxy/model/migrate/versions/0014_pages.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,959 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,959 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,959 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,959 Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,959 Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,959 Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,959 Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,959 Loading script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,960 Script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,960 Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,960 Script lib/galaxy/model/migrate/versions/0019_request_library_folder.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,960 Loading script lib/galaxy/model/migrate/versions/0020_library_upload_job.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,960 Script lib/galaxy/model/migrate/versions/0020_library_upload_job.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,960 Loading script lib/galaxy/model/migrate/versions/0021_user_prefs.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,960 Script lib/galaxy/model/migrate/versions/0021_user_prefs.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,960 Loading script lib/galaxy/model/migrate/versions/0022_visualization_tables.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,960 Script lib/galaxy/model/migrate/versions/0022_visualization_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,961 Loading script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,961 Script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,961 Loading script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,961 Script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,961 Loading script lib/galaxy/model/migrate/versions/0025_user_info.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,961 Script lib/galaxy/model/migrate/versions/0025_user_info.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,961 Loading script lib/galaxy/model/migrate/versions/0026_cloud_tables.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,961 Script lib/galaxy/model/migrate/versions/0026_cloud_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,961 Loading script lib/galaxy/model/migrate/versions/0027_request_events.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,961 Script lib/galaxy/model/migrate/versions/0027_request_events.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,961 Loading script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,962 Script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,962 Loading script lib/galaxy/model/migrate/versions/0029_user_actions.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,962 Script lib/galaxy/model/migrate/versions/0029_user_actions.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,962 Loading script lib/galaxy/model/migrate/versions/0030_history_slug_column.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,962 Script lib/galaxy/model/migrate/versions/0030_history_slug_column.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,962 Loading script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,962 Script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,962 Loading script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,962 Script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,962 Loading script lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,962 Script lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,963 Loading script lib/galaxy/model/migrate/versions/0034_page_user_share_association.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,963 Script lib/galaxy/model/migrate/versions/0034_page_user_share_association.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,963 Loading script lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,963 Script lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,963 Loading script lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,963 Script lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,963 Loading script lib/galaxy/model/migrate/versions/0037_samples_library.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,963 Script lib/galaxy/model/migrate/versions/0037_samples_library.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,963 Loading script lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,963 Script lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,963 Loading script lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,964 Script lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,964 Loading script lib/galaxy/model/migrate/versions/0040_page_annotations.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,964 Script lib/galaxy/model/migrate/versions/0040_page_annotations.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,964 Loading script lib/galaxy/model/migrate/versions/0041_workflow_invocation.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,964 Script lib/galaxy/model/migrate/versions/0041_workflow_invocation.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,964 Loading script lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,964 Script lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,964 Loading script lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,964 Script lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,964 Loading script lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,964 Script lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,965 Loading script lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,965 Script lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,965 Loading script lib/galaxy/model/migrate/versions/0046_post_job_actions.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,965 Script lib/galaxy/model/migrate/versions/0046_post_job_actions.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,965 Loading script lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,965 Script lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,965 Loading script lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,965 Script lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,965 Loading script lib/galaxy/model/migrate/versions/0049_api_keys_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,965 Script lib/galaxy/model/migrate/versions/0049_api_keys_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,965 Loading script lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,966 Script lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,966 Loading script lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,966 Script lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,966 Loading script lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,966 Script lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,966 Loading script lib/galaxy/model/migrate/versions/0053_item_ratings.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,966 Script lib/galaxy/model/migrate/versions/0053_item_ratings.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,966 Loading script lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,966 Script lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,966 Loading script lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,966 Script lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,967 Loading script lib/galaxy/model/migrate/versions/0056_workflow_outputs.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,967 Script lib/galaxy/model/migrate/versions/0056_workflow_outputs.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,967 Loading script lib/galaxy/model/migrate/versions/0057_request_notify.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,967 Script lib/galaxy/model/migrate/versions/0057_request_notify.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,967 Loading script lib/galaxy/model/migrate/versions/0058_history_import_export.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,967 Script lib/galaxy/model/migrate/versions/0058_history_import_export.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,967 Loading script lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,967 Script lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,967 Loading script lib/galaxy/model/migrate/versions/0060_history_archive_import.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,967 Script lib/galaxy/model/migrate/versions/0060_history_archive_import.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,967 Loading script lib/galaxy/model/migrate/versions/0061_tasks.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,968 Script lib/galaxy/model/migrate/versions/0061_tasks.