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pfaucon/gist:67bab93ce44b754348ea

Created November 4, 2014 16:52
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Gist from the latest run - SRR950078 only
Raw
gistfile1.txt
vagrant@vagrant-ubuntu-trusty-64:/vagrant_data/seqc-test/seqc/work$ bcbio_nextgen.py ../config/seqc.yaml -n 8
[2014-10-30 16:28] Using input YAML configuration: /vagrant_data/seqc-test/seqc/config/seqc.yaml
[2014-10-30 16:28] Checking sample YAML configuration: /vagrant_data/seqc-test/seqc/config/seqc.yaml
[2014-10-30 16:28] Testing minimum versions of installed programs
[2014-10-30 16:28] Resource requests: AlienTrimmer, picard; memory: 2.0, 3.5; cores: 1, 1
[2014-10-30 16:28] Configuring 1 jobs to run, using 1 cores each with 3.8g of memory reserved for each job
[2014-10-30 16:28] Timing: adapter trimming
[2014-10-30 16:28] multiprocessing: prepare_sample
[2014-10-30 16:28] Preparing UHRR_rep1
[2014-10-30 16:28] multiprocessing: trim_sample
[2014-10-30 16:28] Trimming low quality ends and read through adapter sequence from /vagrant_data/seqc-test/input/SRR950078_1.fastq.gz, /vagrant_data/seqc-test/input/SRR950078_2.fastq.gz.
[2014-10-30 16:28] Trimming /vagrant_data/seqc-test/input/SRR950078_1.fastq.gz and /vagrant_data/seqc-test/input/SRR950078_2.fastq.gz in single end mode with cutadapt.
[2014-10-30 17:46] cutadapt version 1.4.2
[2014-10-30 17:46] Command line parameters: --times=2 --quality-base=33 --quality-cutoff=5 --format=fastq --adapter=AAAAAAAAAAAAA --adapter=TTTTTTTTTTTTT --adapter=AGATCGGAAGAG --adapter=CTCTTCCGATCT --minimum-length=25 -o /vagrant_data/seqc-test/seqc/work/trimmed/SRR950078_1.trimmed.tmp.fastq.gz -p /vagrant_data/seqc-test/seqc/work/trimmed/SRR950078_2.trimmed.tmp.fastq.gz /vagrant_data/seqc-test/input/SRR950078_1.fastq.gz /vagrant_data/seqc-test/input/SRR950078_2.fastq.gz
[2014-10-30 17:46] Maximum error rate: 10.00%
[2014-10-30 17:46] No. of adapters: 4
[2014-10-30 17:46] Processed reads: 100387010
[2014-10-30 17:46] Processed bases: 10139088010 bp (10139.1 Mbp)
[2014-10-30 17:46] Trimmed reads: 15097779 (15.0%)
[2014-10-30 17:46] Quality-trimmed: 1043832387 bp (1043.8 Mbp) (10.30% of total)
[2014-10-30 17:46] Trimmed bases: 325205040 bp (325.2 Mbp) (3.21% of total)
[2014-10-30 17:46] Too short reads: 7261219 (7.2% of processed reads)
[2014-10-30 17:46] Too long reads: 0 (0.0% of processed reads)
[2014-10-30 17:46] Total time: 4699.45 s
[2014-10-30 17:46] Time per read: 0.047 ms
[2014-10-30 17:46]
[2014-10-30 17:46] === Adapter 1 ===
[2014-10-30 17:46]
[2014-10-30 17:46] Adapter 'AAAAAAAAAAAAA', length 13, was trimmed 7293918 times.
[2014-10-30 17:46]
[2014-10-30 17:46] No. of allowed errors:
[2014-10-30 17:46] 0-9 bp: 0; 10-13 bp: 1
[2014-10-30 17:46]
[2014-10-30 17:46] Overview of removed sequences
[2014-10-30 17:46] length count expect max.err error counts
[2014-10-30 17:46] 3 3652124 1568547.0 0 3652124
[2014-10-30 17:46] 4 1330623 392136.8 0 1330623
[2014-10-30 17:46] 5 532644 98034.2 0 532644
[2014-10-30 17:46] 6 176442 24508.5 0 176442
[2014-10-30 17:46] 7 89141 6127.1 0 89141
[2014-10-30 17:46] 8 46602 1531.8 0 46602
[2014-10-30 17:46] 9 37804 382.9 0 37804
[2014-10-30 17:46] 10 99861 95.7 1 33623 66238
[2014-10-30 17:46] 11 72947 23.9 1 29952 42995
[2014-10-30 17:46] 12 66057 6.0 1 38531 27526
[2014-10-30 17:46] 13 56535 1.5 1 38396 18139
[2014-10-30 17:46] 14 55223 1.5 1 40793 14430
[2014-10-30 17:46] 15 52036 1.5 1 39419 12617
[2014-10-30 17:46] 16 46786 1.5 1 35302 11484
[2014-10-30 17:46] 17 42488 1.5 1 31782 10706
[2014-10-30 17:46] 18 37020 1.5 1 27284 9736
[2014-10-30 17:46] 19 32956 1.5 1 24633 8323
[2014-10-30 17:46] 20 30267 1.5 1 21813 8454
[2014-10-30 17:46] 21 28422 1.5 1 19839 8583
[2014-10-30 17:46] 22 26721 1.5 1 17965 8756
[2014-10-30 17:46] 23 24484 1.5 1 16291 8193
[2014-10-30 17:46] 24 23437 1.5 1 15140 8297
[2014-10-30 17:46] 25 21215 1.5 1 13277 7938
[2014-10-30 17:46] 26 19811 1.5 1 11805 8006
[2014-10-30 17:46] 27 18401 1.5 1 10677 7724
[2014-10-30 17:46] 28 16769 1.5 1 9295 7474
[2014-10-30 17:46] 29 16178 1.5 1 8497 7681
[2014-10-30 17:46] 30 16313 1.5 1 8110 8203
[2014-10-30 17:46] 31 14896 1.5 1 7341 7555
[2014-10-30 17:46] 32 13845 1.5 1 6665 7180
[2014-10-30 17:46] 33 14310 1.5 1 6776 7534
[2014-10-30 17:46] 34 13316 1.5 1 6455 6861
[2014-10-30 17:46] 35 12797 1.5 1 6129 6668
[2014-10-30 17:46] 36 12426 1.5 1 5555 6871
[2014-10-30 17:46] 37 12173 1.5 1 5113 7060
[2014-10-30 17:46] 38 11677 1.5 1 4755 6922
[2014-10-30 17:46] 39 11398 1.5 1 4627 6771
[2014-10-30 17:46] 40 11779 1.5 1 5288 6491
[2014-10-30 17:46] 41 11377 1.5 1 4793 6584
[2014-10-30 17:46] 42 11194 1.5 1 4709 6485
[2014-10-30 17:46] 43 11676 1.5 1 5134 6542
[2014-10-30 17:46] 44 11954 1.5 1 5041 6913
[2014-10-30 17:46] 45 11163 1.5 1 4616 6547
[2014-10-30 17:46] 46 10227 1.5 1 3623 6604
[2014-10-30 17:46] 47 9778 1.5 1 3235 6543
[2014-10-30 17:46] 48 10425 1.5 1 3100 7325
[2014-10-30 17:46] 49 9149 1.5 1 2770 6379
[2014-10-30 17:46] 50 8767 1.5 1 2470 6297
[2014-10-30 17:46] 51 8748 1.5 1 2653 6095
[2014-10-30 17:46] 52 8364 1.5 1 2446 5918
[2014-10-30 17:46] 53 8797 1.5 1 2361 6436
[2014-10-30 17:46] 54 8722 1.5 1 2396 6326
[2014-10-30 17:46] 55 8645 1.5 1 2484 6161
[2014-10-30 17:46] 56 8509 1.5 1 2402 6107
[2014-10-30 17:46] 57 9075 1.5 1 2137 6938
[2014-10-30 17:46] 58 8668 1.5 1 2016 6652
[2014-10-30 17:46] 59 8568 1.5 1 2072 6496
[2014-10-30 17:46] 60 7916 1.5 1 2222 5694
[2014-10-30 17:46] 61 8689 1.5 1 2220 6469
[2014-10-30 17:46] 62 8823 1.5 1 2381 6442
[2014-10-30 17:46] 63 8185 1.5 1 2231 5954
[2014-10-30 17:46] 64 8139 1.5 1 2173 5966
[2014-10-30 17:46] 65 7898 1.5 1 1994 5904
[2014-10-30 17:46] 66 8289 1.5 1 2169 6120
[2014-10-30 17:46] 67 7994 1.5 1 2038 5956
[2014-10-30 17:46] 68 7980 1.5 1 2047 5933
[2014-10-30 17:46] 69 8281 1.5 1 1872 6409
[2014-10-30 17:46] 70 7761 1.5 1 1761 6000
[2014-10-30 17:46] 71 7748 1.5 1 1765 5983
[2014-10-30 17:46] 72 8146 1.5 1 1822 6324
[2014-10-30 17:46] 73 7881 1.5 1 1708 6173
[2014-10-30 17:46] 74 8104 1.5 1 1746 6358
[2014-10-30 17:46] 75 7480 1.5 1 1681 5799
[2014-10-30 17:46] 76 7997 1.5 1 1733 6264
[2014-10-30 17:46] 77 7481 1.5 1 1447 6034
[2014-10-30 17:46] 78 7553 1.5 1 1613 5940
[2014-10-30 17:46] 79 7679 1.5 1 1602 6077
[2014-10-30 17:46] 80 7785 1.5 1 1596 6189
[2014-10-30 17:46] 81 7078 1.5 1 1422 5656
[2014-10-30 17:46] 82 7732 1.5 1 1535 6197
[2014-10-30 17:46] 83 7196 1.5 1 1432 5764
[2014-10-30 17:46] 84 7342 1.5 1 1528 5814
[2014-10-30 17:46] 85 6940 1.5 1 1569 5371
[2014-10-30 17:46] 86 7771 1.5 1 1749 6022
[2014-10-30 17:46] 87 7388 1.5 1 1623 5765
[2014-10-30 17:46] 88 6701 1.5 1 1372 5329
[2014-10-30 17:46] 89 6681 1.5 1 1163 5518
[2014-10-30 17:46] 90 5664 1.5 1 1013 4651
[2014-10-30 17:46] 91 4582 1.5 1 951 3631
[2014-10-30 17:46] 92 8310 1.5 1 1409 6901
[2014-10-30 17:46] 93 8571 1.5 1 1368 7203
[2014-10-30 17:46] 94 7988 1.5 1 1147 6841
[2014-10-30 17:46] 95 4305 1.5 1 610 3695
[2014-10-30 17:46] 96 3474 1.5 1 618 2856
[2014-10-30 17:46] 97 4016 1.5 1 555 3461
[2014-10-30 17:46] 98 4752 1.5 1 630 4122
[2014-10-30 17:46] 99 4014 1.5 1 484 3530
[2014-10-30 17:46] 100 8218 1.5 1 798 7420
[2014-10-30 17:46] 101 15656 1.5 1 1550 14106
[2014-10-30 17:46]
[2014-10-30 17:46] === Adapter 2 ===
[2014-10-30 17:46]
[2014-10-30 17:46] Adapter 'TTTTTTTTTTTTT', length 13, was trimmed 7249835 times.
