-
Notifications
You must be signed in to change notification settings - Fork 0
/
48N_Virus_spades.log
1569 lines (1535 loc) · 197 KB
/
48N_Virus_spades.log
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
Command line: /powerapps/share/SPAdes-3.11.0-Linux/bin/spades.py --meta -k 21,33,45,55,63,77 -t 12 -1 /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/trimmed/paired_R1.fastq -2 /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/trimmed/paired_R2.fastq -o /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades -t 12
System information:
SPAdes version: 3.11.0
Python version: 2.7.13
OS: Linux-3.10.0-514.el7.x86_64-x86_64-with-centos-7.3.1611-Core
Output dir: /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Metagenomic mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/trimmed/paired_R1.fastq']
right reads: ['/scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/trimmed/paired_R2.fastq']
interlaced reads: not specified
single reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed (with gzip)
Assembly parameters:
k: [21, 33, 45, 55, 63, 77]
Repeat resolution is enabled
Mismatch careful mode is turned OFF
MismatchCorrector will be SKIPPED
Coverage cutoff is turned OFF
Other parameters:
Dir for temp files: /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/tmp
Threads: 12
Memory limit (in Gb): 250
======= SPAdes pipeline started. Log can be found here: /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/spades.log
===== Read error correction started.
== Running read error correction tool: /powerapps/share/SPAdes-3.11.0-Linux/bin/hammer /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/corrected/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 83) Starting BayesHammer, built from N/A, git revision N/A
0:00:00.000 4M / 4M INFO General (main.cpp : 84) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/corrected/configs/config.info
0:00:00.001 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 120 Gb
0:00:00.001 4M / 4M INFO General (main.cpp : 93) Trying to determine PHRED offset
0:00:00.001 4M / 4M INFO General (main.cpp : 99) Determined value is 33
0:00:00.002 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.002 4M / 4M INFO General (main.cpp : 120) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.002 4M / 4M INFO K-mer Counting (kmer_data.cpp : 280) Estimating k-mer count
0:00:00.080 196M / 196M INFO K-mer Counting (kmer_data.cpp : 285) Processing /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/trimmed/paired_R1.fastq
0:00:01.169 240M / 240M INFO K-mer Counting (kmer_data.cpp : 294) Processed 580201 reads
0:00:01.169 240M / 240M INFO K-mer Counting (kmer_data.cpp : 285) Processing /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/trimmed/paired_R2.fastq
0:00:02.134 240M / 240M INFO K-mer Counting (kmer_data.cpp : 294) Processed 1160402 reads
0:00:02.134 240M / 240M INFO K-mer Counting (kmer_data.cpp : 299) Total 1160402 reads processed
0:00:03.817 48M / 240M INFO K-mer Counting (kmer_data.cpp : 311) Filtering singleton k-mers
0:00:03.962 560M / 560M INFO K-mer Counting (kmer_data.cpp : 317) Processing /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/trimmed/paired_R1.fastq
0:00:05.829 560M / 560M INFO K-mer Counting (kmer_data.cpp : 326) Processed 580201 reads
0:00:05.829 560M / 560M INFO K-mer Counting (kmer_data.cpp : 317) Processing /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/trimmed/paired_R2.fastq
0:00:07.598 560M / 560M INFO K-mer Counting (kmer_data.cpp : 326) Processed 1160402 reads
0:00:07.598 560M / 560M INFO K-mer Counting (kmer_data.cpp : 331) Total 1160402 reads processed
0:00:07.599 560M / 560M INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index
0:00:07.599 560M / 560M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 192 buckets using 12 threads. This might take a while.
0:00:07.599 560M / 560M INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:07.599 560M / 560M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.31814 Gb
0:00:07.599 560M / 560M INFO General (kmer_splitters.hpp : 82) Using cell size of 349525
0:00:08.515 7G / 7G INFO K-mer Splitting (kmer_data.cpp : 96) Processing /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/trimmed/paired_R1.fastq
0:00:11.856 7G / 7G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 580201 reads
0:00:11.856 7G / 7G INFO K-mer Splitting (kmer_data.cpp : 96) Processing /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/trimmed/paired_R2.fastq
0:00:14.373 7G / 7G INFO K-mer Splitting (kmer_data.cpp : 106) Processed 1160402 reads
0:00:14.373 7G / 7G INFO K-mer Splitting (kmer_data.cpp : 111) Total 1160402 reads processed
0:00:14.684 560M / 7G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:16.466 560M / 7G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 3417908 kmers in total.
0:00:16.466 560M / 7G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:17.344 560M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices
0:00:18.163 560M / 7G INFO General (kmer_index_builder.hpp : 137) Merging final buckets.
0:00:18.449 560M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 1593160 bytes occupied (3.72897 bits per kmer).
0:00:18.451 48M / 7G INFO K-mer Counting (kmer_data.cpp : 357) Arranging kmers in hash map order
0:00:18.818 104M / 7G INFO General (main.cpp : 155) Clustering Hamming graph.
0:00:20.512 104M / 7G INFO General (main.cpp : 162) Extracting clusters
0:00:22.119 104M / 7G INFO General (main.cpp : 174) Clustering done. Total clusters: 599277
0:00:22.119 76M / 7G INFO K-mer Counting (kmer_data.cpp : 379) Collecting K-mer information, this takes a while.
0:00:22.149 156M / 7G INFO K-mer Counting (kmer_data.cpp : 385) Processing /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/trimmed/paired_R1.fastq
0:00:27.043 156M / 7G INFO K-mer Counting (kmer_data.cpp : 385) Processing /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/trimmed/paired_R2.fastq
0:00:31.645 156M / 7G INFO K-mer Counting (kmer_data.cpp : 392) Collection done, postprocessing.
0:00:31.658 156M / 7G INFO K-mer Counting (kmer_data.cpp : 406) There are 3417908 kmers in total. Among them 30 (0.00087773%) are singletons.
0:00:31.658 156M / 7G INFO General (main.cpp : 180) Subclustering Hamming graph
0:00:33.311 156M / 7G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated.
0:00:33.311 156M / 7G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics:
0:00:33.311 156M / 7G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 544044. Among them 457066 (84.0127%) are good
0:00:33.311 156M / 7G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 208317. Among them 208317 (100%) are good
0:00:33.311 156M / 7G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 358676. Among them 350296 (97.6636%) are good
0:00:33.311 156M / 7G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 8.01242 kmers
0:00:33.311 156M / 7G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 10.2655
0:00:33.311 156M / 7G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1015679
0:00:33.311 156M / 7G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.943247,0.0251791,0.00778813,0.0237856),(0.0201797,0.954633,0.0195373,0.00565002),(0.00562972,0.0195324,0.954602,0.0202361),(0.0237732,0.00775758,0.0252322,0.943237))
0:00:33.316 156M / 7G INFO General (main.cpp : 185) Finished clustering.
0:00:33.316 156M / 7G INFO General (main.cpp : 204) Starting solid k-mers expansion in 12 threads.
0:00:35.331 156M / 7G INFO General (main.cpp : 225) Solid k-mers iteration 0 produced 242210 new k-mers.
0:00:37.290 156M / 7G INFO General (main.cpp : 225) Solid k-mers iteration 1 produced 16251 new k-mers.
0:00:39.249 156M / 7G INFO General (main.cpp : 225) Solid k-mers iteration 2 produced 471 new k-mers.
0:00:41.206 156M / 7G INFO General (main.cpp : 225) Solid k-mers iteration 3 produced 32 new k-mers.
0:00:43.165 156M / 7G INFO General (main.cpp : 225) Solid k-mers iteration 4 produced 0 new k-mers.
0:00:43.165 156M / 7G INFO General (main.cpp : 229) Solid k-mers finalized
0:00:43.165 156M / 7G INFO General (hammer_tools.cpp : 211) Starting read correction in 12 threads.
0:00:43.165 156M / 7G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/trimmed/paired_R1.fastq and /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/trimmed/paired_R2.fastq
0:00:44.905 760M / 7G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 580201 reads.