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,968 Loading script lib/galaxy/model/migrate/versions/0062_user_openid_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,968 Script lib/galaxy/model/migrate/versions/0062_user_openid_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,968 Loading script lib/galaxy/model/migrate/versions/0063_sequencer_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,968 Script lib/galaxy/model/migrate/versions/0063_sequencer_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,968 Loading script lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,968 Script lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,968 Loading script lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,968 Script lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,968 Loading script lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,968 Script lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,969 Loading script lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,969 Script lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,969 Loading script lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,969 Script lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,969 Loading script lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,969 Script lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,969 Loading script lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,969 Script lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,969 Loading script lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,969 Script lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,969 Loading script lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,970 Script lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,970 Loading script lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,970 Script lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,970 Loading script lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,970 Script lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,970 Loading script lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,970 Script lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,970 Loading script lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,970 Script lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,970 Loading script lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,970 Script lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,971 Loading script lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,971 Script lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,971 Loading script lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,971 Script lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,971 Loading script lib/galaxy/model/migrate/versions/0080_quota_tables.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,971 Script lib/galaxy/model/migrate/versions/0080_quota_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,971 Loading script lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,971 Script lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,971 Loading script lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,971 Script lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,971 Loading script lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,972 Script lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,972 Loading script lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,972 Script lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,972 Loading script lib/galaxy/model/migrate/versions/0085_add_task_info.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,972 Script lib/galaxy/model/migrate/versions/0085_add_task_info.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,972 Loading script lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,972 Script lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,972 Loading script lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,972 Script lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,972 Loading script lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,972 Script lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,973 Loading script lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,973 Script lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,973 Loading script lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,973 Script lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,973 Loading script lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,973 Script lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,973 Loading script lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,973 Script lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,973 Loading script lib/galaxy/model/migrate/versions/0093_add_job_params_col.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,973 Script lib/galaxy/model/migrate/versions/0093_add_job_params_col.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,974 Loading script lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,974 Script lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,974 Loading script lib/galaxy/model/migrate/versions/0095_hda_subsets.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,974 Script lib/galaxy/model/migrate/versions/0095_hda_subsets.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,974 Loading script lib/galaxy/model/migrate/versions/0096_openid_provider.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,974 Script lib/galaxy/model/migrate/versions/0096_openid_provider.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,974 Loading script lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,974 Script lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,974 Loading script lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,974 Script lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,974 Loading script lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,975 Script lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,975 Loading script lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,975 Script lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,975 Loading script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,975 Script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,975 Loading script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,975 Script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,975 Loading script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,975 Script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,975 Loading script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,975 Script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,976 Loading script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,976 Script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,976 Loading script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,976 Script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,976 Loading script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,976 Script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,976 Loading script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,976 Script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,976 Loading script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,976 Script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,976 Loading script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,977 Script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,977 Loading script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,977 Script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,977 Loading script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,977 Script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,977 Loading script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,977 Script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,977 Loading script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,977 Script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,977 Loading script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,977 Script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,978 Loading script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,978 Script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,978 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,978 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,978 Loading script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,978 Script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,978 Loading script lib/galaxy/model/migrate/versions/0119_job_metrics.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,978 Script lib/galaxy/model/migrate/versions/0119_job_metrics.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,978 Loading script lib/galaxy/model/migrate/versions/0120_dataset_collections.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,978 Script lib/galaxy/model/migrate/versions/0120_dataset_collections.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,978 Loading script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,979 Script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,979 Loading script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,979 Script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,979 Loading script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,979 Script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,979 Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,979 Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,979 Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,979 Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,979 Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,979 Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,980 Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,980 Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,980 Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,980 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,980 Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,980 Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,980 Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,980 Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,980 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,980 Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,980 Loading script lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,980 Script lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py loaded successfully
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,981 Loading script lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py...
migrate.versioning.script.base DEBUG 2017-01-12 16:13:30,981 Script lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py loaded successfully
migrate.versioning.repository DEBUG 2017-01-12 16:13:30,981 Repository lib/galaxy/model/migrate loaded successfully
migrate.versioning.repository DEBUG 2017-01-12 16:13:30,981 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))])
galaxy.model.migrate.check INFO 2017-01-12 16:13:31,031 Migrating 127 -> 128...