[2014-10-30 17:46]
[2014-10-30 17:46] No. of allowed errors:
[2014-10-30 17:46] 0-9 bp: 0; 10-13 bp: 1
[2014-10-30 17:46]
[2014-10-30 17:46] Overview of removed sequences
[2014-10-30 17:46] length count expect max.err error counts
[2014-10-30 17:46] 3 3598839 1568547.0 0 3598839
[2014-10-30 17:46] 4 1303670 392136.8 0 1303670
[2014-10-30 17:46] 5 497282 98034.2 0 497282
[2014-10-30 17:46] 6 170574 24508.5 0 170574
[2014-10-30 17:46] 7 89960 6127.1 0 89960
[2014-10-30 17:46] 8 38013 1531.8 0 38013
[2014-10-30 17:46] 9 28850 382.9 0 28850
[2014-10-30 17:46] 10 94764 95.7 1 25552 69212
[2014-10-30 17:46] 11 69241 23.9 1 23627 45614
[2014-10-30 17:46] 12 70706 6.0 1 41059 29647
[2014-10-30 17:46] 13 65486 1.5 1 45059 20427
[2014-10-30 17:46] 14 70202 1.5 1 52899 17303
[2014-10-30 17:46] 15 70552 1.5 1 56490 14062
[2014-10-30 17:46] 16 66836 1.5 1 54437 12399
[2014-10-30 17:46] 17 59544 1.5 1 48020 11524
[2014-10-30 17:46] 18 49786 1.5 1 39261 10525
[2014-10-30 17:46] 19 42551 1.5 1 32229 10322
[2014-10-30 17:46] 20 45179 1.5 1 28342 16837
[2014-10-30 17:46] 21 34779 1.5 1 24645 10134
[2014-10-30 17:46] 22 30810 1.5 1 21644 9166
[2014-10-30 17:46] 23 27729 1.5 1 18608 9121
[2014-10-30 17:46] 24 26216 1.5 1 16034 10182
[2014-10-30 17:46] 25 24067 1.5 1 13905 10162
[2014-10-30 17:46] 26 20532 1.5 1 11709 8823
[2014-10-30 17:46] 27 18412 1.5 1 10276 8136
[2014-10-30 17:46] 28 17773 1.5 1 8865 8908
[2014-10-30 17:46] 29 16879 1.5 1 7970 8909
[2014-10-30 17:46] 30 15191 1.5 1 6851 8340
[2014-10-30 17:46] 31 14097 1.5 1 6040 8057
[2014-10-30 17:46] 32 13416 1.5 1 5292 8124
[2014-10-30 17:46] 33 12457 1.5 1 4798 7659
[2014-10-30 17:46] 34 11783 1.5 1 4145 7638
[2014-10-30 17:46] 35 11101 1.5 1 3787 7314
[2014-10-30 17:46] 36 10633 1.5 1 3353 7280
[2014-10-30 17:46] 37 10587 1.5 1 3328 7259
[2014-10-30 17:46] 38 10645 1.5 1 3237 7408
[2014-10-30 17:46] 39 10836 1.5 1 3091 7745
[2014-10-30 17:46] 40 10450 1.5 1 2946 7504
[2014-10-30 17:46] 41 10362 1.5 1 3003 7359
[2014-10-30 17:46] 42 10675 1.5 1 3035 7640
[2014-10-30 17:46] 43 10776 1.5 1 2913 7863
[2014-10-30 17:46] 44 10113 1.5 1 2814 7299
[2014-10-30 17:46] 45 10394 1.5 1 2919 7475
[2014-10-30 17:46] 46 9743 1.5 1 2855 6888
[2014-10-30 17:46] 47 9657 1.5 1 2620 7037
[2014-10-30 17:46] 48 9537 1.5 1 2395 7142
[2014-10-30 17:46] 49 9499 1.5 1 2431 7068
[2014-10-30 17:46] 50 9560 1.5 1 2387 7173
[2014-10-30 17:46] 51 8463 1.5 1 2062 6401
[2014-10-30 17:46] 52 8467 1.5 1 1948 6519
[2014-10-30 17:46] 53 7925 1.5 1 1913 6012
[2014-10-30 17:46] 54 8350 1.5 1 1943 6407
[2014-10-30 17:46] 55 8184 1.5 1 1876 6308
[2014-10-30 17:46] 56 8263 1.5 1 1905 6358
[2014-10-30 17:46] 57 8263 1.5 1 1799 6464
[2014-10-30 17:46] 58 7900 1.5 1 1669 6231
[2014-10-30 17:46] 59 8610 1.5 1 1740 6870
[2014-10-30 17:46] 60 7852 1.5 1 1637 6215
[2014-10-30 17:46] 61 8258 1.5 1 1628 6630
[2014-10-30 17:46] 62 7606 1.5 1 1515 6091
[2014-10-30 17:46] 63 7636 1.5 1 1484 6152
[2014-10-30 17:46] 64 7567 1.5 1 1402 6165
[2014-10-30 17:46] 65 7553 1.5 1 1377 6176
[2014-10-30 17:46] 66 7438 1.5 1 1300 6138
[2014-10-30 17:46] 67 7483 1.5 1 1435 6048
[2014-10-30 17:46] 68 7490 1.5 1 1331 6159
[2014-10-30 17:46] 69 7391 1.5 1 1399 5992
[2014-10-30 17:46] 70 7249 1.5 1 1259 5990
[2014-10-30 17:46] 71 7151 1.5 1 1335 5816
[2014-10-30 17:46] 72 7702 1.5 1 1403 6299
[2014-10-30 17:46] 73 6839 1.5 1 1263 5576
[2014-10-30 17:46] 74 6890 1.5 1 1250 5640
[2014-10-30 17:46] 75 6631 1.5 1 1148 5483
[2014-10-30 17:46] 76 6925 1.5 1 1175 5750
[2014-10-30 17:46] 77 7407 1.5 1 1207 6200
[2014-10-30 17:46] 78 6971 1.5 1 1154 5817
[2014-10-30 17:46] 79 6610 1.5 1 1132 5478
[2014-10-30 17:46] 80 7215 1.5 1 1017 6198
[2014-10-30 17:46] 81 7211 1.5 1 1056 6155
[2014-10-30 17:46] 82 6929 1.5 1 997 5932
[2014-10-30 17:46] 83 6393 1.5 1 1030 5363
[2014-10-30 17:46] 84 6498 1.5 1 969 5529
[2014-10-30 17:46] 85 6349 1.5 1 1020 5329
[2014-10-30 17:46] 86 6485 1.5 1 983 5502
[2014-10-30 17:46] 87 6179 1.5 1 904 5275
[2014-10-30 17:46] 88 6452 1.5 1 919 5533
[2014-10-30 17:46] 89 6266 1.5 1 852 5414
[2014-10-30 17:46] 90 8910 1.5 1 1066 7844
[2014-10-30 17:46] 91 7335 1.5 1 915 6420
[2014-10-30 17:46] 92 7182 1.5 1 833 6349
[2014-10-30 17:46] 93 6335 1.5 1 841 5494
[2014-10-30 17:46] 94 4094 1.5 1 507 3587
[2014-10-30 17:46] 95 5735 1.5 1 735 5000
[2014-10-30 17:46] 96 5246 1.5 1 585 4661
[2014-10-30 17:46] 97 5494 1.5 1 464 5030
[2014-10-30 17:46] 98 3639 1.5 1 386 3253
[2014-10-30 17:46] 99 2776 1.5 1 234 2542
[2014-10-30 17:46] 100 13060 1.5 1 706 12354
[2014-10-30 17:46] 101 12234 1.5 1 966 11268
[2014-10-30 17:46]
[2014-10-30 17:46] === Adapter 3 ===
[2014-10-30 17:46]
[2014-10-30 17:46] Adapter 'AGATCGGAAGAG', length 12, was trimmed 10436624 times.
[2014-10-30 17:46]
[2014-10-30 17:46] No. of allowed errors:
[2014-10-30 17:46] 0-9 bp: 0; 10-12 bp: 1
[2014-10-30 17:46]
[2014-10-30 17:46] Overview of removed sequences
[2014-10-30 17:46] length count expect max.err error counts
[2014-10-30 17:46] 3 4215345 1568547.0 0 4215345
[2014-10-30 17:46] 4 1186170 392136.8 0 1186170
[2014-10-30 17:46] 5 489229 98034.2 0 489229
[2014-10-30 17:46] 6 441172 24508.5 0 441172
[2014-10-30 17:46] 7 294260 6127.1 0 294260
[2014-10-30 17:46] 8 349988 1531.8 0 349988
[2014-10-30 17:46] 9 280334 382.9 0 276073 4261
[2014-10-30 17:46] 10 224435 95.7 1 216422 8013
[2014-10-30 17:46] 11 181733 23.9 1 175398 6335
[2014-10-30 17:46] 12 168633 6.0 1 164634 3999
[2014-10-30 17:46] 13 121398 6.0 1 118692 2706
[2014-10-30 17:46] 14 114248 6.0 1 111608 2640
[2014-10-30 17:46] 15 105839 6.0 1 103016 2823
[2014-10-30 17:46] 16 95216 6.0 1 92542 2674
[2014-10-30 17:46] 17 95434 6.0 1 92613 2821
[2014-10-30 17:46] 18 89028 6.0 1 86601 2427
[2014-10-30 17:46] 19 58340 6.0 1 56691 1649
[2014-10-30 17:46] 20 57697 6.0 1 55744 1953
[2014-10-30 17:46] 21 46534 6.0 1 44682 1852
[2014-10-30 17:46] 22 37276 6.0 1 34630 2646
[2014-10-30 17:46] 23 39100 6.0 1 37092 2008
[2014-10-30 17:46] 24 28681 6.0 1 27145 1536
[2014-10-30 17:46] 25 29675 6.0 1 28175 1500
[2014-10-30 17:46] 26 23014 6.0 1 21444 1570
[2014-10-30 17:46] 27 28712 6.0 1 25461 3251
[2014-10-30 17:46] 28 21881 6.0 1 19952 1929
[2014-10-30 17:46] 29 22949 6.0 1 20666 2283
[2014-10-30 17:46] 30 23866 6.0 1 21958 1908
[2014-10-30 17:46] 31 13938 6.0 1 12620 1318
[2014-10-30 17:46] 32 10427 6.0 1 6564 3863
[2014-10-30 17:46] 33 12671 6.0 1 10412 2259
[2014-10-30 17:46] 34 13363 6.0 1 9475 3888
[2014-10-30 17:46] 35 14979 6.0 1 11854 3125
[2014-10-30 17:46] 36 11451 6.0 1 8644 2807
[2014-10-30 17:46] 37 11856 6.0 1 8449 3407
[2014-10-30 17:46] 38 14950 6.0 1 8222 6728
[2014-10-30 17:46] 39 18691 6.0 1 12277 6414
[2014-10-30 17:46] 40 16084 6.0 1 10539 5545
[2014-10-30 17:46] 41 15195 6.0 1 12160 3035
[2014-10-30 17:46] 42 7846 6.0 1 6131 1715
[2014-10-30 17:46] 43 5130 6.0 1 3612 1518
[2014-10-30 17:46] 44 5448 6.0 1 2701 2747
[2014-10-30 17:46] 45 6669 6.0 1 3854 2815
[2014-10-30 17:46] 46 6520 6.0 1 4525 1995
[2014-10-30 17:46] 47 5451 6.0 1 3223 2228
[2014-10-30 17:46] 48 5793 6.0 1 3612 2181
[2014-10-30 17:46] 49 5472 6.0 1 3887 1585
[2014-10-30 17:46] 50 5133 6.0 1 2748 2385
[2014-10-30 17:46] 51 7479 6.0 1 4101 3378
[2014-10-30 17:46] 52 8757 6.0 1 4827 3930
[2014-10-30 17:46] 53 6685 6.0 1 4772 1913
[2014-10-30 17:46] 54 3757 6.0 1 2003 1754
[2014-10-30 17:46] 55 4877 6.0 1 2333 2544
[2014-10-30 17:46] 56 6643 6.0 1 3525 3118
[2014-10-30 17:46] 57 7328 6.0 1 3423 3905
[2014-10-30 17:46] 58 8395 6.0 1 3941 4454