0:00:48.875 888M / 7G INFO General (hammer_tools.cpp : 175) Processed batch 0
0:00:49.920 888M / 7G INFO General (hammer_tools.cpp : 185) Written batch 0
0:00:57.144 156M / 7G INFO General (hammer_tools.cpp : 270) Correction done. Changed 610320 bases in 325218 reads.
0:00:57.144 156M / 7G INFO General (hammer_tools.cpp : 271) Failed to correct 190 bases out of 158688966.
0:00:57.145 48M / 7G INFO General (main.cpp : 262) Saving corrected dataset description to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/corrected/corrected.yaml
0:00:57.148 48M / 7G INFO General (main.cpp : 269) All done. Exiting.
== Compressing corrected reads (with gzip)
== Dataset description file was created: /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/corrected/corrected.yaml
===== Read error correction finished.
===== Assembling started.
== Running assembler: K21
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K21/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K21/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K21/configs/meta_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 120 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 89) Starting SPAdes, built from N/A, git revision N/A
0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum k-mer length: 128
0:00:00.000 4M / 4M INFO General (main.cpp : 91) Assembling dataset (/scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/dataset.info) with K=21
0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction
0:00:00.001 4M / 4M INFO General (launch.hpp : 61) Two-step RR enabled: 0
0:00:00.020 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction
0:00:00.023 4M / 4M INFO General (read_converter.hpp : 84) Converting reads to binary format for library #0 (takes a while)
0:00:00.023 4M / 4M INFO General (read_converter.hpp : 85) Converting paired reads
0:00:00.282 112M / 112M INFO General (binary_converter.hpp : 139) 16384 reads processed
0:00:00.432 128M / 128M INFO General (binary_converter.hpp : 139) 32768 reads processed
0:00:00.728 156M / 156M INFO General (binary_converter.hpp : 139) 65536 reads processed
0:00:01.473 216M / 216M INFO General (binary_converter.hpp : 139) 131072 reads processed
0:00:03.397 332M / 332M INFO General (binary_converter.hpp : 139) 262144 reads processed
0:00:05.378 568M / 568M INFO General (binary_converter.hpp : 139) 524288 reads processed
0:00:06.228 612M / 612M INFO General (binary_converter.hpp : 159) 575305 reads written
0:00:06.679 4M / 612M INFO General (read_converter.hpp : 94) Converting single reads
0:00:06.871 148M / 612M INFO General (binary_converter.hpp : 159) 3711 reads written
0:00:07.745 4M / 612M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=21
0:00:07.748 4M / 612M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 144 buckets using 12 threads. This might take a while.
0:00:07.748 4M / 612M INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:07.748 4M / 612M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.33322 Gb
0:00:07.748 4M / 612M INFO General (kmer_splitters.hpp : 82) Using cell size of 466033
0:00:11.224 6G / 6G INFO General (kmer_splitters.hpp : 291) Processed 2308642 reads
0:00:11.224 6G / 6G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K
0:00:11.484 48M / 6G INFO General (kmer_splitters.hpp : 310) Used 2308642 reads. Maximum read length 151
0:00:11.484 48M / 6G INFO General (kmer_splitters.hpp : 311) Average read length 136.96
0:00:11.484 48M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:12.766 48M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 1426252 kmers in total.
0:00:12.766 48M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:13.834 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index
0:00:13.834 48M / 6G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 192 buckets using 12 threads. This might take a while.
0:00:13.834 48M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:13.834 48M / 6G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.33203 Gb
0:00:13.834 48M / 6G INFO General (kmer_splitters.hpp : 82) Using cell size of 349525
0:00:16.545 6G / 6G INFO General (kmer_splitters.hpp : 381) Processed 1426252 kmers
0:00:16.545 6G / 6G INFO General (kmer_splitters.hpp : 386) Used 1426252 kmers.
0:00:16.993 48M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:18.174 48M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 1385175 kmers in total.
0:00:18.174 48M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:19.024 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices
0:00:19.164 48M / 6G INFO General (kmer_index_builder.hpp : 137) Merging final buckets.
0:00:19.309 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 650744 bytes occupied (3.75834 bits per kmer).
0:00:19.311 48M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers
0:00:19.370 48M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished.
0:00:19.371 48M / 6G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping
0:00:19.636 48M / 6G INFO Early tip clipping (early_simplification.hpp : 184) 242186 22-mers were removed by early tip clipper
0:00:19.636 48M / 6G INFO General (graph_construction.hpp : 136) Condensing graph
0:00:19.695 48M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
0:00:19.786 52M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 117891 sequences extracted
0:00:19.832 52M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
0:00:19.955 52M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 2 loops collected
0:00:20.017 52M / 6G INFO General (graph_construction.hpp : 141) Building index with from graph
0:00:20.018 52M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index
0:00:20.018 52M / 6G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 192 buckets using 12 threads. This might take a while.
0:00:20.018 52M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:20.019 52M / 6G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.33192 Gb
0:00:20.019 52M / 6G INFO General (kmer_splitters.hpp : 82) Using cell size of 349525
0:00:22.449 6G / 6G INFO General (edge_index_builders.hpp : 75) Processed 235769 edges
0:00:22.449 6G / 6G INFO General (edge_index_builders.hpp : 80) Used 235769 sequences.
0:00:22.894 52M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:24.103 52M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 1184066 kmers in total.
0:00:24.103 52M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:24.908 52M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices
0:00:25.019 72M / 6G INFO General (kmer_index_builder.hpp : 137) Merging final buckets.
0:00:25.139 72M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 557504 bytes occupied (3.76671 bits per kmer).
0:00:25.158 100M / 6G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while.
0:00:25.208 100M / 6G INFO General (edge_index.hpp : 91) Index refilled
0:00:25.254 96M / 6G INFO General (graph_construction.hpp : 173) Filling coverage index
0:00:25.254 96M / 6G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while.