galaxy.model.migrate.check INFO 2017-01-12 16:13:32,099
galaxy.model.migrate.check INFO 2017-01-12 16:13:32,099 Migration script to add session update time (used for timeouts)
galaxy.model.migrate.check INFO 2017-01-12 16:13:32,100
galaxy.model.migrate.check INFO 2017-01-12 16:13:32,100
galaxy.model.migrate.check INFO 2017-01-12 16:13:32,100 Migrating 128 -> 129...
galaxy.model.migrate.check INFO 2017-01-12 16:13:32,791
galaxy.model.migrate.check INFO 2017-01-12 16:13:32,792 Migration script to allow invalidation of job external output metadata temp files
galaxy.model.migrate.check INFO 2017-01-12 16:13:32,792
galaxy.model.migrate.check INFO 2017-01-12 16:13:32,792
galaxy.model.migrate.check INFO 2017-01-12 16:13:32,792 Migrating 129 -> 130...
galaxy.model.migrate.check INFO 2017-01-12 16:13:33,835
galaxy.model.migrate.check INFO 2017-01-12 16:13:33,836 Migration script to change the value column of user_preference from varchar to text.
galaxy.model.migrate.check INFO 2017-01-12 16:13:33,836
galaxy.model.migrate.check INFO 2017-01-12 16:13:33,836
galaxy.model.migrate.check INFO 2017-01-12 16:13:33,836 Migrating 130 -> 131...
galaxy.model.migrate.check INFO 2017-01-12 16:13:35,084
galaxy.model.migrate.check INFO 2017-01-12 16:13:35,084 Migration script to support subworkflows and workflow request input parameters
galaxy.model.migrate.check INFO 2017-01-12 16:13:35,085
galaxy.model.migrate.check INFO 2017-01-12 16:13:35,085
galaxy.model.migrate.check INFO 2017-01-12 16:13:35,085 Migrating 131 -> 132...
galaxy.model.migrate.check INFO 2017-01-12 16:13:35,184
galaxy.model.migrate.check INFO 2017-01-12 16:13:35,184 Migrating 132 -> 133...
galaxy.model.migrate.check INFO 2017-01-12 16:13:36,231
galaxy.model.migrate.check INFO 2017-01-12 16:13:36,231 Add dependencies column to jobs table
galaxy.model.migrate.check INFO 2017-01-12 16:13:36,232
galaxy.model.migrate.check INFO 2017-01-12 16:13:36,232
galaxy.config INFO 2017-01-12 16:13:36,264 Install database targetting Galaxy's database configuration.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,376 Loading datatypes from ./config/datatypes_conf.xml.sample
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,377 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,380 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,380 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,380 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,380 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,380 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,382 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,382 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,383 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,383 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,383 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,383 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,383 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,384 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,384 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,384 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,385 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,385 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,385 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,385 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,386 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,386 Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,386 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,387 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,388 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,388 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,388 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,388 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,388 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,388 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,389 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,389 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,389 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,389 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,390 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,390 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,390 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,390 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,390 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,390 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,390 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,391 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,391 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,391 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,391 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,392 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,392 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,392 Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,392 Retrieved datatype module galaxy.datatypes.text:Markdown from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,392 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,393 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,393 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,393 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,393 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,394 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,394 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,394 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,395 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,395 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,395 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,395 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,396 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,396 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,396 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,397 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,397 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,397 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,397 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,398 Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,398 Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,398 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,398 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,398 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,398 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,399 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,399 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,399 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,399 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,399 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,399 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,399 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,400 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,400 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,400 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,400 Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,400 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,407 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,408 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,408 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,408 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,408 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,409 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,409 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,409 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,409 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,409 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,410 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,410 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,410 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,410 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,410 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,410 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,411 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,411 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,411 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,411 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,411 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,411 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,412 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,412 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,412 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,412 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,412 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,412 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,413 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,413 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,413 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,413 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,413 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,414 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,414 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,414 Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,414 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,414 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,415 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,415 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,415 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,415 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,415 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,415 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,416 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,416 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,416 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,416 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,416 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,416 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,417 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,417 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,417 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,417 Roadmaps is not lower case, that could cause troubles in the future. Please change it to lower case
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,417 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,417 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,417 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,418 Sequences is not lower case, that could cause troubles in the future. Please change it to lower case