[2014-10-30 17:46] 59 8475 6.0 1 4792 3683
[2014-10-30 17:46] 60 8381 6.0 1 3435 4946
[2014-10-30 17:46] 61 11460 6.0 1 4411 7049
[2014-10-30 17:46] 62 22689 6.0 1 7050 15639
[2014-10-30 17:46] 63 35852 6.0 1 11535 24317
[2014-10-30 17:46] 64 28653 6.0 1 17433 11220
[2014-10-30 17:46] 65 21539 6.0 1 8425 13114
[2014-10-30 17:46] 66 32045 6.0 1 10207 21838
[2014-10-30 17:46] 67 53796 6.0 1 15712 38084
[2014-10-30 17:46] 68 102738 6.0 1 28241 74497
[2014-10-30 17:46] 69 181441 6.0 1 49929 131512
[2014-10-30 17:46] 70 203896 6.0 1 89599 114297
[2014-10-30 17:46] 71 202441 6.0 1 69312 133129
[2014-10-30 17:46] 72 197918 6.0 1 78686 119232
[2014-10-30 17:46] 73 122283 6.0 1 68005 54278
[2014-10-30 17:46] 74 31334 6.0 1 28863 2471
[2014-10-30 17:46] 75 3397 6.0 1 2614 783
[2014-10-30 17:46] 76 1185 6.0 1 521 664
[2014-10-30 17:46] 77 1221 6.0 1 183 1038
[2014-10-30 17:46] 78 975 6.0 1 151 824
[2014-10-30 17:46] 79 826 6.0 1 151 675
[2014-10-30 17:46] 80 862 6.0 1 165 697
[2014-10-30 17:46] 81 1016 6.0 1 156 860
[2014-10-30 17:46] 82 1069 6.0 1 175 894
[2014-10-30 17:46] 83 1022 6.0 1 154 868
[2014-10-30 17:46] 84 1004 6.0 1 186 818
[2014-10-30 17:46] 85 1012 6.0 1 198 814
[2014-10-30 17:46] 86 964 6.0 1 187 777
[2014-10-30 17:46] 87 1115 6.0 1 243 872
[2014-10-30 17:46] 88 1095 6.0 1 217 878
[2014-10-30 17:46] 89 1051 6.0 1 232 819
[2014-10-30 17:46] 90 1185 6.0 1 274 911
[2014-10-30 17:46] 91 1319 6.0 1 246 1073
[2014-10-30 17:46] 92 1564 6.0 1 254 1310
[2014-10-30 17:46] 93 1325 6.0 1 314 1011
[2014-10-30 17:46] 94 1242 6.0 1 354 888
[2014-10-30 17:46] 95 1225 6.0 1 328 897
[2014-10-30 17:46] 96 1450 6.0 1 340 1110
[2014-10-30 17:46] 97 1152 6.0 1 304 848
[2014-10-30 17:46] 98 2140 6.0 1 406 1734
[2014-10-30 17:46] 99 1064 6.0 1 296 768
[2014-10-30 17:46] 100 772 6.0 1 196 576
[2014-10-30 17:46] 101 8256 6.0 1 3140 5116
[2014-10-30 17:46]
[2014-10-30 17:46] === Adapter 4 ===
[2014-10-30 17:46]
[2014-10-30 17:46] Adapter 'CTCTTCCGATCT', length 12, was trimmed 5215181 times.
[2014-10-30 17:46]
[2014-10-30 17:46] No. of allowed errors:
[2014-10-30 17:46] 0-9 bp: 0; 10-12 bp: 1
[2014-10-30 17:46]
[2014-10-30 17:46] Overview of removed sequences
[2014-10-30 17:46] length count expect max.err error counts
[2014-10-30 17:46] 3 3751914 1568547.0 0 3751914
[2014-10-30 17:46] 4 948036 392136.8 0 948036
[2014-10-30 17:46] 5 298653 98034.2 0 298653
[2014-10-30 17:46] 6 104665 24508.5 0 104665
[2014-10-30 17:46] 7 36236 6127.1 0 36236
[2014-10-30 17:46] 8 1635 1531.8 0 1635
[2014-10-30 17:46] 9 3376 382.9 0 282 3094
[2014-10-30 17:46] 10 10834 95.7 1 57 10777
[2014-10-30 17:46] 11 2406 23.9 1 60 2346
[2014-10-30 17:46] 12 796 6.0 1 82 714
[2014-10-30 17:46] 13 525 6.0 1 6 519
[2014-10-30 17:46] 14 590 6.0 1 15 575
[2014-10-30 17:46] 15 520 6.0 1 4 516
[2014-10-30 17:46] 16 507 6.0 1 11 496
[2014-10-30 17:46] 17 587 6.0 1 11 576
[2014-10-30 17:46] 18 521 6.0 1 9 512
[2014-10-30 17:46] 19 529 6.0 1 10 519
[2014-10-30 17:46] 20 522 6.0 1 10 512
[2014-10-30 17:46] 21 543 6.0 1 9 534
[2014-10-30 17:46] 22 773 6.0 1 15 758
[2014-10-30 17:46] 23 675 6.0 1 15 660
[2014-10-30 17:46] 24 661 6.0 1 1 660
[2014-10-30 17:46] 25 741 6.0 1 8 733
[2014-10-30 17:46] 26 531 6.0 1 8 523
[2014-10-30 17:46] 27 563 6.0 1 10 553
[2014-10-30 17:46] 28 633 6.0 1 9 624
[2014-10-30 17:46] 29 658 6.0 1 19 639
[2014-10-30 17:46] 30 825 6.0 1 12 813
[2014-10-30 17:46] 31 700 6.0 1 11 689
[2014-10-30 17:46] 32 857 6.0 1 6 851
[2014-10-30 17:46] 33 739 6.0 1 9 730
[2014-10-30 17:46] 34 813 6.0 1 10 803
[2014-10-30 17:46] 35 709 6.0 1 17 692
[2014-10-30 17:46] 36 574 6.0 1 16 558
[2014-10-30 17:46] 37 883 6.0 1 16 867
[2014-10-30 17:46] 38 683 6.0 1 46 637
[2014-10-30 17:46] 39 542 6.0 1 13 529
[2014-10-30 17:46] 40 503 6.0 1 14 489
[2014-10-30 17:46] 41 437 6.0 1 16 421
[2014-10-30 17:46] 42 542 6.0 1 13 529
[2014-10-30 17:46] 43 551 6.0 1 6 545
[2014-10-30 17:46] 44 589 6.0 1 10 579
[2014-10-30 17:46] 45 526 6.0 1 4 522
[2014-10-30 17:46] 46 537 6.0 1 11 526
[2014-10-30 17:46] 47 770 6.0 1 16 754
[2014-10-30 17:46] 48 538 6.0 1 14 524
[2014-10-30 17:46] 49 555 6.0 1 9 546
[2014-10-30 17:46] 50 550 6.0 1 14 536
[2014-10-30 17:46] 51 552 6.0 1 24 528
[2014-10-30 17:46] 52 652 6.0 1 20 632
[2014-10-30 17:46] 53 664 6.0 1 18 646
[2014-10-30 17:46] 54 560 6.0 1 5 555
[2014-10-30 17:46] 55 572 6.0 1 14 558
[2014-10-30 17:46] 56 528 6.0 1 21 507
[2014-10-30 17:46] 57 544 6.0 1 14 530
[2014-10-30 17:46] 58 621 6.0 1 12 609
[2014-10-30 17:46] 59 526 6.0 1 12 514
[2014-10-30 17:46] 60 483 6.0 1 20 463
[2014-10-30 17:46] 61 561 6.0 1 14 547
[2014-10-30 17:46] 62 568 6.0 1 9 559
[2014-10-30 17:46] 63 472 6.0 1 16 456
[2014-10-30 17:46] 64 565 6.0 1 17 548
[2014-10-30 17:46] 65 490 6.0 1 16 474
[2014-10-30 17:46] 66 456 6.0 1 18 438
[2014-10-30 17:46] 67 537 6.0 1 10 527
[2014-10-30 17:46] 68 631 6.0 1 10 621
[2014-10-30 17:46] 69 565 6.0 1 13 552
[2014-10-30 17:46] 70 515 6.0 1 6 509
[2014-10-30 17:46] 71 501 6.0 1 8 493
[2014-10-30 17:46] 72 446 6.0 1 24 422
[2014-10-30 17:46] 73 544 6.0 1 11 533
[2014-10-30 17:46] 74 567 6.0 1 6 561
[2014-10-30 17:46] 75 685 6.0 1 14 671
[2014-10-30 17:46] 76 590 6.0 1 20 570
[2014-10-30 17:46] 77 549 6.0 1 18 531
[2014-10-30 17:46] 78 451 6.0 1 22 429
[2014-10-30 17:46] 79 665 6.0 1 18 647
[2014-10-30 17:46] 80 490 6.0 1 26 464
[2014-10-30 17:46] 81 570 6.0 1 40 530
[2014-10-30 17:46] 82 559 6.0 1 36 523
[2014-10-30 17:46] 83 828 6.0 1 44 784
[2014-10-30 17:46] 84 588 6.0 1 36 552
[2014-10-30 17:46] 85 649 6.0 1 35 614
[2014-10-30 17:46] 86 486 6.0 1 42 444
[2014-10-30 17:46] 87 639 6.0 1 36 603
[2014-10-30 17:46] 88 556 6.0 1 62 494
[2014-10-30 17:46] 89 628 6.0 1 40 588
[2014-10-30 17:46] 90 721 6.0 1 54 667
[2014-10-30 17:46] 91 645 6.0 1 84 561
[2014-10-30 17:46] 92 707 6.0 1 80 627
[2014-10-30 17:46] 93 766 6.0 1 174 592
[2014-10-30 17:46] 94 1288 6.0 1 450 838
[2014-10-30 17:46] 95 659 6.0 1 144 515
[2014-10-30 17:46] 96 1513 6.0 1 402 1111
[2014-10-30 17:46] 97 558 6.0 1 124 434
[2014-10-30 17:46] 98 2236 6.0 1 1592 644
[2014-10-30 17:46] 99 1016 6.0 1 218 798
[2014-10-30 17:46] 100 452 6.0 1 216 236
[2014-10-30 17:46] 101 514 6.0 1 128 386
[2014-10-30 17:46]
[2014-10-30 18:54] cutadapt version 1.4.2
[2014-10-30 18:54] Command line parameters: --times=2 --quality-base=33 --quality-cutoff=5 --format=fastq --adapter=AAAAAAAAAAAAA --adapter=TTTTTTTTTTTTT --adapter=AGATCGGAAGAG --adapter=CTCTTCCGATCT --minimum-length=25 -o /vagrant_data/seqc-test/seqc/work/trimmed/SRR950078_2.trimmed.fastq.gz -p /vagrant_data/seqc-test/seqc/work/trimmed/SRR950078_1.trimmed.fastq.gz /vagrant_data/seqc-test/seqc/work/trimmed/SRR950078_2.trimmed.tmp.fastq.gz /vagrant_data/seqc-test/seqc/work/trimmed/SRR950078_1.trimmed.tmp.fastq.gz
[2014-10-30 18:54] Maximum error rate: 10.00%
[2014-10-30 18:54] No. of adapters: 4
[2014-10-30 18:54] Processed reads: 93125791
[2014-10-30 18:54] Processed bases: 9405704891 bp (9405.7 Mbp)
[2014-10-30 18:54] Trimmed reads: 13396473 (14.4%)
[2014-10-30 18:54] Quality-trimmed: 284365128 bp (284.4 Mbp) (3.02% of total)
[2014-10-30 18:54] Trimmed bases: 231972386 bp (232.0 Mbp) (2.47% of total)
[2014-10-30 18:54] Too short reads: 1255183 (1.3% of processed reads)
[2014-10-30 18:54] Too long reads: 0 (0.0% of processed reads)
[2014-10-30 18:54] Total time: 4063.67 s
[2014-10-30 18:54] Time per read: 0.044 ms
[2014-10-30 18:54]
[2014-10-30 18:54] === Adapter 1 ===
[2014-10-30 18:54]
[2014-10-30 18:54] Adapter 'AAAAAAAAAAAAA', length 13, was trimmed 6137496 times.