0:00:29.016 80M / 6G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index
0:00:29.123 80M / 6G INFO General (construction.cpp : 30) Figured out: read length = 151
0:00:29.124 80M / 6G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding
0:00:29.285 80M / 6G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 38
0:00:29.285 80M / 6G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 112.836
0:00:29.285 80M / 6G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 342
0:00:29.294 80M / 6G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 112.836
0:00:29.294 80M / 6G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0
0:00:29.294 80M / 6G INFO StageManager (stage.cpp : 126) STAGE == Simplification
0:00:29.294 52M / 6G INFO General (simplification.cpp : 387) Graph simplification started
0:00:29.294 52M / 6G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning
0:00:29.294 52M / 6G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled
0:00:29.294 52M / 6G INFO General (simplification.cpp : 356) Running Self conjugate edge remover
0:00:29.301 52M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:29.301 52M / 6G INFO General (simplification.cpp : 356) Running Initial isolated edge remover
0:00:29.313 52M / 6G INFO General (simplification.cpp : 358) Triggered 1226 times
0:00:29.313 52M / 6G INFO General (simplification.cpp : 356) Running Initial tip clipper
0:00:29.331 52M / 6G INFO General (simplification.cpp : 358) Triggered 1060 times
0:00:29.331 52M / 6G INFO General (simplification.cpp : 356) Running Initial ec remover
0:00:29.339 52M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:29.340 52M / 6G INFO General (graph_simplification.hpp : 617) Creating parallel br instance
0:00:29.340 52M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1
0:00:29.340 52M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:29.349 52M / 6G INFO General (simplification.cpp : 358) Triggered 81 times
0:00:29.349 52M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:30.420 56M / 6G INFO General (simplification.cpp : 358) Triggered 5598 times
0:00:30.421 56M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:30.440 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:30.440 56M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2
0:00:30.440 56M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:30.447 56M / 6G INFO General (simplification.cpp : 358) Triggered 28 times
0:00:30.447 56M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:30.449 56M / 6G INFO General (simplification.cpp : 358) Triggered 3 times
0:00:30.449 56M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:30.677 56M / 6G INFO General (simplification.cpp : 358) Triggered 12440 times
0:00:30.677 56M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3
0:00:30.677 56M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:30.687 56M / 6G INFO General (simplification.cpp : 358) Triggered 290 times
0:00:30.687 56M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:31.734 56M / 6G INFO General (simplification.cpp : 358) Triggered 4251 times
0:00:31.734 56M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:31.848 56M / 6G INFO General (simplification.cpp : 358) Triggered 5055 times
0:00:31.848 56M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4
0:00:31.848 56M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:31.855 56M / 6G INFO General (simplification.cpp : 358) Triggered 14 times
0:00:31.855 56M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:32.507 56M / 6G INFO General (simplification.cpp : 358) Triggered 3471 times
0:00:32.507 56M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:32.508 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.508 56M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5
0:00:32.508 56M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:32.510 56M / 6G INFO General (simplification.cpp : 358) Triggered 1 times
0:00:32.510 56M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:32.510 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.510 56M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:32.510 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.510 56M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 6
0:00:32.510 56M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:32.510 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.510 56M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:32.510 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.510 56M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:32.510 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.510 56M / 6G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification
0:00:32.510 56M / 6G INFO General (graph_simplification.hpp : 617) Creating parallel br instance
0:00:32.510 56M / 6G INFO General (simplification.cpp : 301) Iteration 1
0:00:32.510 56M / 6G INFO General (simplification.cpp : 356) Running Relative coverage component remover
0:00:32.897 52M / 6G INFO General (simplification.cpp : 358) Triggered 11252 times
0:00:32.897 52M / 6G INFO General (simplification.cpp : 356) Running Disconnecting edges with relatively low coverage
0:00:32.936 52M / 6G INFO General (simplification.cpp : 358) Triggered 329 times
0:00:32.936 52M / 6G INFO General (simplification.cpp : 356) Running Complex tip clipper
0:00:32.943 52M / 6G INFO General (simplification.cpp : 358) Triggered 80 times
0:00:32.943 52M / 6G INFO General (simplification.cpp : 356) Running Complex bulge remover
0:00:32.952 52M / 6G INFO General (simplification.cpp : 358) Triggered 1 times
0:00:32.952 52M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:32.954 52M / 6G INFO General (simplification.cpp : 358) Triggered 35 times
0:00:32.954 52M / 6G INFO General (simplification.cpp : 356) Running Final tip clipper
0:00:32.955 52M / 6G INFO General (simplification.cpp : 358) Triggered 6 times
0:00:32.955 52M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:32.956 52M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.956 52M / 6G INFO General (simplification.cpp : 356) Running Thorn remover (meta)
0:00:32.956 52M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.957 52M / 6G INFO General (simplification.cpp : 301) Iteration 2
0:00:32.957 52M / 6G INFO General (simplification.cpp : 356) Running Relative coverage component remover
0:00:32.957 52M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.957 52M / 6G INFO General (simplification.cpp : 356) Running Disconnecting edges with relatively low coverage
0:00:32.958 52M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.958 52M / 6G INFO General (simplification.cpp : 356) Running Complex tip clipper
0:00:32.958 52M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.958 52M / 6G INFO General (simplification.cpp : 356) Running Complex bulge remover
0:00:32.967 52M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.967 52M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:32.967 52M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.967 52M / 6G INFO General (simplification.cpp : 356) Running Final tip clipper
0:00:32.968 52M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.968 52M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:32.968 52M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.968 52M / 6G INFO General (simplification.cpp : 356) Running Thorn remover (meta)
0:00:32.969 52M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.969 52M / 6G INFO General (simplification.cpp : 328) Running Hidden EC remover (meta)
0:00:32.969 52M / 6G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges
0:00:32.970 52M / 6G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup
0:00:32.970 52M / 6G INFO General (simplification.cpp : 547) Removing isolated edges
0:00:32.973 52M / 6G INFO General (simplification.cpp : 570) Counting average coverage
0:00:32.974 52M / 6G INFO General (simplification.cpp : 575) Average coverage = 345.248
0:00:32.974 52M / 6G INFO StageManager (stage.cpp : 126) STAGE == Contig Output
0:00:32.974 52M / 6G INFO General (contig_output_stage.cpp : 40) Writing GFA to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K21/assembly_graph_with_scaffolds.gfa
0:00:33.005 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K21/before_rr.fasta
0:00:33.019 52M / 6G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K21/assembly_graph.fastg
0:00:33.048 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K21/simplified_contigs.fasta
0:00:33.062 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K21/final_contigs.fasta
0:00:33.083 52M / 6G INFO StageManager (stage.cpp : 126) STAGE == Contig Output
0:00:33.083 52M / 6G INFO General (contig_output_stage.cpp : 40) Writing GFA to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K21/assembly_graph_with_scaffolds.gfa
0:00:33.089 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K21/before_rr.fasta
0:00:33.104 52M / 6G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K21/assembly_graph.fastg
0:00:33.135 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K21/simplified_contigs.fasta
0:00:33.154 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K21/final_contigs.fasta
0:00:33.187 52M / 6G INFO General (launch.hpp : 137) SPAdes finished
0:00:33.213 48M / 6G INFO General (main.cpp : 110) Assembling time: 0 hours 0 minutes 33 seconds
== Running assembler: K33
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K33/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K33/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K33/configs/meta_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 120 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 89) Starting SPAdes, built from N/A, git revision N/A
0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum k-mer length: 128
0:00:00.000 4M / 4M INFO General (main.cpp : 91) Assembling dataset (/scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/dataset.info) with K=33
0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction
0:00:00.000 4M / 4M INFO General (launch.hpp : 61) Two-step RR enabled: 0
0:00:00.003 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction
0:00:00.008 4M / 4M INFO General (read_converter.hpp : 67) Binary reads detected
0:00:00.031 4M / 4M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=33
0:00:00.035 4M / 4M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 144 buckets using 12 threads. This might take a while.
0:00:00.035 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:00.035 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.33322 Gb
0:00:00.035 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 233016
0:00:03.333 6G / 6G INFO General (kmer_splitters.hpp : 291) Processed 2308642 reads
0:00:03.333 6G / 6G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K
0:00:04.449 48M / 6G INFO General (kmer_splitters.hpp : 310) Used 2308642 reads. Maximum read length 151
0:00:04.449 48M / 6G INFO General (kmer_splitters.hpp : 311) Average read length 136.96
0:00:04.449 48M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:05.894 48M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 2161561 kmers in total.
0:00:05.894 48M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:07.142 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index
0:00:07.142 48M / 6G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 192 buckets using 12 threads. This might take a while.
0:00:07.143 48M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:07.143 48M / 6G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.33203 Gb
0:00:07.143 48M / 6G INFO General (kmer_splitters.hpp : 82) Using cell size of 174762
0:00:11.437 6G / 6G INFO General (kmer_splitters.hpp : 381) Processed 2161561 kmers
0:00:11.437 6G / 6G INFO General (kmer_splitters.hpp : 386) Used 2161561 kmers.
0:00:11.875 48M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:13.629 48M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 2087413 kmers in total.
0:00:13.629 48M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:15.345 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices
0:00:16.675 48M / 6G INFO General (kmer_index_builder.hpp : 137) Merging final buckets.
0:00:17.401 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 976360 bytes occupied (3.74189 bits per kmer).
0:00:17.405 48M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers
0:00:17.510 48M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished.
0:00:17.512 48M / 6G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping
0:00:18.059 48M / 6G INFO Early tip clipping (early_simplification.hpp : 184) 378559 34-mers were removed by early tip clipper
0:00:18.060 48M / 6G INFO General (graph_construction.hpp : 136) Condensing graph
0:00:18.113 48M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
0:00:18.244 60M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 220476 sequences extracted
0:00:18.321 60M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
0:00:18.406 60M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected
0:00:18.487 104M / 6G INFO General (graph_construction.hpp : 141) Building index with from graph
0:00:18.488 104M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index
0:00:18.488 104M / 6G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 192 buckets using 12 threads. This might take a while.