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,418 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,418 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,418 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,418 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,419 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,419 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,419 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,419 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,419 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,420 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,420 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,420 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,420 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,420 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,420 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,420 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,421 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,421 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,421 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,421 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,421 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,422 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,422 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,422 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,423 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,423 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,423 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,423 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,435 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,435 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,435 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,436 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,436 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,436 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,436 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,436 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,437 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,437 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,437 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,437 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,438 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,438 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,438 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,438 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,438 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,438 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,439 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,439 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,442 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,442 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,445 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,445 Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,445 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,445 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,446 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,446 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,446 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,446 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,446 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,447 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,447 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,447 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,447 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,448 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,448 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,448 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,448 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,449 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,449 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,449 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,450 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,450 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,450 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,450 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,451 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,451 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,451 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,451 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,452 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,452 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,452 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,452 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,453 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,453 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,453 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,453 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,454 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,454 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,454 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,455 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,455 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,455 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,455 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,456 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,456 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,456 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,456 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,457 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,457 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,457 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,457 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,458 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,458 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,458 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,458 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,459 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,459 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,461 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,461 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,461 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,461 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,462 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,462 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,462 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,462 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,463 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,463 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,463 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,463 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,464 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,464 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,464 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,464 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,465 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,465 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,465 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,466 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry WARNING 2017-01-12 16:13:36,466 Cannot specify edam_format without setting subclass to True, skipping datatype.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,466 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,466 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,466 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,467 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,467 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,467 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,468 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,468 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,468 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,468 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,469 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,469 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,469 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,469 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,470 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,470 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,470 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,471 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,471 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,471 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,471 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,472 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,472 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,476 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,476 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,476 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,476 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,476 Retrieved datatype module galaxy.datatypes.binary:Cel from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,476 RData is not lower case, that could cause troubles in the future. Please change it to lower case
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,477 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,477 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,477 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,477 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,477 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,477 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,477 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,483 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,483 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,484 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,484 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,484 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,484 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,485 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,494 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,494 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,495 Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,495 Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,495 Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,495 Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,495 Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,495 Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,496 Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,496 Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,507 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,508 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,508 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,508 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,508 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,509 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,509 Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,509 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,509 Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,510 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,510 Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,510 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,510 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,510 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,511 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,511 Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,511 Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,511 Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,511 Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,512 Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,512 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,512 Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,512 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,512 Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,513 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,513 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,513 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,513 Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,514 Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,514 Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,514 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,514 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,514 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,515 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,515 Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,515 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,515 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,517 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,518 Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,522 Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,522 Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,522 Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,522 Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,523 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,523 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,523 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry.