[2014-10-30 18:54]
[2014-10-30 18:54] No. of allowed errors:
[2014-10-30 18:54] 0-9 bp: 0; 10-13 bp: 1
[2014-10-30 18:54]
[2014-10-30 18:54] Overview of removed sequences
[2014-10-30 18:54] length count expect max.err error counts
[2014-10-30 18:54] 3 3122602 1455090.5 0 3122602
[2014-10-30 18:54] 4 1081092 363772.6 0 1081092
[2014-10-30 18:54] 5 401607 90943.2 0 401607
[2014-10-30 18:54] 6 117951 22735.8 0 117951
[2014-10-30 18:54] 7 55546 5683.9 0 55546
[2014-10-30 18:54] 8 26585 1421.0 0 26585
[2014-10-30 18:54] 9 21613 355.2 0 21613
[2014-10-30 18:54] 10 68637 88.8 1 19429 49208
[2014-10-30 18:54] 11 48976 22.2 1 18779 30197
[2014-10-30 18:54] 12 45261 5.6 1 27157 18104
[2014-10-30 18:54] 13 39433 1.4 1 28784 10649
[2014-10-30 18:54] 14 41943 1.4 1 32758 9185
[2014-10-30 18:54] 15 41832 1.4 1 33224 8608
[2014-10-30 18:54] 16 39237 1.4 1 31446 7791
[2014-10-30 18:54] 17 36012 1.4 1 28071 7941
[2014-10-30 18:54] 18 31448 1.4 1 24294 7154
[2014-10-30 18:54] 19 29254 1.4 1 22963 6291
[2014-10-30 18:54] 20 27144 1.4 1 20775 6369
[2014-10-30 18:54] 21 25437 1.4 1 18812 6625
[2014-10-30 18:54] 22 23350 1.4 1 16758 6592
[2014-10-30 18:54] 23 21326 1.4 1 14899 6427
[2014-10-30 18:54] 24 20800 1.4 1 14108 6692
[2014-10-30 18:54] 25 18929 1.4 1 12556 6373
[2014-10-30 18:54] 26 17886 1.4 1 11260 6626
[2014-10-30 18:54] 27 16445 1.4 1 9783 6662
[2014-10-30 18:54] 28 15194 1.4 1 8541 6653
[2014-10-30 18:54] 29 14481 1.4 1 7958 6523
[2014-10-30 18:54] 30 14350 1.4 1 7231 7119
[2014-10-30 18:54] 31 13171 1.4 1 6682 6489
[2014-10-30 18:54] 32 12651 1.4 1 6243 6408
[2014-10-30 18:54] 33 12852 1.4 1 6111 6741
[2014-10-30 18:54] 34 12421 1.4 1 6177 6244
[2014-10-30 18:54] 35 12607 1.4 1 6300 6307
[2014-10-30 18:54] 36 12467 1.4 1 5845 6622
[2014-10-30 18:54] 37 11749 1.4 1 5268 6481
[2014-10-30 18:54] 38 10955 1.4 1 4809 6146
[2014-10-30 18:54] 39 11292 1.4 1 4750 6542
[2014-10-30 18:54] 40 11567 1.4 1 5264 6303
[2014-10-30 18:54] 41 10716 1.4 1 4544 6172
[2014-10-30 18:54] 42 10555 1.4 1 4386 6169
[2014-10-30 18:54] 43 11345 1.4 1 4925 6420
[2014-10-30 18:54] 44 12202 1.4 1 4890 7312
[2014-10-30 18:54] 45 10789 1.4 1 4425 6364
[2014-10-30 18:54] 46 10301 1.4 1 3555 6746
[2014-10-30 18:54] 47 10162 1.4 1 3436 6726
[2014-10-30 18:54] 48 11028 1.4 1 3403 7625
[2014-10-30 18:54] 49 9577 1.4 1 2940 6637
[2014-10-30 18:54] 50 9377 1.4 1 2893 6484
[2014-10-30 18:54] 51 8344 1.4 1 2470 5874
[2014-10-30 18:54] 52 8962 1.4 1 2845 6117
[2014-10-30 18:54] 53 9061 1.4 1 2700 6361
[2014-10-30 18:54] 54 9379 1.4 1 2774 6605
[2014-10-30 18:54] 55 9688 1.4 1 2948 6740
[2014-10-30 18:54] 56 9385 1.4 1 2782 6603
[2014-10-30 18:54] 57 9624 1.4 1 2500 7124
[2014-10-30 18:54] 58 9185 1.4 1 2339 6846
[2014-10-30 18:54] 59 9206 1.4 1 2403 6803
[2014-10-30 18:54] 60 8773 1.4 1 2332 6441
[2014-10-30 18:54] 61 9729 1.4 1 2624 7105
[2014-10-30 18:54] 62 9461 1.4 1 2623 6838
[2014-10-30 18:54] 63 8824 1.4 1 2547 6277
[2014-10-30 18:54] 64 8788 1.4 1 2478 6310
[2014-10-30 18:54] 65 8670 1.4 1 2354 6316
[2014-10-30 18:54] 66 8870 1.4 1 2381 6489
[2014-10-30 18:54] 67 8819 1.4 1 2380 6439
[2014-10-30 18:54] 68 8766 1.4 1 2493 6273
[2014-10-30 18:54] 69 9276 1.4 1 2317 6959
[2014-10-30 18:54] 70 8276 1.4 1 1991 6285
[2014-10-30 18:54] 71 8634 1.4 1 2098 6536
[2014-10-30 18:54] 72 8889 1.4 1 2153 6736
[2014-10-30 18:54] 73 8967 1.4 1 2094 6873
[2014-10-30 18:54] 74 9305 1.4 1 2237 7068
[2014-10-30 18:54] 75 8628 1.4 1 2113 6515
[2014-10-30 18:54] 76 9490 1.4 1 2279 7211
[2014-10-30 18:54] 77 8664 1.4 1 1972 6692
[2014-10-30 18:54] 78 8512 1.4 1 2111 6401
[2014-10-30 18:54] 79 9178 1.4 1 2210 6968
[2014-10-30 18:54] 80 9468 1.4 1 2160 7308
[2014-10-30 18:54] 81 8289 1.4 1 2003 6286
[2014-10-30 18:54] 82 9044 1.4 1 1950 7094
[2014-10-30 18:54] 83 8294 1.4 1 1970 6324
[2014-10-30 18:54] 84 8428 1.4 1 2079 6349
[2014-10-30 18:54] 85 8501 1.4 1 2213 6288
[2014-10-30 18:54] 86 8828 1.4 1 2202 6626
[2014-10-30 18:54] 87 8809 1.4 1 2002 6807
[2014-10-30 18:54] 88 8005 1.4 1 1762 6243
[2014-10-30 18:54] 89 7857 1.4 1 1631 6226
[2014-10-30 18:54] 90 6566 1.4 1 1342 5224
[2014-10-30 18:54] 91 5646 1.4 1 1474 4172
[2014-10-30 18:54] 92 10523 1.4 1 2136 8387
[2014-10-30 18:54] 93 11025 1.4 1 1996 9029
[2014-10-30 18:54] 94 9860 1.4 1 1769 8091
[2014-10-30 18:54] 95 4876 1.4 1 890 3986
[2014-10-30 18:54] 96 3953 1.4 1 896 3057
[2014-10-30 18:54] 97 4714 1.4 1 1011 3703
[2014-10-30 18:54] 98 5202 1.4 1 991 4211
[2014-10-30 18:54] 99 5014 1.4 1 948 4066
[2014-10-30 18:54] 100 11166 1.4 1 1446 9720
[2014-10-30 18:54] 101 19920 1.4 1 2352 17568
[2014-10-30 18:54]
[2014-10-30 18:54] === Adapter 2 ===
[2014-10-30 18:54]
[2014-10-30 18:54] Adapter 'TTTTTTTTTTTTT', length 13, was trimmed 6276294 times.