0:00:18.488 104M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:18.488 104M / 6G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.33051 Gb
0:00:18.488 104M / 6G INFO General (kmer_splitters.hpp : 82) Using cell size of 174762
0:00:23.330 6G / 6G INFO General (edge_index_builders.hpp : 75) Processed 440941 edges
0:00:23.331 6G / 6G INFO General (edge_index_builders.hpp : 80) Used 440941 sequences.
0:00:23.649 104M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:25.137 104M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 1783002 kmers in total.
0:00:25.137 104M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:26.650 104M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices
0:00:26.952 104M / 6G INFO General (kmer_index_builder.hpp : 137) Merging final buckets.
0:00:27.846 104M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 835024 bytes occupied (3.7466 bits per kmer).
0:00:27.873 148M / 6G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while.
0:00:27.947 148M / 6G INFO General (edge_index.hpp : 91) Index refilled
0:00:27.991 144M / 6G INFO General (graph_construction.hpp : 173) Filling coverage index
0:00:27.991 144M / 6G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while.
0:00:32.019 144M / 6G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index
0:00:32.192 144M / 6G INFO General (construction.cpp : 30) Figured out: read length = 151
0:00:32.192 144M / 6G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding
0:00:32.505 144M / 6G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 25
0:00:32.505 144M / 6G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 67.0811
0:00:32.505 144M / 6G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 185
0:00:32.511 144M / 6G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 67.0811
0:00:32.511 144M / 6G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0
0:00:32.511 144M / 6G INFO StageManager (stage.cpp : 126) STAGE == Simplification
0:00:32.512 100M / 6G INFO General (simplification.cpp : 387) Graph simplification started
0:00:32.512 100M / 6G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning
0:00:32.512 100M / 6G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled
0:00:32.512 100M / 6G INFO General (simplification.cpp : 356) Running Self conjugate edge remover
0:00:32.525 100M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:32.525 100M / 6G INFO General (simplification.cpp : 356) Running Initial isolated edge remover
0:00:32.548 100M / 6G INFO General (simplification.cpp : 358) Triggered 2185 times
0:00:32.548 100M / 6G INFO General (simplification.cpp : 356) Running Initial tip clipper
0:00:32.581 100M / 6G INFO General (simplification.cpp : 358) Triggered 1637 times
0:00:32.581 100M / 6G INFO General (simplification.cpp : 356) Running Initial ec remover
0:00:32.600 100M / 6G INFO General (simplification.cpp : 358) Triggered 7 times
0:00:32.600 100M / 6G INFO General (graph_simplification.hpp : 617) Creating parallel br instance
0:00:32.600 100M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1
0:00:32.600 100M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:32.620 100M / 6G INFO General (simplification.cpp : 358) Triggered 194 times
0:00:32.620 100M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:33.417 108M / 6G INFO General (simplification.cpp : 358) Triggered 1980 times
0:00:33.417 108M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:33.473 108M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:33.473 108M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2
0:00:33.473 108M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:33.481 104M / 6G INFO General (simplification.cpp : 358) Triggered 6 times
0:00:33.481 104M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:33.481 104M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:33.481 104M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:34.374 108M / 6G INFO General (simplification.cpp : 358) Triggered 40511 times
0:00:34.374 108M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3
0:00:34.374 108M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:34.391 108M / 6G INFO General (simplification.cpp : 358) Triggered 378 times
0:00:34.391 108M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:35.846 108M / 6G INFO General (simplification.cpp : 358) Triggered 3649 times
0:00:35.846 108M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:36.111 108M / 6G INFO General (simplification.cpp : 358) Triggered 11592 times
0:00:36.111 108M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4
0:00:36.111 108M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:36.122 104M / 6G INFO General (simplification.cpp : 358) Triggered 23 times
0:00:36.122 104M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:37.685 104M / 6G INFO General (simplification.cpp : 358) Triggered 5412 times
0:00:37.685 104M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:37.685 104M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:37.685 104M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5
0:00:37.685 104M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:37.688 104M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:37.688 104M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:37.688 104M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:37.688 104M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:37.688 104M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:37.688 104M / 6G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification
0:00:37.688 104M / 6G INFO General (graph_simplification.hpp : 617) Creating parallel br instance
0:00:37.688 104M / 6G INFO General (simplification.cpp : 301) Iteration 1
0:00:37.688 104M / 6G INFO General (simplification.cpp : 356) Running Relative coverage component remover
0:00:38.162 56M / 6G INFO General (simplification.cpp : 358) Triggered 12064 times
0:00:38.162 56M / 6G INFO General (simplification.cpp : 356) Running Disconnecting edges with relatively low coverage
0:00:38.205 56M / 6G INFO General (simplification.cpp : 358) Triggered 356 times
0:00:38.205 56M / 6G INFO General (simplification.cpp : 356) Running Complex tip clipper
0:00:38.213 56M / 6G INFO General (simplification.cpp : 358) Triggered 80 times
0:00:38.213 56M / 6G INFO General (simplification.cpp : 356) Running Complex bulge remover
0:00:38.222 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:38.222 56M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:38.223 56M / 6G INFO General (simplification.cpp : 358) Triggered 36 times
0:00:38.223 56M / 6G INFO General (simplification.cpp : 356) Running Final tip clipper
0:00:38.224 56M / 6G INFO General (simplification.cpp : 358) Triggered 1 times
0:00:38.224 56M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:38.225 56M / 6G INFO General (simplification.cpp : 358) Triggered 2 times
0:00:38.225 56M / 6G INFO General (simplification.cpp : 356) Running Thorn remover (meta)
0:00:38.225 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:38.225 56M / 6G INFO General (simplification.cpp : 301) Iteration 2
0:00:38.225 56M / 6G INFO General (simplification.cpp : 356) Running Relative coverage component remover
0:00:38.225 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:38.225 56M / 6G INFO General (simplification.cpp : 356) Running Disconnecting edges with relatively low coverage
0:00:38.225 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:38.226 56M / 6G INFO General (simplification.cpp : 356) Running Complex tip clipper
0:00:38.226 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:38.226 56M / 6G INFO General (simplification.cpp : 356) Running Complex bulge remover
0:00:38.234 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:38.234 56M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:38.234 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:38.234 56M / 6G INFO General (simplification.cpp : 356) Running Final tip clipper
0:00:38.234 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:38.235 56M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:38.235 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:38.235 56M / 6G INFO General (simplification.cpp : 356) Running Thorn remover (meta)
0:00:38.235 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:38.235 56M / 6G INFO General (simplification.cpp : 328) Running Hidden EC remover (meta)
0:00:38.235 56M / 6G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges
0:00:38.237 56M / 6G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup
0:00:38.237 56M / 6G INFO General (simplification.cpp : 547) Removing isolated edges
0:00:38.240 52M / 6G INFO General (simplification.cpp : 570) Counting average coverage
0:00:38.241 52M / 6G INFO General (simplification.cpp : 575) Average coverage = 334.105
0:00:38.241 52M / 6G INFO StageManager (stage.cpp : 126) STAGE == Contig Output
0:00:38.241 52M / 6G INFO General (contig_output_stage.cpp : 40) Writing GFA to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K33/assembly_graph_with_scaffolds.gfa
0:00:38.257 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K33/before_rr.fasta
0:00:38.269 52M / 6G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K33/assembly_graph.fastg
0:00:38.292 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K33/simplified_contigs.fasta
0:00:38.303 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K33/final_contigs.fasta
0:00:38.320 52M / 6G INFO StageManager (stage.cpp : 126) STAGE == Contig Output
0:00:38.320 52M / 6G INFO General (contig_output_stage.cpp : 40) Writing GFA to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K33/assembly_graph_with_scaffolds.gfa
0:00:38.324 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K33/before_rr.fasta
0:00:38.337 52M / 6G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K33/assembly_graph.fastg
0:00:38.359 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K33/simplified_contigs.fasta
0:00:38.371 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K33/final_contigs.fasta
0:00:38.391 52M / 6G INFO General (launch.hpp : 137) SPAdes finished
0:00:38.416 48M / 6G INFO General (main.cpp : 110) Assembling time: 0 hours 0 minutes 38 seconds
== Running assembler: K45
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K45/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K45/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K45/configs/meta_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 120 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 89) Starting SPAdes, built from N/A, git revision N/A
0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum k-mer length: 128
0:00:00.000 4M / 4M INFO General (main.cpp : 91) Assembling dataset (/scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/dataset.info) with K=45
0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction
0:00:00.000 4M / 4M INFO General (launch.hpp : 61) Two-step RR enabled: 0
0:00:00.002 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction
0:00:00.005 4M / 4M INFO General (read_converter.hpp : 67) Binary reads detected
0:00:00.023 4M / 4M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=45
0:00:00.026 4M / 4M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 144 buckets using 12 threads. This might take a while.