galaxy.datatypes.registry ERROR 2017-01-12 16:13:36,524 Error importing datatype module galaxy.datatypes.estscan: No module named estscan
Traceback (most recent call last):
File "/tmp/tmpVCld0W/galaxy-dev/lib/galaxy/datatypes/registry.py", line 209, in load_datatypes
module = __import__( datatype_module )
ImportError: No module named estscan
galaxy.datatypes.registry ERROR 2017-01-12 16:13:36,524 Error importing datatype class for 'galaxy.datatypes.estscan:Smat': No module named estscan
Traceback (most recent call last):
File "/tmp/tmpVCld0W/galaxy-dev/lib/galaxy/datatypes/registry.py", line 380, in load_datatype_sniffers
module = __import__( datatype_module )
ImportError: No module named estscan
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,525 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,525 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,525 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,525 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,525 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,525 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,525 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,525 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,525 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,526 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,526 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,526 Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,526 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,526 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,526 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,526 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,526 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,526 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,527 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,527 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,527 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,527 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,527 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,527 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,527 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,527 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,528 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,528 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,528 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,528 Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,528 Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,528 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,528 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,528 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,529 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,529 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,529 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,529 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,529 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,529 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,529 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,529 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,530 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,530 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,530 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,530 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,530 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,530 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,530 Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,531 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,531 Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,531 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,531 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,531 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,531 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,531 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,531 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,532 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,532 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,532 Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,532 Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,532 Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,532 Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,532 Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,532 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,533 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,533 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,533 Loaded sniffer for datatype 'galaxy.datatypes.text:Html'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,533 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,533 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,533 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,533 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,534 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,534 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,534 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,534 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,534 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,534 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,534 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,535 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,535 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,535 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,535 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,535 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,535 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,535 Loaded sniffer for datatype 'galaxy.datatypes.text:Json'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,536 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,536 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,536 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,536 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,536 Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,536 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,536 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,537 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,537 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,537 Loaded sniffer for datatype 'galaxy.datatypes.binary:Cel'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,537 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,537 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,537 Loaded sniffer for datatype 'galaxy.datatypes.images:Png'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,538 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,538 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,538 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,538 Loaded sniffer for datatype 'galaxy.datatypes.images:Im'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,538 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,538 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,539 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,539 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,539 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,539 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,539 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,539 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,539 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,540 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,540 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,540 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,540 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,540 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,540 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,541 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,541 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels'
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,541 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,541 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,541 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,541 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,542 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt
galaxy.datatypes.registry DEBUG 2017-01-12 16:13:36,542 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt
galaxy.visualization.genomes ERROR 2017-01-12 16:13:37,236 Error reading twobit.loc: [Errno 2] No such file or directory: '/tmp/tmpVCld0W/galaxy-dev/tool-data/twobit.loc'
Traceback (most recent call last):
File "/tmp/tmpVCld0W/galaxy-dev/lib/galaxy/visualization/genomes.py", line 210, in reload_genomes
for line in open( os.path.join( self.app.config.tool_data_path, "twobit.loc" ) ):
IOError: [Errno 2] No such file or directory: '/tmp/tmpVCld0W/galaxy-dev/tool-data/twobit.loc'
galaxy.jobs DEBUG 2017-01-12 16:13:37,250 Loading job configuration from /tmp/tmpVCld0W/job_conf.xml
galaxy.jobs DEBUG 2017-01-12 16:13:37,250 Read definition for handler 'main'
galaxy.jobs INFO 2017-01-12 16:13:37,250 Setting <handlers> default to child with id 'main'
galaxy.jobs DEBUG 2017-01-12 16:13:37,250 <destinations> default set to child with id or tag 'planemo_dest'
galaxy.jobs DEBUG 2017-01-12 16:13:37,251 Done loading job configuration
beaker.container DEBUG 2017-01-12 16:13:37,289 data file /tmp/tmpVCld0W/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache
galaxy.tools.toolbox.watcher INFO 2017-01-12 16:13:37,312 Watchdog library unavailable, cannot monitor tools.
galaxy.tools.toolbox.base INFO 2017-01-12 16:13:37,313 Parsing the tool configuration /tmp/tmpVCld0W/tool_conf.xml
galaxy.tools.toolbox.base DEBUG 2017-01-12 16:13:37,329 Loaded tool id: upload1, version: 1.1.4 into tool panel..
galaxy.tools.toolbox.base DEBUG 2017-01-12 16:13:37,343 Loaded tool id: ipo4xcmsSet, version: 0.0.3 into tool panel..
galaxy.tools.toolbox.base INFO 2017-01-12 16:13:37,343 Parsing the tool configuration /tmp/tmpVCld0W/shed_tools_conf.xml
galaxy.tools.toolbox.base INFO 2017-01-12 16:13:37,344 Parsing the tool configuration /tmp/tmpVCld0W/empty_tool_conf.xml
galaxy.tools.toolbox.base DEBUG 2017-01-12 16:13:37,344 Reading tools from config files took 0 seconds
PREFIX=/tmp/mc
installing: _cache-0.0-py27_x0 ...
installing: python-2.7.11-0 ...
installing: conda-env-2.4.5-py27_0 ...
installing: openssl-1.0.2g-0 ...
installing: pycosat-0.6.1-py27_0 ...
installing: pyyaml-3.11-py27_1 ...
installing: readline-6.2-2 ...
installing: requests-2.9.1-py27_0 ...
installing: sqlite-3.9.2-0 ...
installing: tk-8.5.18-0 ...
installing: yaml-0.1.6-0 ...
installing: zlib-1.2.8-0 ...
installing: conda-4.0.5-py27_0 ...
installing: pycrypto-2.6.1-py27_0 ...
installing: pip-8.1.1-py27_1 ...
installing: wheel-0.29.0-py27_0 ...
installing: setuptools-20.3-py27_0 ...
Python 2.7.11 :: Continuum Analytics, Inc.
creating default environment...
installation finished.
Fetching package metadata: ........
Solving package specifications: .........
Package plan for installation in environment /tmp/mc:
The following packages will be downloaded:
package | build
---------------------------|-----------------
conda-env-2.6.0 | 0 502 B
sqlite-3.13.0 | 0 4.0 MB
python-2.7.13 | 0 11.5 MB
enum34-1.1.6 | py27_0 53 KB
ruamel_yaml-0.11.14 | py27_1 361 KB
conda-4.2.13 | py27_0 391 KB
------------------------------------------------------------
Total: 16.2 MB