[2014-10-30 18:54]
[2014-10-30 18:54] No. of allowed errors:
[2014-10-30 18:54] 0-9 bp: 0; 10-13 bp: 1
[2014-10-30 18:54]
[2014-10-30 18:54] Overview of removed sequences
[2014-10-30 18:54] length count expect max.err error counts
[2014-10-30 18:54] 3 3145675 1455090.5 0 3145675
[2014-10-30 18:54] 4 1107872 363772.6 0 1107872
[2014-10-30 18:54] 5 392764 90943.2 0 392764
[2014-10-30 18:54] 6 126354 22735.8 0 126354
[2014-10-30 18:54] 7 61832 5683.9 0 61832
[2014-10-30 18:54] 8 24550 1421.0 0 24550
[2014-10-30 18:54] 9 20749 355.2 0 20749
[2014-10-30 18:54] 10 72361 88.8 1 19028 53333
[2014-10-30 18:54] 11 52775 22.2 1 18026 34749
[2014-10-30 18:54] 12 53113 5.6 1 31945 21168
[2014-10-30 18:54] 13 50177 1.4 1 36706 13471
[2014-10-30 18:54] 14 56566 1.4 1 44920 11646
[2014-10-30 18:54] 15 60110 1.4 1 49866 10244
[2014-10-30 18:54] 16 58387 1.4 1 49114 9273
[2014-10-30 18:54] 17 50848 1.4 1 42363 8485
[2014-10-30 18:54] 18 44032 1.4 1 35804 8228
[2014-10-30 18:54] 19 38672 1.4 1 30569 8103
[2014-10-30 18:54] 20 40882 1.4 1 26423 14459
[2014-10-30 18:54] 21 31015 1.4 1 23080 7935
[2014-10-30 18:54] 22 27046 1.4 1 19819 7227
[2014-10-30 18:54] 23 24441 1.4 1 16805 7636
[2014-10-30 18:54] 24 22841 1.4 1 14328 8513
[2014-10-30 18:54] 25 20518 1.4 1 11807 8711
[2014-10-30 18:54] 26 17790 1.4 1 10511 7279
[2014-10-30 18:54] 27 16026 1.4 1 9268 6758
[2014-10-30 18:54] 28 15744 1.4 1 8240 7504
[2014-10-30 18:54] 29 15054 1.4 1 7101 7953
[2014-10-30 18:54] 30 13722 1.4 1 6558 7164
[2014-10-30 18:54] 31 12577 1.4 1 5676 6901
[2014-10-30 18:54] 32 12297 1.4 1 4984 7313
[2014-10-30 18:54] 33 11791 1.4 1 4544 7247
[2014-10-30 18:54] 34 11034 1.4 1 3855 7179
[2014-10-30 18:54] 35 10669 1.4 1 3621 7048
[2014-10-30 18:54] 36 10435 1.4 1 3256 7179
[2014-10-30 18:54] 37 10150 1.4 1 3244 6906
[2014-10-30 18:54] 38 10033 1.4 1 3162 6871
[2014-10-30 18:54] 39 10299 1.4 1 2976 7323
[2014-10-30 18:54] 40 10174 1.4 1 2934 7240
[2014-10-30 18:54] 41 9975 1.4 1 2890 7085
[2014-10-30 18:54] 42 10325 1.4 1 2956 7369
[2014-10-30 18:54] 43 10429 1.4 1 2822 7607
[2014-10-30 18:54] 44 9629 1.4 1 2831 6798
[2014-10-30 18:54] 45 10192 1.4 1 2920 7272
[2014-10-30 18:54] 46 9716 1.4 1 2858 6858
[2014-10-30 18:54] 47 9914 1.4 1 2870 7044
[2014-10-30 18:54] 48 9731 1.4 1 2577 7154
[2014-10-30 18:54] 49 9542 1.4 1 2286 7256
[2014-10-30 18:54] 50 9894 1.4 1 2448 7446
[2014-10-30 18:54] 51 8683 1.4 1 2141 6542
[2014-10-30 18:54] 52 8547 1.4 1 1975 6572
[2014-10-30 18:54] 53 7946 1.4 1 1923 6023
[2014-10-30 18:54] 54 8528 1.4 1 1875 6653
[2014-10-30 18:54] 55 8466 1.4 1 2135 6331
[2014-10-30 18:54] 56 8641 1.4 1 2083 6558
[2014-10-30 18:54] 57 8322 1.4 1 1893 6429
[2014-10-30 18:54] 58 8125 1.4 1 1840 6285
[2014-10-30 18:54] 59 9136 1.4 1 1824 7312
[2014-10-30 18:54] 60 8312 1.4 1 1669 6643
[2014-10-30 18:54] 61 8635 1.4 1 1746 6889
[2014-10-30 18:54] 62 8043 1.4 1 1636 6407
[2014-10-30 18:54] 63 8231 1.4 1 1719 6512
[2014-10-30 18:54] 64 8272 1.4 1 1654 6618
[2014-10-30 18:54] 65 8127 1.4 1 1633 6494
[2014-10-30 18:54] 66 8330 1.4 1 1680 6650
[2014-10-30 18:54] 67 8206 1.4 1 1681 6525
[2014-10-30 18:54] 68 8015 1.4 1 1684 6331
[2014-10-30 18:54] 69 8111 1.4 1 1623 6488
[2014-10-30 18:54] 70 8077 1.4 1 1522 6555
[2014-10-30 18:54] 71 7921 1.4 1 1601 6320
[2014-10-30 18:54] 72 8395 1.4 1 1599 6796
[2014-10-30 18:54] 73 7786 1.4 1 1549 6237
[2014-10-30 18:54] 74 7498 1.4 1 1461 6037
[2014-10-30 18:54] 75 7174 1.4 1 1420 5754
[2014-10-30 18:54] 76 7476 1.4 1 1382 6094
[2014-10-30 18:54] 77 7765 1.4 1 1318 6447
[2014-10-30 18:54] 78 7284 1.4 1 1465 5819
[2014-10-30 18:54] 79 7651 1.4 1 1530 6121
[2014-10-30 18:54] 80 8198 1.4 1 1334 6864
[2014-10-30 18:54] 81 8182 1.4 1 1400 6782
[2014-10-30 18:54] 82 7780 1.4 1 1234 6546
[2014-10-30 18:54] 83 7180 1.4 1 1278 5902
[2014-10-30 18:54] 84 7173 1.4 1 1287 5886
[2014-10-30 18:54] 85 7112 1.4 1 1299 5813
[2014-10-30 18:54] 86 7536 1.4 1 1194 6342
[2014-10-30 18:54] 87 6959 1.4 1 1188 5771
[2014-10-30 18:54] 88 6957 1.4 1 1077 5880
[2014-10-30 18:54] 89 7309 1.4 1 1225 6084
[2014-10-30 18:54] 90 10438 1.4 1 1395 9043
[2014-10-30 18:54] 91 8393 1.4 1 1204 7189
[2014-10-30 18:54] 92 8362 1.4 1 1141 7221
[2014-10-30 18:54] 93 7271 1.4 1 1002 6269
[2014-10-30 18:54] 94 4836 1.4 1 806 4030
[2014-10-30 18:54] 95 6782 1.4 1 873 5909
[2014-10-30 18:54] 96 6030 1.4 1 713 5317
[2014-10-30 18:54] 97 5540 1.4 1 647 4893
[2014-10-30 18:54] 98 3663 1.4 1 490 3173
[2014-10-30 18:54] 99 3666 1.4 1 518 3148
[2014-10-30 18:54] 100 15562 1.4 1 1208 14354
[2014-10-30 18:54] 101 14940 1.4 1 1128 13812
[2014-10-30 18:54]
[2014-10-30 18:54] === Adapter 3 ===
[2014-10-30 18:54]
[2014-10-30 18:54] Adapter 'AGATCGGAAGAG', length 12, was trimmed 9380943 times.
[2014-10-30 18:54]
[2014-10-30 18:54] No. of allowed errors:
[2014-10-30 18:54] 0-9 bp: 0; 10-12 bp: 1
[2014-10-30 18:54]
[2014-10-30 18:54] Overview of removed sequences
[2014-10-30 18:54] length count expect max.err error counts
[2014-10-30 18:54] 3 4126946 1455090.5 0 4126946
[2014-10-30 18:54] 4 1225274 363772.6 0 1225274
[2014-10-30 18:54] 5 550912 90943.2 0 550912
[2014-10-30 18:54] 6 453287 22735.8 0 453287
[2014-10-30 18:54] 7 352275 5683.9 0 352275
[2014-10-30 18:54] 8 352822 1421.0 0 352822
[2014-10-30 18:54] 9 289137 355.2 0 285433 3704
[2014-10-30 18:54] 10 256749 88.8 1 248254 8495
[2014-10-30 18:54] 11 187784 22.2 1 180810 6974
[2014-10-30 18:54] 12 184946 5.6 1 180304 4642
[2014-10-30 18:54] 13 149705 5.6 1 145838 3867
[2014-10-30 18:54] 14 163675 5.6 1 159887 3788
[2014-10-30 18:54] 15 97082 5.6 1 94620 2462
[2014-10-30 18:54] 16 104822 5.6 1 102099 2723
[2014-10-30 18:54] 17 119871 5.6 1 116896 2975
[2014-10-30 18:54] 18 74300 5.6 1 72322 1978
[2014-10-30 18:54] 19 80827 5.6 1 78787 2040
[2014-10-30 18:54] 20 69504 5.6 1 67715 1789
[2014-10-30 18:54] 21 28591 5.6 1 27400 1191
[2014-10-30 18:54] 22 40161 5.6 1 38936 1225
[2014-10-30 18:54] 23 37550 5.6 1 36190 1360
[2014-10-30 18:54] 24 36817 5.6 1 35451 1366
[2014-10-30 18:54] 25 31109 5.6 1 29905 1204
[2014-10-30 18:54] 26 29662 5.6 1 28217 1445
[2014-10-30 18:54] 27 20988 5.6 1 19902 1086
[2014-10-30 18:54] 28 24954 5.6 1 23794 1160
[2014-10-30 18:54] 29 18037 5.6 1 17114 923
[2014-10-30 18:54] 30 30535 5.6 1 29335 1200
[2014-10-30 18:54] 31 7381 5.6 1 6604 777
[2014-10-30 18:54] 32 11789 5.6 1 11011 778
[2014-10-30 18:54] 33 7416 5.6 1 6700 716
[2014-10-30 18:54] 34 8790 5.6 1 7971 819
[2014-10-30 18:54] 35 9018 5.6 1 8085 933
[2014-10-30 18:54] 36 8477 5.6 1 7663 814
[2014-10-30 18:54] 37 8496 5.6 1 7726 770
[2014-10-30 18:54] 38 8448 5.6 1 7586 862
[2014-10-30 18:54] 39 8556 5.6 1 7777 779
[2014-10-30 18:54] 40 7470 5.6 1 6795 675
[2014-10-30 18:54] 41 8432 5.6 1 7471 961
[2014-10-30 18:54] 42 10138 5.6 1 9172 966
[2014-10-30 18:54] 43 3687 5.6 1 2893 794
[2014-10-30 18:54] 44 6509 5.6 1 5655 854
[2014-10-30 18:54] 45 6681 5.6 1 5898 783
[2014-10-30 18:54] 46 2987 5.6 1 2267 720
[2014-10-30 18:54] 47 4111 5.6 1 3501 610
[2014-10-30 18:54] 48 3482 5.6 1 2839 643
[2014-10-30 18:54] 49 4014 5.6 1 3227 787
[2014-10-30 18:54] 50 4488 5.6 1 3743 745
[2014-10-30 18:54] 51 4453 5.6 1 3817 636
[2014-10-30 18:54] 52 2991 5.6 1 2404 587
[2014-10-30 18:54] 53 2504 5.6 1 1733 771
[2014-10-30 18:54] 54 3113 5.6 1 2372 741
[2014-10-30 18:54] 55 3438 5.6 1 2770 668
[2014-10-30 18:54] 56 3116 5.6 1 2485 631
[2014-10-30 18:54] 57 3480 5.6 1 2592 888
[2014-10-30 18:54] 58 3852 5.6 1 3162 690
[2014-10-30 18:54] 59 3639 5.6 1 2946 693
[2014-10-30 18:54] 60 3669 5.6 1 2890 779
[2014-10-30 18:54] 61 3799 5.6 1 2864 935
[2014-10-30 18:54] 62 5704 5.6 1 4473 1231
[2014-10-30 18:54] 63 7070 5.6 1 5438 1632
[2014-10-30 18:54] 64 8364 5.6 1 5260 3104
[2014-10-30 18:54] 65 11585 5.6 1 6845 4740
[2014-10-30 18:54] 66 9240 5.6 1 6601 2639
[2014-10-30 18:54] 67 3481 5.6 1 2018 1463
[2014-10-30 18:54] 68 1799 5.6 1 1183 616
[2014-10-30 18:54] 69 913 5.6 1 369 544
[2014-10-30 18:54] 70 659 5.6 1 26 633
[2014-10-30 18:54] 71 495 5.6 1 6 489
[2014-10-30 18:54] 72 596 5.6 1 8 588
[2014-10-30 18:54] 73 515 5.6 1 8 507
[2014-10-30 18:54] 74 512 5.6 1 2 510
[2014-10-30 18:54] 75 548 5.6 1 6 542
[2014-10-30 18:54] 76 491 5.6 1 4 487
[2014-10-30 18:54] 77 835 5.6 1 2 833
[2014-10-30 18:54] 78 528 5.6 1 0 528
[2014-10-30 18:54] 79 442 5.6 1 8 434
[2014-10-30 18:54] 80 473 5.6 1 7 466
[2014-10-30 18:54] 81 501 5.6 1 4 497
[2014-10-30 18:54] 82 618 5.6 1 4 614
[2014-10-30 18:54] 83 628 5.6 1 8 620
[2014-10-30 18:54] 84 484 5.6 1 12 472
[2014-10-30 18:54] 85 374 5.6 1 3 371
[2014-10-30 18:54] 86 528 5.6 1 4 524
[2014-10-30 18:54] 87 382 5.6 1 12 370
[2014-10-30 18:54] 88 517 5.6 1 4 513
[2014-10-30 18:54] 89 420 5.6 1 2 418
[2014-10-30 18:54] 90 354 5.6 1 4 350
[2014-10-30 18:54] 91 503 5.6 1 0 503
[2014-10-30 18:54] 92 712 5.6 1 2 710
[2014-10-30 18:54] 93 454 5.6 1 8 446
[2014-10-30 18:54] 94 290 5.6 1 8 282
[2014-10-30 18:54] 95 218 5.6 1 2 216
[2014-10-30 18:54] 96 538 5.6 1 4 534
[2014-10-30 18:54] 97 295 5.6 1 10 285
[2014-10-30 18:54] 98 1243 5.6 1 12 1231
[2014-10-30 18:54] 99 406 5.6 1 10 396
[2014-10-30 18:54] 100 244 5.6 1 4 240
[2014-10-30 18:54] 101 238 5.6 1 48 190
[2014-10-30 18:54]
[2014-10-30 18:54] === Adapter 4 ===
[2014-10-30 18:54]
[2014-10-30 18:54] Adapter 'CTCTTCCGATCT', length 12, was trimmed 4998213 times.