0:00:00.026 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:00.026 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.33322 Gb
0:00:00.026 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 233016
0:00:03.555 6G / 6G INFO General (kmer_splitters.hpp : 291) Processed 2308642 reads
0:00:03.556 6G / 6G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K
0:00:05.002 48M / 6G INFO General (kmer_splitters.hpp : 310) Used 2308642 reads. Maximum read length 151
0:00:05.002 48M / 6G INFO General (kmer_splitters.hpp : 311) Average read length 136.96
0:00:05.002 48M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:09.834 48M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 3120614 kmers in total.
0:00:09.834 48M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:12.019 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index
0:00:12.019 48M / 6G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 192 buckets using 12 threads. This might take a while.
0:00:12.019 48M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:12.019 48M / 6G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.33203 Gb
0:00:12.019 48M / 6G INFO General (kmer_splitters.hpp : 82) Using cell size of 174762
0:00:15.943 6G / 6G INFO General (kmer_splitters.hpp : 381) Processed 3120614 kmers
0:00:15.943 6G / 6G INFO General (kmer_splitters.hpp : 386) Used 3120614 kmers.
0:00:16.369 48M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:18.789 48M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 3038261 kmers in total.
0:00:18.789 48M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:20.595 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices
0:00:21.609 48M / 6G INFO General (kmer_index_builder.hpp : 137) Merging final buckets.
0:00:22.489 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 1417280 bytes occupied (3.73182 bits per kmer).
0:00:22.497 52M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers
0:00:22.646 52M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished.
0:00:22.647 52M / 6G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping
0:00:23.299 52M / 6G INFO Early tip clipping (early_simplification.hpp : 184) 642931 46-mers were removed by early tip clipper
0:00:23.299 52M / 6G INFO General (graph_construction.hpp : 136) Condensing graph
0:00:23.349 52M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
0:00:23.512 60M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 254412 sequences extracted
0:00:23.610 60M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
0:00:23.703 60M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected
0:00:23.798 104M / 6G INFO General (graph_construction.hpp : 141) Building index with from graph
0:00:23.799 104M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index
0:00:23.799 104M / 6G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 192 buckets using 12 threads. This might take a while.
0:00:23.799 104M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:23.799 104M / 6G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.33051 Gb
0:00:23.799 104M / 6G INFO General (kmer_splitters.hpp : 82) Using cell size of 174762
0:00:26.473 6G / 6G INFO General (edge_index_builders.hpp : 75) Processed 508815 edges
0:00:26.473 6G / 6G INFO General (edge_index_builders.hpp : 80) Used 508815 sequences.
0:00:26.920 104M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:29.461 104M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 2477683 kmers in total.
0:00:29.461 104M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:33.448 104M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices
0:00:33.849 104M / 6G INFO General (kmer_index_builder.hpp : 137) Merging final buckets.
0:00:34.647 104M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 1157360 bytes occupied (3.73691 bits per kmer).
0:00:34.680 164M / 6G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while.
0:00:34.783 168M / 6G INFO General (edge_index.hpp : 91) Index refilled
0:00:34.836 164M / 6G INFO General (graph_construction.hpp : 173) Filling coverage index
0:00:34.836 164M / 6G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while.
0:00:38.892 164M / 6G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index
0:00:39.259 164M / 6G INFO General (construction.cpp : 30) Figured out: read length = 151
0:00:39.259 164M / 6G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding
0:00:39.692 164M / 6G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 17
0:00:39.693 164M / 6G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 42.5931
0:00:39.693 164M / 6G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 159
0:00:39.697 164M / 6G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 42.5931
0:00:39.697 164M / 6G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0
0:00:39.697 164M / 6G INFO StageManager (stage.cpp : 126) STAGE == Simplification
0:00:39.697 104M / 6G INFO General (simplification.cpp : 387) Graph simplification started
0:00:39.697 104M / 6G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning
0:00:39.698 104M / 6G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled
0:00:39.698 104M / 6G INFO General (simplification.cpp : 356) Running Self conjugate edge remover
0:00:39.715 104M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:39.715 104M / 6G INFO General (simplification.cpp : 356) Running Initial isolated edge remover
0:00:39.751 104M / 6G INFO General (simplification.cpp : 358) Triggered 3857 times
0:00:39.751 104M / 6G INFO General (simplification.cpp : 356) Running Initial tip clipper
0:00:39.794 104M / 6G INFO General (simplification.cpp : 358) Triggered 2235 times
0:00:39.794 104M / 6G INFO General (simplification.cpp : 356) Running Initial ec remover
0:00:39.817 104M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:39.817 104M / 6G INFO General (graph_simplification.hpp : 617) Creating parallel br instance
0:00:39.817 104M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1
0:00:39.817 104M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:39.842 104M / 6G INFO General (simplification.cpp : 358) Triggered 335 times
0:00:39.842 104M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:40.716 108M / 6G INFO General (simplification.cpp : 358) Triggered 1243 times
0:00:40.716 108M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:40.792 108M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:40.792 108M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2
0:00:40.792 108M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:40.802 108M / 6G INFO General (simplification.cpp : 358) Triggered 13 times
0:00:40.802 108M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:40.802 108M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:40.802 108M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:42.196 108M / 6G INFO General (simplification.cpp : 358) Triggered 53143 times
0:00:42.196 108M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3
0:00:42.196 108M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:42.224 108M / 6G INFO General (simplification.cpp : 358) Triggered 965 times
0:00:42.224 108M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:44.491 108M / 6G INFO General (simplification.cpp : 358) Triggered 4149 times
0:00:44.492 108M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:44.829 108M / 6G INFO General (simplification.cpp : 358) Triggered 11755 times
0:00:44.829 108M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4
0:00:44.829 108M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:44.847 108M / 6G INFO General (simplification.cpp : 358) Triggered 69 times
0:00:44.847 108M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:47.174 104M / 6G INFO General (simplification.cpp : 358) Triggered 6320 times
0:00:47.174 104M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:47.174 104M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.174 104M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5
0:00:47.174 104M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:47.176 104M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.176 104M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:47.176 104M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.176 104M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:47.176 104M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.176 104M / 6G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification
0:00:47.176 104M / 6G INFO General (graph_simplification.hpp : 617) Creating parallel br instance
0:00:47.176 104M / 6G INFO General (simplification.cpp : 301) Iteration 1
0:00:47.176 104M / 6G INFO General (simplification.cpp : 356) Running Relative coverage component remover
0:00:47.569 56M / 6G INFO General (simplification.cpp : 358) Triggered 8448 times
0:00:47.569 56M / 6G INFO General (simplification.cpp : 356) Running Disconnecting edges with relatively low coverage
0:00:47.590 56M / 6G INFO General (simplification.cpp : 358) Triggered 192 times
0:00:47.590 56M / 6G INFO General (simplification.cpp : 356) Running Complex tip clipper
0:00:47.595 56M / 6G INFO General (simplification.cpp : 358) Triggered 40 times
0:00:47.595 56M / 6G INFO General (simplification.cpp : 356) Running Complex bulge remover
0:00:47.603 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.603 56M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:47.604 56M / 6G INFO General (simplification.cpp : 358) Triggered 16 times
0:00:47.604 56M / 6G INFO General (simplification.cpp : 356) Running Final tip clipper
0:00:47.605 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.605 56M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:47.605 56M / 6G INFO General (simplification.cpp : 358) Triggered 2 times
0:00:47.605 56M / 6G INFO General (simplification.cpp : 356) Running Thorn remover (meta)
0:00:47.605 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.605 56M / 6G INFO General (simplification.cpp : 301) Iteration 2
0:00:47.605 56M / 6G INFO General (simplification.cpp : 356) Running Relative coverage component remover
0:00:47.606 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.606 56M / 6G INFO General (simplification.cpp : 356) Running Disconnecting edges with relatively low coverage
0:00:47.606 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.606 56M / 6G INFO General (simplification.cpp : 356) Running Complex tip clipper
0:00:47.606 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.606 56M / 6G INFO General (simplification.cpp : 356) Running Complex bulge remover
0:00:47.614 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.614 56M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:47.614 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.614 56M / 6G INFO General (simplification.cpp : 356) Running Final tip clipper
0:00:47.614 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.614 56M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:47.614 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.614 56M / 6G INFO General (simplification.cpp : 356) Running Thorn remover (meta)
0:00:47.614 56M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.614 56M / 6G INFO General (simplification.cpp : 328) Running Hidden EC remover (meta)
0:00:47.615 56M / 6G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges
0:00:47.616 56M / 6G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup
0:00:47.616 56M / 6G INFO General (simplification.cpp : 547) Removing isolated edges
0:00:47.619 52M / 6G INFO General (simplification.cpp : 570) Counting average coverage
0:00:47.619 52M / 6G INFO General (simplification.cpp : 575) Average coverage = 326.754
0:00:47.619 52M / 6G INFO StageManager (stage.cpp : 126) STAGE == Contig Output
0:00:47.619 52M / 6G INFO General (contig_output_stage.cpp : 40) Writing GFA to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K45/assembly_graph_with_scaffolds.gfa
0:00:47.624 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K45/before_rr.fasta
0:00:47.634 52M / 6G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K45/assembly_graph.fastg
0:00:47.652 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K45/simplified_contigs.fasta
0:00:47.662 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K45/final_contigs.fasta
0:00:47.676 52M / 6G INFO StageManager (stage.cpp : 126) STAGE == Contig Output
0:00:47.676 52M / 6G INFO General (contig_output_stage.cpp : 40) Writing GFA to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K45/assembly_graph_with_scaffolds.gfa
0:00:47.679 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K45/before_rr.fasta
0:00:47.690 52M / 6G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K45/assembly_graph.fastg
0:00:47.709 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K45/simplified_contigs.fasta
0:00:47.719 52M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K45/final_contigs.fasta
0:00:47.735 52M / 6G INFO General (launch.hpp : 137) SPAdes finished
0:00:47.757 48M / 6G INFO General (main.cpp : 110) Assembling time: 0 hours 0 minutes 47 seconds
== Running assembler: K55
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K55/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K55/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K55/configs/meta_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 120 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 89) Starting SPAdes, built from N/A, git revision N/A
0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum k-mer length: 128
0:00:00.000 4M / 4M INFO General (main.cpp : 91) Assembling dataset (/scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/dataset.info) with K=55
0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction
0:00:00.000 4M / 4M INFO General (launch.hpp : 61) Two-step RR enabled: 0
0:00:00.001 4M / 4M INFO General (launch.hpp : 79) Will need read mapping, kmer mapper will be attached
0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction
0:00:00.004 4M / 4M INFO General (read_converter.hpp : 67) Binary reads detected
0:00:00.010 4M / 4M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=55
0:00:00.012 4M / 4M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 144 buckets using 12 threads. This might take a while.
0:00:00.012 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:00.012 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.33322 Gb
0:00:00.012 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 233016
0:00:04.077 6G / 6G INFO General (kmer_splitters.hpp : 291) Processed 2308642 reads
0:00:04.077 6G / 6G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K
0:00:04.866 48M / 6G INFO General (kmer_splitters.hpp : 310) Used 2308642 reads. Maximum read length 151
0:00:04.866 48M / 6G INFO General (kmer_splitters.hpp : 311) Average read length 136.96
0:00:04.866 48M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:07.554 48M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 3907177 kmers in total.
0:00:07.554 48M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:12.757 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index
0:00:12.757 48M / 6G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 192 buckets using 12 threads. This might take a while.
0:00:12.757 48M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:12.757 48M / 6G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.33203 Gb
0:00:12.757 48M / 6G INFO General (kmer_splitters.hpp : 82) Using cell size of 174762
0:00:17.151 6G / 6G INFO General (kmer_splitters.hpp : 381) Processed 3907177 kmers
0:00:17.151 6G / 6G INFO General (kmer_splitters.hpp : 386) Used 3907177 kmers.
0:00:17.572 48M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:20.137 48M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 3832513 kmers in total.
0:00:20.137 48M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:22.178 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices
0:00:23.736 48M / 6G INFO General (kmer_index_builder.hpp : 137) Merging final buckets.
0:00:24.348 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 1785288 bytes occupied (3.72662 bits per kmer).
0:00:24.358 52M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers
0:00:24.545 52M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished.
0:00:24.547 52M / 6G INFO General (graph_construction.hpp : 136) Condensing graph
0:00:24.626 52M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
0:00:25.703 64M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 380378 sequences extracted
0:00:25.865 64M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
0:00:25.971 64M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected
0:00:26.132 156M / 6G INFO General (graph_construction.hpp : 141) Building index with from graph
0:00:26.137 156M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index
0:00:26.137 156M / 6G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 192 buckets using 12 threads. This might take a while.
0:00:26.137 156M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:26.137 156M / 6G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.3291 Gb
0:00:26.137 156M / 6G INFO General (kmer_splitters.hpp : 82) Using cell size of 174762
0:00:29.381 6G / 6G INFO General (edge_index_builders.hpp : 75) Processed 760751 edges
0:00:29.381 6G / 6G INFO General (edge_index_builders.hpp : 80) Used 760751 sequences.
0:00:29.826 156M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:32.287 156M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 3907177 kmers in total.
0:00:32.287 156M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:34.528 156M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices
0:00:37.234 160M / 6G INFO General (kmer_index_builder.hpp : 137) Merging final buckets.
0:00:39.569 160M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 1820168 bytes occupied (3.72682 bits per kmer).
0:00:39.623 252M / 6G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while.
0:00:39.791 252M / 6G INFO General (edge_index.hpp : 91) Index refilled
0:00:40.067 248M / 6G INFO General (graph_construction.hpp : 173) Filling coverage index
0:00:40.067 248M / 6G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while.