[2014-10-30 18:54]
[2014-10-30 18:54] No. of allowed errors:
[2014-10-30 18:54] 0-9 bp: 0; 10-12 bp: 1
[2014-10-30 18:54]
[2014-10-30 18:54] Overview of removed sequences
[2014-10-30 18:54] length count expect max.err error counts
[2014-10-30 18:54] 3 3566034 1455090.5 0 3566034
[2014-10-30 18:54] 4 933642 363772.6 0 933642
[2014-10-30 18:54] 5 289738 90943.2 0 289738
[2014-10-30 18:54] 6 98248 22735.8 0 98248
[2014-10-30 18:54] 7 34753 5683.9 0 34753
[2014-10-30 18:54] 8 1589 1421.0 0 1589
[2014-10-30 18:54] 9 3594 355.2 0 283 3311
[2014-10-30 18:54] 10 12024 88.8 1 55 11969
[2014-10-30 18:54] 11 2332 22.2 1 29 2303
[2014-10-30 18:54] 12 671 5.6 1 20 651
[2014-10-30 18:54] 13 506 5.6 1 55 451
[2014-10-30 18:54] 14 449 5.6 1 12 437
[2014-10-30 18:54] 15 383 5.6 1 6 377
[2014-10-30 18:54] 16 415 5.6 1 6 409
[2014-10-30 18:54] 17 432 5.6 1 4 428
[2014-10-30 18:54] 18 423 5.6 1 9 414
[2014-10-30 18:54] 19 441 5.6 1 3 438
[2014-10-30 18:54] 20 496 5.6 1 8 488
[2014-10-30 18:54] 21 482 5.6 1 3 479
[2014-10-30 18:54] 22 652 5.6 1 5 647
[2014-10-30 18:54] 23 608 5.6 1 6 602
[2014-10-30 18:54] 24 622 5.6 1 2 620
[2014-10-30 18:54] 25 757 5.6 1 7 750
[2014-10-30 18:54] 26 515 5.6 1 6 509
[2014-10-30 18:54] 27 577 5.6 1 6 571
[2014-10-30 18:54] 28 553 5.6 1 3 550
[2014-10-30 18:54] 29 677 5.6 1 2 675
[2014-10-30 18:54] 30 683 5.6 1 2 681
[2014-10-30 18:54] 31 675 5.6 1 0 675
[2014-10-30 18:54] 32 958 5.6 1 4 954
[2014-10-30 18:54] 33 698 5.6 1 0 698
[2014-10-30 18:54] 34 702 5.6 1 4 698
[2014-10-30 18:54] 35 701 5.6 1 12 689
[2014-10-30 18:54] 36 631 5.6 1 2 629
[2014-10-30 18:54] 37 924 5.6 1 2 922
[2014-10-30 18:54] 38 666 5.6 1 0 666
[2014-10-30 18:54] 39 510 5.6 1 0 510
[2014-10-30 18:54] 40 504 5.6 1 2 502
[2014-10-30 18:54] 41 437 5.6 1 10 427
[2014-10-30 18:54] 42 417 5.6 1 2 415
[2014-10-30 18:54] 43 613 5.6 1 7 606
[2014-10-30 18:54] 44 585 5.6 1 2 583
[2014-10-30 18:54] 45 587 5.6 1 6 581
[2014-10-30 18:54] 46 613 5.6 1 11 602
[2014-10-30 18:54] 47 743 5.6 1 13 730
[2014-10-30 18:54] 48 560 5.6 1 6 554
[2014-10-30 18:54] 49 510 5.6 1 2 508
[2014-10-30 18:54] 50 571 5.6 1 0 571
[2014-10-30 18:54] 51 554 5.6 1 4 550
[2014-10-30 18:54] 52 700 5.6 1 8 692
[2014-10-30 18:54] 53 613 5.6 1 12 601
[2014-10-30 18:54] 54 594 5.6 1 22 572
[2014-10-30 18:54] 55 564 5.6 1 4 560
[2014-10-30 18:54] 56 559 5.6 1 6 553
[2014-10-30 18:54] 57 582 5.6 1 8 574
[2014-10-30 18:54] 58 667 5.6 1 7 660
[2014-10-30 18:54] 59 504 5.6 1 3 501
[2014-10-30 18:54] 60 497 5.6 1 6 491
[2014-10-30 18:54] 61 593 5.6 1 0 593
[2014-10-30 18:54] 62 546 5.6 1 6 540
[2014-10-30 18:54] 63 514 5.6 1 2 512
[2014-10-30 18:54] 64 555 5.6 1 7 548
[2014-10-30 18:54] 65 450 5.6 1 6 444
[2014-10-30 18:54] 66 503 5.6 1 6 497
[2014-10-30 18:54] 67 518 5.6 1 2 516
[2014-10-30 18:54] 68 618 5.6 1 6 612
[2014-10-30 18:54] 69 594 5.6 1 9 585
[2014-10-30 18:54] 70 525 5.6 1 8 517
[2014-10-30 18:54] 71 516 5.6 1 4 512
[2014-10-30 18:54] 72 541 5.6 1 4 537
[2014-10-30 18:54] 73 555 5.6 1 8 547
[2014-10-30 18:54] 74 646 5.6 1 10 636
[2014-10-30 18:54] 75 643 5.6 1 18 625
[2014-10-30 18:54] 76 565 5.6 1 22 543
[2014-10-30 18:54] 77 575 5.6 1 20 555
[2014-10-30 18:54] 78 484 5.6 1 22 462
[2014-10-30 18:54] 79 683 5.6 1 14 669
[2014-10-30 18:54] 80 510 5.6 1 38 472
[2014-10-30 18:54] 81 607 5.6 1 50 557
[2014-10-30 18:54] 82 582 5.6 1 28 554
[2014-10-30 18:54] 83 994 5.6 1 141 853
[2014-10-30 18:54] 84 522 5.6 1 18 504
[2014-10-30 18:54] 85 612 5.6 1 38 574
[2014-10-30 18:54] 86 492 5.6 1 26 466
[2014-10-30 18:54] 87 642 5.6 1 59 583
[2014-10-30 18:54] 88 505 5.6 1 68 437
[2014-10-30 18:54] 89 678 5.6 1 54 624
[2014-10-30 18:54] 90 762 5.6 1 78 684
[2014-10-30 18:54] 91 755 5.6 1 112 643
[2014-10-30 18:54] 92 628 5.6 1 58 570
[2014-10-30 18:54] 93 788 5.6 1 126 662
[2014-10-30 18:54] 94 1314 5.6 1 398 916
[2014-10-30 18:54] 95 639 5.6 1 116 523
[2014-10-30 18:54] 96 1672 5.6 1 520 1152
[2014-10-30 18:54] 97 593 5.6 1 96 497
[2014-10-30 18:54] 98 1461 5.6 1 750 711
[2014-10-30 18:54] 99 1238 5.6 1 308 930
[2014-10-30 18:54] 100 394 5.6 1 114 280
[2014-10-30 18:54] 101 466 5.6 1 62 404
[2014-10-30 18:54]
[2014-10-30 18:54] Resource requests: picard, tophat2; memory: 0.4; cores: 1, 16
[2014-10-30 18:54] Configuring 1 jobs to run, using 8 cores each with 8.2g of memory reserved for each job
[2014-10-30 18:54] Timing: alignment
[2014-10-30 18:54] multiprocessing: process_alignment
[2014-10-30 18:54] Aligning lane 1_2014-10-08_seqc with tophat2 aligner
[2014-10-30 18:54] Aligning /vagrant_data/seqc-test/seqc/work/trimmed/SRR950078_1.trimmed.fastq.gz and /vagrant_data/seqc-test/seqc/work/trimmed/SRR950078_2.trimmed.fastq.gz with Bowtie2.
[2014-10-30 18:57] 250000 reads; of these:
[2014-10-30 18:57] 250000 (100.00%) were paired; of these:
[2014-10-30 18:57] 51621 (20.65%) aligned concordantly 0 times
[2014-10-30 18:57] 119683 (47.87%) aligned concordantly exactly 1 time
[2014-10-30 18:57] 78696 (31.48%) aligned concordantly >1 times
[2014-10-30 18:57] ----
[2014-10-30 18:57] 51621 pairs aligned concordantly 0 times; of these:
[2014-10-30 18:57] 3797 (7.36%) aligned discordantly 1 time
[2014-10-30 18:57] ----
[2014-10-30 18:57] 47824 pairs aligned 0 times concordantly or discordantly; of these:
[2014-10-30 18:57] 95648 mates make up the pairs; of these:
[2014-10-30 18:57] 62751 (65.61%) aligned 0 times
[2014-10-30 18:57] 27672 (28.93%) aligned exactly 1 time
[2014-10-30 18:57] 5225 (5.46%) aligned >1 times
[2014-10-30 18:57] 87.45% overall alignment rate
[2014-10-30 19:02] Running Tophat on /vagrant_data/seqc-test/seqc/work/trimmed/SRR950078_1.trimmed.fastq.gz and /vagrant_data/seqc-test/seqc/work/trimmed/SRR950078_2.trimmed.fastq.gz.
[2014-10-30 19:02]
[2014-10-30 19:02] [2014-10-30 19:02:38] Beginning TopHat run (v2.0.12)
[2014-10-30 19:02] -----------------------------------------------
[2014-10-30 19:02] [2014-10-30 19:02:38] Checking for Bowtie
[2014-10-30 19:02] Bowtie version: 2.2.3.0
[2014-10-30 19:02] [2014-10-30 19:02:38] Checking for Samtools
[2014-10-30 19:02] Samtools version: 1.1.0.0
[2014-10-30 19:02] [2014-10-30 19:02:38] Checking for Bowtie index files (transcriptome)..
[2014-10-30 19:02] [2014-10-30 19:02:38] Checking for Bowtie index files (genome)..
[2014-10-30 19:02] [2014-10-30 19:02:38] Checking for reference FASTA file
[2014-10-30 19:02] [2014-10-30 19:02:38] Generating SAM header for /usr/local/share/bcbio/genomes/Hsapiens/GRCh37/bowtie2/GRCh37
[2014-10-30 19:02] [2014-10-30 19:02:39] Reading known junctions from GTF file
[2014-10-30 19:02] [2014-10-30 19:02:52] Preparing reads
[2014-10-30 19:55] left reads: min. length=25, max. length=101, 91870599 kept reads (9 discarded)
[2014-10-30 19:55] right reads: min. length=25, max. length=101, 91870545 kept reads (63 discarded)
[2014-10-30 19:55] [2014-10-30 19:55:29] Using pre-built transcriptome data..
[2014-10-30 19:55] [2014-10-30 19:55:45] Mapping left_kept_reads to transcriptome GRCh37_transcriptome with Bowtie2
[2014-10-31 01:13] [2014-10-31 01:13:48] Mapping right_kept_reads to transcriptome GRCh37_transcriptome with Bowtie2
[2014-10-31 06:08] [2014-10-31 06:08:10] Resuming TopHat pipeline with unmapped reads
[2014-10-31 06:08] samtools: writing to standard output failed: Broken pipe
[2014-10-31 06:08] samtools: error closing standard output: -1
[2014-10-31 06:08] samtools: writing to standard output failed: Broken pipe
[2014-10-31 06:08] [2014-10-31 06:08:11] Mapping left_kept_reads.m2g_um to genome GRCh37 with Bowtie2
[2014-10-31 06:08] samtools: error closing standard output: -1
[2014-10-31 07:31] samtools: writing to standard output failed: Broken pipe
[2014-10-31 07:31] samtools: error closing standard output: -1
[2014-10-31 07:36] [2014-10-31 07:36:46] Mapping left_kept_reads.m2g_um_seg1 to genome GRCh37 with Bowtie2 (1/4)
[2014-10-31 07:43] [2014-10-31 07:43:16] Mapping left_kept_reads.m2g_um_seg2 to genome GRCh37 with Bowtie2 (2/4)
[2014-10-31 07:50] [2014-10-31 07:50:24] Mapping left_kept_reads.m2g_um_seg3 to genome GRCh37 with Bowtie2 (3/4)
[2014-10-31 07:57] [2014-10-31 07:57:43] Mapping left_kept_reads.m2g_um_seg4 to genome GRCh37 with Bowtie2 (4/4)
[2014-10-31 08:04] samtools: writing to standard output failed: Broken pipe
[2014-10-31 08:04] [2014-10-31 08:04:22] Mapping right_kept_reads.m2g_um to genome GRCh37 with Bowtie2
[2014-10-31 08:04] samtools: error closing standard output: -1
[2014-10-31 09:30] samtools: writing to standard output failed: Broken pipe
[2014-10-31 09:30] samtools: error closing standard output: -1
[2014-10-31 09:36] [2014-10-31 09:36:22] Mapping right_kept_reads.m2g_um_seg1 to genome GRCh37 with Bowtie2 (1/4)
[2014-10-31 09:43] [2014-10-31 09:43:20] Mapping right_kept_reads.m2g_um_seg2 to genome GRCh37 with Bowtie2 (2/4)
[2014-10-31 09:50] [2014-10-31 09:50:37] Mapping right_kept_reads.m2g_um_seg3 to genome GRCh37 with Bowtie2 (3/4)
[2014-10-31 09:58] [2014-10-31 09:58:25] Mapping right_kept_reads.m2g_um_seg4 to genome GRCh37 with Bowtie2 (4/4)
[2014-10-31 10:05] [2014-10-31 10:05:57] Searching for junctions via segment mapping
[2014-10-31 11:09] [2014-10-31 11:09:28] Retrieving sequences for splices
[2014-10-31 11:12] [2014-10-31 11:12:11] Indexing splices
[2014-10-31 11:12] Building a SMALL index
[2014-10-31 11:14] samtools: writing to standard output failed: Broken pipe
[2014-10-31 11:14] [2014-10-31 11:14:44] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-10-31 11:14] samtools: error closing standard output: -1
[2014-10-31 11:16] [2014-10-31 11:16:40] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-10-31 11:18] [2014-10-31 11:18:50] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-10-31 11:21] [2014-10-31 11:21:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-10-31 11:23] [2014-10-31 11:23:24] Joining segment hits
[2014-10-31 11:31] samtools: writing to standard output failed: Broken pipe
[2014-10-31 11:31] samtools: error closing standard output: -1
[2014-10-31 11:31] samtools: writing to standard output failed: Broken pipe
[2014-10-31 11:31] samtools: error closing standard output: -1
[2014-10-31 11:31] samtools: writing to standard output failed: Broken pipe
[2014-10-31 11:31] samtools: error closing standard output: -1
[2014-10-31 11:31] samtools: writing to standard output failed: Broken pipe
[2014-10-31 11:31] samtools: error closing standard output: -1
[2014-10-31 11:31] [2014-10-31 11:31:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-10-31 11:33] [2014-10-31 11:33:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-10-31 11:35] [2014-10-31 11:35:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-10-31 11:37] [2014-10-31 11:37:53] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-10-31 11:40] [2014-10-31 11:40:33] Joining segment hits
[2014-10-31 11:46] samtools: writing to standard output failed: Broken pipe
[2014-10-31 11:46] samtools: error closing standard output: -1
[2014-10-31 11:46] samtools: writing to standard output failed: Broken pipe
[2014-10-31 11:46] samtools: error closing standard output: -1
[2014-10-31 11:46] samtools: writing to standard output failed: Broken pipe
[2014-10-31 11:46] samtools: error closing standard output: -1
[2014-10-31 11:46] [2014-10-31 11:46:08] Reporting output tracks
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:54] samtools: writing to standard output failed: Broken pipe
[2014-10-31 19:54] samtools: error closing standard output: -1
[2014-10-31 19:57] -----------------------------------------------
[2014-10-31 19:57] [2014-10-31 19:57:57] A summary of the alignment counts can be found in /vagrant_data/seqc-test/seqc/work/align/UHRR_rep1/tx/tmpuvcooL/1_2014-10-08_seqc_tophat/align_summary.txt
[2014-10-31 19:57] [2014-10-31 19:57:57] Run complete: 1 days 00:55:19 elapsed
[2014-10-31 19:57] Removing reads with empty read names from Tophat output.
[2014-10-31 21:42] Fix mate pairs in TopHat output
[2014-10-31 22:12] Convert SAM to BAM (8 cores): /vagrant_data/seqc-test/seqc/work/align/UHRR_rep1/1_2014-10-08_seqc_tophat/1_2014-10-08_seqc-align.sam to /vagrant_data/seqc-test/seqc/work/align/UHRR_rep1/1_2014-10-08_seqc_tophat/1_2014-10-08_seqc-align.bam
[2014-10-31 22:45] Merge ['/vagrant_data/seqc-test/seqc/work/align/UHRR_rep1/1_2014-10-08_seqc_tophat/1_2014-10-08_seqc-align.bam', '/vagrant_data/seqc-test/seqc/work/align/UHRR_rep1/1_2014-10-08_seqc_tophat/unmapped.bam'] into /vagrant_data/seqc-test/seqc/work/align/UHRR_rep1/1_2014-10-08_seqc_tophat/merged.bam.