0:00:43.986 244M / 6G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index
0:00:44.374 244M / 6G INFO General (construction.cpp : 30) Figured out: read length = 151
0:00:44.374 244M / 6G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding
0:00:44.939 244M / 6G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 12
0:00:44.939 244M / 6G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 24.2897
0:00:44.939 244M / 6G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 9
0:00:44.942 244M / 6G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 9
0:00:44.942 244M / 6G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0
0:00:44.942 244M / 6G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer
0:00:44.949 244M / 6G INFO General (gap_closer.cpp : 159) Preparing shift maps
0:00:45.228 260M / 6G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
0:00:47.272 260M / 6G INFO General (gap_closer.cpp : 138) Used 575305 paired reads
0:00:47.272 260M / 6G INFO General (gap_closer.cpp : 140) Merging paired indices
0:00:47.343 248M / 6G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
0:00:47.865 248M / 6G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 3 gaps after checking 1710 candidates
0:00:47.883 248M / 6G INFO StageManager (stage.cpp : 126) STAGE == Simplification
0:00:47.885 156M / 6G INFO General (simplification.cpp : 387) Graph simplification started
0:00:47.885 156M / 6G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning
0:00:47.885 156M / 6G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled
0:00:47.885 156M / 6G INFO General (simplification.cpp : 356) Running Self conjugate edge remover
0:00:47.910 156M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:47.910 156M / 6G INFO General (simplification.cpp : 356) Running Initial isolated edge remover
0:00:47.962 152M / 6G INFO General (simplification.cpp : 358) Triggered 5090 times
0:00:47.962 152M / 6G INFO General (simplification.cpp : 356) Running Initial tip clipper
0:00:48.709 160M / 6G INFO General (simplification.cpp : 358) Triggered 78280 times
0:00:48.709 160M / 6G INFO General (simplification.cpp : 356) Running Initial ec remover
0:00:48.732 160M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:48.742 156M / 6G INFO General (graph_simplification.hpp : 617) Creating parallel br instance
0:00:48.742 156M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1
0:00:48.742 156M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:48.773 156M / 6G INFO General (simplification.cpp : 358) Triggered 1070 times
0:00:48.773 156M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:49.671 164M / 6G INFO General (simplification.cpp : 358) Triggered 1057 times
0:00:49.671 164M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:49.742 164M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:49.742 164M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2
0:00:49.742 164M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:49.750 164M / 6G INFO General (simplification.cpp : 358) Triggered 17 times
0:00:49.750 164M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:49.750 164M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:49.750 164M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:51.030 164M / 6G INFO General (simplification.cpp : 358) Triggered 51921 times
0:00:51.030 164M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3
0:00:51.030 164M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:51.069 164M / 6G INFO General (simplification.cpp : 358) Triggered 1782 times
0:00:51.069 164M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:55.120 188M / 6G INFO General (simplification.cpp : 358) Triggered 5312 times
0:00:55.120 188M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:55.357 184M / 6G INFO General (simplification.cpp : 358) Triggered 9279 times
0:00:55.357 184M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 4
0:00:55.357 184M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:55.368 184M / 6G INFO General (simplification.cpp : 358) Triggered 140 times
0:00:55.368 184M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:58.926 200M / 6G INFO General (simplification.cpp : 358) Triggered 6699 times
0:00:58.926 200M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:58.926 200M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:58.926 200M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 5
0:00:58.926 200M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:58.928 200M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:58.928 200M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:58.928 200M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:58.928 200M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:58.928 200M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:58.928 200M / 6G INFO General (simplification.cpp : 167) PROCEDURE == Post simplification
0:00:58.928 200M / 6G INFO General (graph_simplification.hpp : 617) Creating parallel br instance
0:00:58.928 200M / 6G INFO General (simplification.cpp : 301) Iteration 1
0:00:58.928 200M / 6G INFO General (simplification.cpp : 356) Running Relative coverage component remover
0:00:59.174 172M / 6G INFO General (simplification.cpp : 358) Triggered 5027 times
0:00:59.174 172M / 6G INFO General (simplification.cpp : 356) Running Disconnecting edges with relatively low coverage
0:00:59.178 172M / 6G INFO General (simplification.cpp : 358) Triggered 69 times
0:00:59.178 172M / 6G INFO General (simplification.cpp : 356) Running Complex tip clipper
0:00:59.180 172M / 6G INFO General (simplification.cpp : 358) Triggered 10 times
0:00:59.180 172M / 6G INFO General (simplification.cpp : 356) Running Complex bulge remover
0:00:59.188 172M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:59.188 172M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:59.189 172M / 6G INFO General (simplification.cpp : 358) Triggered 10 times
0:00:59.189 172M / 6G INFO General (simplification.cpp : 356) Running Final tip clipper
0:00:59.189 172M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:59.189 172M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:59.190 172M / 6G INFO General (simplification.cpp : 358) Triggered 2 times
0:00:59.190 172M / 6G INFO General (simplification.cpp : 356) Running Thorn remover (meta)
0:00:59.190 172M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:59.190 172M / 6G INFO General (simplification.cpp : 301) Iteration 2
0:00:59.190 172M / 6G INFO General (simplification.cpp : 356) Running Relative coverage component remover
0:00:59.190 172M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:59.190 172M / 6G INFO General (simplification.cpp : 356) Running Disconnecting edges with relatively low coverage
0:00:59.190 172M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:59.190 172M / 6G INFO General (simplification.cpp : 356) Running Complex tip clipper
0:00:59.191 172M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:59.191 172M / 6G INFO General (simplification.cpp : 356) Running Complex bulge remover
0:00:59.199 172M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:59.199 172M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:59.199 172M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:59.199 172M / 6G INFO General (simplification.cpp : 356) Running Final tip clipper
0:00:59.199 172M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:59.199 172M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:59.199 172M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:59.199 172M / 6G INFO General (simplification.cpp : 356) Running Thorn remover (meta)
0:00:59.200 172M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:59.200 172M / 6G INFO General (simplification.cpp : 328) Running Hidden EC remover (meta)
0:00:59.200 172M / 6G INFO General (simplification.cpp : 333) Disrupting self-conjugate edges
0:00:59.201 172M / 6G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer
0:00:59.201 172M / 6G INFO General (graph_pack.hpp : 99) Index refill
0:00:59.202 172M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index
0:00:59.202 172M / 6G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 192 buckets using 12 threads. This might take a while.
0:00:59.202 172M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:59.202 172M / 6G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.32867 Gb
0:00:59.202 172M / 6G INFO General (kmer_splitters.hpp : 82) Using cell size of 174762
0:01:01.142 6G / 6G INFO General (edge_index_builders.hpp : 75) Processed 2886 edges
0:01:01.142 6G / 6G INFO General (edge_index_builders.hpp : 80) Used 2886 sequences.
0:01:01.589 172M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:01:02.591 172M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 309785 kmers in total.
0:01:02.591 172M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:01:03.281 172M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices
0:01:03.339 172M / 6G INFO General (kmer_index_builder.hpp : 137) Merging final buckets.
0:01:03.408 172M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 152048 bytes occupied (3.92654 bits per kmer).
0:01:03.413 180M / 6G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while.
0:01:03.427 180M / 6G INFO General (edge_index.hpp : 91) Index refilled
0:01:03.431 180M / 6G INFO General (gap_closer.cpp : 159) Preparing shift maps
0:01:03.435 180M / 6G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
0:01:05.107 180M / 6G INFO General (gap_closer.cpp : 138) Used 575305 paired reads
0:01:05.107 180M / 6G INFO General (gap_closer.cpp : 140) Merging paired indices
0:01:05.111 180M / 6G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
0:01:05.123 180M / 6G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 3 gaps after checking 243 candidates
0:01:05.126 180M / 6G INFO StageManager (stage.cpp : 126) STAGE == Simplification Cleanup
0:01:05.126 180M / 6G INFO General (simplification.cpp : 547) Removing isolated edges
0:01:05.160 180M / 6G INFO General (simplification.cpp : 570) Counting average coverage
0:01:05.161 180M / 6G INFO General (simplification.cpp : 575) Average coverage = 322.292
0:01:05.161 180M / 6G INFO StageManager (stage.cpp : 126) STAGE == Contig Output
0:01:05.161 180M / 6G INFO General (contig_output_stage.cpp : 40) Writing GFA to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K55/assembly_graph_with_scaffolds.gfa
0:01:05.171 180M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K55/before_rr.fasta
0:01:05.183 180M / 6G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K55/assembly_graph.fastg
0:01:05.205 180M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K55/simplified_contigs.fasta
0:01:05.216 180M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K55/final_contigs.fasta
0:01:05.231 180M / 6G INFO StageManager (stage.cpp : 126) STAGE == Contig Output
0:01:05.231 180M / 6G INFO General (contig_output_stage.cpp : 40) Writing GFA to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K55/assembly_graph_with_scaffolds.gfa
0:01:05.234 180M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K55/before_rr.fasta
0:01:05.245 180M / 6G INFO General (contig_output_stage.cpp : 50) Outputting FastG graph to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K55/assembly_graph.fastg
0:01:05.265 180M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K55/simplified_contigs.fasta
0:01:05.278 180M / 6G INFO General (contig_output.hpp : 22) Outputting contigs to /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades//K55/final_contigs.fasta
0:01:05.296 180M / 6G INFO General (launch.hpp : 137) SPAdes finished
0:01:05.831 52M / 6G INFO General (main.cpp : 110) Assembling time: 0 hours 1 minutes 5 seconds
== Running assembler: K63
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K63/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K63/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/K63/configs/meta_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 51) Memory limit set to 120 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 89) Starting SPAdes, built from N/A, git revision N/A
0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum k-mer length: 128
0:00:00.000 4M / 4M INFO General (main.cpp : 91) Assembling dataset (/scratch200/urineri/Not_my_raw_reads/IS7/viral_IS7/output/meta_spades/dataset.info) with K=63
0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction
0:00:00.000 4M / 4M INFO General (launch.hpp : 61) Two-step RR enabled: 0
0:00:00.001 4M / 4M INFO General (launch.hpp : 79) Will need read mapping, kmer mapper will be attached
0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction
0:00:00.003 4M / 4M INFO General (read_converter.hpp : 67) Binary reads detected
0:00:00.012 4M / 4M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=63
0:00:00.013 4M / 4M INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 144 buckets using 12 threads. This might take a while.
0:00:00.013 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:00.013 4M / 4M INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.33322 Gb
0:00:00.013 4M / 4M INFO General (kmer_splitters.hpp : 82) Using cell size of 233016
0:00:04.628 6G / 6G INFO General (kmer_splitters.hpp : 291) Processed 2308642 reads
0:00:04.628 6G / 6G INFO General (kmer_splitters.hpp : 297) Adding contigs from previous K
0:00:05.552 48M / 6G INFO General (kmer_splitters.hpp : 310) Used 2308642 reads. Maximum read length 151
0:00:05.552 48M / 6G INFO General (kmer_splitters.hpp : 311) Average read length 136.96
0:00:05.552 48M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:08.590 48M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 4450455 kmers in total.
0:00:08.590 48M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:10.959 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index
0:00:10.959 48M / 6G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 192 buckets using 12 threads. This might take a while.
0:00:10.959 48M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:10.959 48M / 6G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.33203 Gb
0:00:10.960 48M / 6G INFO General (kmer_splitters.hpp : 82) Using cell size of 174762
0:00:16.628 6G / 6G INFO General (kmer_splitters.hpp : 381) Processed 4450455 kmers
0:00:16.628 6G / 6G INFO General (kmer_splitters.hpp : 386) Used 4450455 kmers.
0:00:17.064 48M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:19.391 48M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 4388076 kmers in total.
0:00:19.391 48M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:23.222 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices
0:00:26.648 48M / 6G INFO General (kmer_index_builder.hpp : 137) Merging final buckets.
0:00:29.673 48M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 2042904 bytes occupied (3.72446 bits per kmer).
0:00:29.682 56M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 87) Building k-mer extensions from k+1-mers
0:00:29.883 56M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 91) Building k-mer extensions from k+1-mers finished.
0:00:29.885 56M / 6G INFO General (graph_construction.hpp : 136) Condensing graph
0:00:29.944 56M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
0:00:31.103 68M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 383574 sequences extracted
0:00:31.278 68M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
0:00:31.654 68M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected
0:00:31.824 164M / 6G INFO General (graph_construction.hpp : 141) Building index with from graph
0:00:31.825 164M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 289) Building kmer index
0:00:31.825 164M / 6G INFO General (kmer_index_builder.hpp : 106) Splitting kmer instances into 192 buckets using 12 threads. This might take a while.
0:00:31.825 164M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:31.825 164M / 6G INFO General (kmer_splitters.hpp : 74) Memory available for splitting buffers: 3.32888 Gb
0:00:31.825 164M / 6G INFO General (kmer_splitters.hpp : 82) Using cell size of 174762
0:00:36.197 6G / 6G INFO General (edge_index_builders.hpp : 75) Processed 767145 edges
0:00:36.197 6G / 6G INFO General (edge_index_builders.hpp : 80) Used 767145 sequences.
0:00:36.681 164M / 6G INFO General (kmer_index_builder.hpp : 109) Starting k-mer counting.
0:00:38.638 164M / 6G INFO General (kmer_index_builder.hpp : 115) K-mer counting done. There are 4450455 kmers in total.
0:00:38.638 164M / 6G INFO General (kmer_index_builder.hpp : 121) Merging temporary buckets.
0:00:40.892 164M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 298) Building perfect hash indices
0:00:42.847 164M / 6G INFO General (kmer_index_builder.hpp : 137) Merging final buckets.
0:00:44.495 164M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 320) Index built. Total 2071888 bytes occupied (3.72436 bits per kmer).
0:00:44.554 268M / 6G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from graph, this takes a while.
0:00:44.739 268M / 6G INFO General (edge_index.hpp : 91) Index refilled
0:00:44.796 260M / 6G INFO General (graph_construction.hpp : 173) Filling coverage index
0:00:44.796 260M / 6G INFO General (edge_index_builders.hpp : 183) Collecting k-mer coverage information from reads, this takes a while.
0:00:48.539 260M / 6G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index
0:00:48.917 260M / 6G INFO General (construction.cpp : 30) Figured out: read length = 151
0:00:48.917 260M / 6G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding
0:00:49.517 260M / 6G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 10
0:00:49.517 260M / 6G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 19.3195
0:00:49.517 260M / 6G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 7
0:00:49.520 260M / 6G INFO General (genomic_info_filler.cpp : 141) EC coverage threshold value was calculated as 7
0:00:49.520 260M / 6G INFO General (genomic_info_filler.cpp : 142) Trusted kmer low bound: 0
0:00:49.520 260M / 6G INFO StageManager (stage.cpp : 126) STAGE == Gap Closer
0:00:49.527 260M / 6G INFO General (gap_closer.cpp : 159) Preparing shift maps
0:00:49.832 276M / 6G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
0:00:51.505 276M / 6G INFO General (gap_closer.cpp : 138) Used 575305 paired reads
0:00:51.505 276M / 6G INFO General (gap_closer.cpp : 140) Merging paired indices
0:00:51.578 260M / 6G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
0:00:52.136 260M / 6G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 2 gaps after checking 2000 candidates
0:00:52.176 260M / 6G INFO StageManager (stage.cpp : 126) STAGE == Simplification
0:00:52.177 156M / 6G INFO General (simplification.cpp : 387) Graph simplification started
0:00:52.177 156M / 6G INFO General (simplification.cpp : 77) PROCEDURE == InitialCleaning
0:00:52.177 156M / 6G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled
0:00:52.177 156M / 6G INFO General (simplification.cpp : 356) Running Self conjugate edge remover
0:00:52.213 156M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:52.213 156M / 6G INFO General (simplification.cpp : 356) Running Initial isolated edge remover
0:00:52.275 156M / 6G INFO General (simplification.cpp : 358) Triggered 6874 times
0:00:52.275 156M / 6G INFO General (simplification.cpp : 356) Running Initial tip clipper
0:00:53.171 160M / 6G INFO General (simplification.cpp : 358) Triggered 92518 times
0:00:53.171 160M / 6G INFO General (simplification.cpp : 356) Running Initial ec remover
0:00:53.192 160M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:53.203 160M / 6G INFO General (graph_simplification.hpp : 617) Creating parallel br instance
0:00:53.203 160M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 1
0:00:53.203 160M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:53.233 160M / 6G INFO General (simplification.cpp : 358) Triggered 1305 times
0:00:53.233 160M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:54.055 164M / 6G INFO General (simplification.cpp : 358) Triggered 885 times
0:00:54.055 164M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:54.115 164M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:54.115 164M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 2
0:00:54.115 164M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:54.121 164M / 6G INFO General (simplification.cpp : 358) Triggered 20 times
0:00:54.121 164M / 6G INFO General (simplification.cpp : 356) Running Bulge remover
0:00:54.122 164M / 6G INFO General (simplification.cpp : 358) Triggered 0 times
0:00:54.122 164M / 6G INFO General (simplification.cpp : 356) Running Low coverage edge remover
0:00:55.260 164M / 6G INFO General (simplification.cpp : 358) Triggered 45583 times
0:00:55.260 164M / 6G INFO General (simplification.cpp : 410) PROCEDURE == Simplification cycle, iteration 3
0:00:55.260 164M / 6G INFO General (simplification.cpp : 356) Running Tip clipper
0:00:55.306 164M / 6G INFO General (simplification.cpp : 358) Triggered 2407 times