[2014-10-31 23:10] Index BAM file: merged.bam
[2014-10-31 23:13] Picard AddOrReplaceReadGroups
[2014-10-31 23:13] [Fri Oct 31 23:13:44 UTC 2014] net.sf.picard.sam.AddOrReplaceReadGroups INPUT=/vagrant_data/seqc-test/seqc/work/align/UHRR_rep1/1_2014-10-08_seqc_tophat/merged.bam OUTPUT=/vagrant_data/seqc-test/seqc/work/align/UHRR_rep1/1_2014-10-08_seqc_tophat/tx/tmpNIHlU1/merged-fixrgs.bam SORT_ORDER=coordinate RGID=1 RGLB=unknown RGPL=illumina RGPU=1_2014-10-08_seqc RGSM=UHRR_rep1 TMP_DIR=[/vagrant_data/seqc-test/seqc/work/tx/tmpB0SIYI] VALIDATION_STRINGENCY=SILENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[2014-10-31 23:13] [Fri Oct 31 23:13:44 UTC 2014] Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01; Picard version: 1.96(1510)
[2014-10-31 23:13] INFO 2014-10-31 23:13:44 AddOrReplaceReadGroups Created read group ID=1 PL=illumina LB=unknown SM=UHRR_rep1
[2014-10-31 23:13]
[2014-10-31 23:14] INFO 2014-10-31 23:14:02 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 18s. Last read position: 1:569,320
[2014-10-31 23:14] INFO 2014-10-31 23:14:22 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 19s. Last read position: 1:8,921,439
[2014-10-31 23:14] INFO 2014-10-31 23:14:41 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 19s. Last read position: 1:16,721,707
[2014-10-31 23:15] INFO 2014-10-31 23:15:00 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 18s. Last read position: 1:25,168,834
[2014-10-31 23:15] INFO 2014-10-31 23:15:18 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 18s. Last read position: 1:32,661,744
[2014-10-31 23:15] INFO 2014-10-31 23:15:38 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 19s. Last read position: 1:40,888,571
[2014-10-31 23:15] INFO 2014-10-31 23:15:57 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 19s. Last read position: 1:46,738,138
[2014-10-31 23:16] INFO 2014-10-31 23:16:17 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 19s. Last read position: 1:68,591,613
[2014-10-31 23:16] INFO 2014-10-31 23:16:36 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 19s. Last read position: 1:100,488,374
[2014-10-31 23:16] INFO 2014-10-31 23:16:56 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 19s. Last read position: 1:116,937,768
[2014-10-31 23:17] INFO 2014-10-31 23:17:16 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 19s. Last read position: 1:147,575,043
[2014-10-31 23:17] INFO 2014-10-31 23:17:35 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 19s. Last read position: 1:153,637,809
[2014-10-31 23:17] INFO 2014-10-31 23:17:54 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 19s. Last read position: 1:156,256,165
[2014-10-31 23:18] INFO 2014-10-31 23:18:14 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 19s. Last read position: 1:168,054,387
[2014-10-31 23:18] INFO 2014-10-31 23:18:34 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 19s. Last read position: 1:199,065,756
[2014-10-31 23:18] INFO 2014-10-31 23:18:53 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 19s. Last read position: 1:216,231,553
[2014-10-31 23:19] INFO 2014-10-31 23:19:13 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 19s. Last read position: 1:233,270,902
[2014-10-31 23:19] INFO 2014-10-31 23:19:33 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 19s. Last read position: 10:7,773,853
[2014-10-31 23:19] INFO 2014-10-31 23:19:53 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 19s. Last read position: 10:35,500,642
[2014-10-31 23:20] INFO 2014-10-31 23:20:13 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 19s. Last read position: 10:73,578,382
[2014-10-31 23:20] INFO 2014-10-31 23:20:32 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 19s. Last read position: 10:89,729,090
[2014-10-31 23:20] INFO 2014-10-31 23:20:52 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 19s. Last read position: 10:103,547,240
[2014-10-31 23:21] INFO 2014-10-31 23:21:12 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 19s. Last read position: 10:133,782,059
[2014-10-31 23:21] INFO 2014-10-31 23:21:31 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 19s. Last read position: 11:5,275,636
[2014-10-31 23:21] INFO 2014-10-31 23:21:50 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 19s. Last read position: 11:17,096,709
[2014-10-31 23:22] INFO 2014-10-31 23:22:09 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 19s. Last read position: 11:43,465,019
[2014-10-31 23:22] INFO 2014-10-31 23:22:29 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 19s. Last read position: 11:61,590,879
[2014-10-31 23:22] INFO 2014-10-31 23:22:48 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 18s. Last read position: 11:62,445,066
[2014-10-31 23:23] INFO 2014-10-31 23:23:07 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 18s. Last read position: 11:65,270,237
[2014-10-31 23:23] INFO 2014-10-31 23:23:26 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 19s. Last read position: 11:70,316,382
[2014-10-31 23:23] INFO 2014-10-31 23:23:45 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 19s. Last read position: 11:85,669,139
[2014-10-31 23:24] INFO 2014-10-31 23:24:05 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 19s. Last read position: 11:118,453,908
[2014-10-31 23:24] INFO 2014-10-31 23:24:24 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 19s. Last read position: 11:126,147,373
[2014-10-31 23:24] INFO 2014-10-31 23:24:43 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 18s. Last read position: 12:6,646,172
[2014-10-31 23:25] INFO 2014-10-31 23:25:01 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 17s. Last read position: 12:6,978,517
[2014-10-31 23:25] INFO 2014-10-31 23:25:20 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 19s. Last read position: 12:19,449,954
[2014-10-31 23:25] INFO 2014-10-31 23:25:40 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 19s. Last read position: 12:49,218,113
[2014-10-31 23:25] INFO 2014-10-31 23:25:58 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 18s. Last read position: 12:51,141,085
[2014-10-31 23:26] INFO 2014-10-31 23:26:17 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 18s. Last read position: 12:54,579,848
[2014-10-31 23:26] INFO 2014-10-31 23:26:36 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 18s. Last read position: 12:56,495,787
[2014-10-31 23:26] INFO 2014-10-31 23:26:54 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 18s. Last read position: 12:57,449,963
[2014-10-31 23:27] INFO 2014-10-31 23:27:14 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 19s. Last read position: 12:76,447,081
[2014-10-31 23:27] INFO 2014-10-31 23:27:33 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 19s. Last read position: 12:104,728,077
[2014-10-31 23:27] INFO 2014-10-31 23:27:53 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:14:09s. Time for last 1,000,000: 19s. Last read position: 12:118,503,795
[2014-10-31 23:28] INFO 2014-10-31 23:28:12 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:14:28s. Time for last 1,000,000: 19s. Last read position: 12:123,422,778
[2014-10-31 23:28] INFO 2014-10-31 23:28:31 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:14:46s. Time for last 1,000,000: 18s. Last read position: 13:21,947,547
[2014-10-31 23:28] INFO 2014-10-31 23:28:50 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:15:05s. Time for last 1,000,000: 18s. Last read position: 13:46,104,828
[2014-10-31 23:29] INFO 2014-10-31 23:29:10 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:15:25s. Time for last 1,000,000: 19s. Last read position: 13:103,450,895
[2014-10-31 23:29] INFO 2014-10-31 23:29:29 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:15:45s. Time for last 1,000,000: 19s. Last read position: 14:23,495,247
[2014-10-31 23:29] INFO 2014-10-31 23:29:49 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:16:04s. Time for last 1,000,000: 19s. Last read position: 14:50,053,321
[2014-10-31 23:30] INFO 2014-10-31 23:30:06 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:16:22s. Time for last 1,000,000: 17s. Last read position: 14:56,079,016
[2014-10-31 23:30] INFO 2014-10-31 23:30:26 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:16:42s. Time for last 1,000,000: 19s. Last read position: 14:75,598,453
[2014-10-31 23:30] INFO 2014-10-31 23:30:46 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:17:01s. Time for last 1,000,000: 19s. Last read position: 14:102,516,192
[2014-10-31 23:31] INFO 2014-10-31 23:31:06 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:17:21s. Time for last 1,000,000: 19s. Last read position: 15:34,634,224
[2014-10-31 23:31] INFO 2014-10-31 23:31:25 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:17:41s. Time for last 1,000,000: 19s. Last read position: 15:45,707,829
[2014-10-31 23:31] INFO 2014-10-31 23:31:45 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:18:00s. Time for last 1,000,000: 19s. Last read position: 15:64,452,392
[2014-10-31 23:32] INFO 2014-10-31 23:32:04 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:18:20s. Time for last 1,000,000: 19s. Last read position: 15:72,491,411
[2014-10-31 23:32] INFO 2014-10-31 23:32:23 AddOrReplaceReadGroups Processed 58,000,000 records. Elapsed time: 00:18:39s. Time for last 1,000,000: 19s. Last read position: 15:80,429,949
[2014-10-31 23:32] INFO 2014-10-31 23:32:41 AddOrReplaceReadGroups Processed 59,000,000 records. Elapsed time: 00:18:57s. Time for last 1,000,000: 18s. Last read position: 15:90,619,674
[2014-10-31 23:33] INFO 2014-10-31 23:33:01 AddOrReplaceReadGroups Processed 60,000,000 records. Elapsed time: 00:19:16s. Time for last 1,000,000: 19s. Last read position: 16:2,013,203
[2014-10-31 23:33] INFO 2014-10-31 23:33:20 AddOrReplaceReadGroups Processed 61,000,000 records. Elapsed time: 00:19:36s. Time for last 1,000,000: 19s. Last read position: 16:14,852,814
[2014-10-31 23:33] INFO 2014-10-31 23:33:39 AddOrReplaceReadGroups Processed 62,000,000 records. Elapsed time: 00:19:55s. Time for last 1,000,000: 18s. Last read position: 16:19,564,516
[2014-10-31 23:33] INFO 2014-10-31 23:33:58 AddOrReplaceReadGroups Processed 63,000,000 records. Elapsed time: 00:20:14s. Time for last 1,000,000: 19s. Last read position: 16:28,725,994
[2014-10-31 23:34] INFO 2014-10-31 23:34:17 AddOrReplaceReadGroups Processed 64,000,000 records. Elapsed time: 00:20:32s. Time for last 1,000,000: 18s. Last read position: 16:30,536,516
[2014-10-31 23:34] INFO 2014-10-31 23:34:37 AddOrReplaceReadGroups Processed 65,000,000 records. Elapsed time: 00:20:52s. Time for last 1,000,000: 19s. Last read position: 16:58,752,113
[2014-10-31 23:34] INFO 2014-10-31 23:34:56 AddOrReplaceReadGroups Processed 66,000,000 records. Elapsed time: 00:21:12s. Time for last 1,000,000: 19s. Last read position: 16:74,335,480
[2014-10-31 23:35] INFO 2014-10-31 23:35:16 AddOrReplaceReadGroups Processed 67,000,000 records. Elapsed time: 00:21:31s. Time for last 1,000,000: 19s. Last read position: 16:89,629,295
[2014-10-31 23:35] INFO 2014-10-31 23:35:35 AddOrReplaceReadGroups Processed 68,000,000 records. Elapsed time: 00:21:51s. Time for last 1,000,000: 19s. Last read position: 17:5,253,814
[2014-10-31 23:35] INFO 2014-10-31 23:35:55 AddOrReplaceReadGroups Processed 69,000,000 records. Elapsed time: 00:22:10s. Time for last 1,000,000: 19s. Last read position: 17:12,045,556
[2014-10-31 23:36] INFO 2014-10-31 23:36:14 AddOrReplaceReadGroups Processed 70,000,000 records. Elapsed time: 00:22:29s. Time for last 1,000,000: 19s. Last read position: 17:26,946,966
[2014-10-31 23:36] INFO 2014-10-31 23:36:34 AddOrReplaceReadGroups Processed 71,000,000 records. Elapsed time: 00:22:49s. Time for last 1,000,000: 19s. Last read position: 17:36,891,094
[2014-10-31 23:36] INFO 2014-10-31 23:36:52 AddOrReplaceReadGroups Processed 72,000,000 records. Elapsed time: 00:23:08s. Time for last 1,000,000: 18s. Last read position: 17:40,175,916
[2014-10-31 23:37] INFO 2014-10-31 23:37:12 AddOrReplaceReadGroups Processed 73,000,000 records. Elapsed time: 00:23:27s. Time for last 1,000,000: 19s. Last read position: 17:44,604,329
[2014-10-31 23:37] INFO 2014-10-31 23:37:31 AddOrReplaceReadGroups Processed 74,000,000 records. Elapsed time: 00:23:47s. Time for last 1,000,000: 19s. Last read position: 17:55,693,393
[2014-10-31 23:37] INFO 2014-10-31 23:37:51 AddOrReplaceReadGroups Processed 75,000,000 records. Elapsed time: 00:24:06s. Time for last 1,000,000: 19s. Last read position: 17:63,005,916
[2014-10-31 23:38] INFO 2014-10-31 23:38:11 AddOrReplaceReadGroups Processed 76,000,000 records. Elapsed time: 00:24:26s. Time for last 1,000,000: 19s. Last read position: 17:75,086,938
[2014-10-31 23:38] INFO 2014-10-31 23:38:30 AddOrReplaceReadGroups Processed 77,000,000 records. Elapsed time: 00:24:46s. Time for last 1,000,000: 19s. Last read position: 17:79,805,152
[2014-10-31 23:38] INFO 2014-10-31 23:38:49 AddOrReplaceReadGroups Processed 78,000,000 records. Elapsed time: 00:25:05s. Time for last 1,000,000: 19s. Last read position: 18:19,450,015
[2014-10-31 23:39] INFO 2014-10-31 23:39:08 AddOrReplaceReadGroups Processed 79,000,000 records. Elapsed time: 00:25:24s. Time for last 1,000,000: 19s. Last read position: 18:57,569,981
[2014-10-31 23:39] INFO 2014-10-31 23:39:28 AddOrReplaceReadGroups Processed 80,000,000 records. Elapsed time: 00:25:43s. Time for last 1,000,000: 19s. Last read position: 19:3,976,135
[2014-10-31 23:39] INFO 2014-10-31 23:39:46 AddOrReplaceReadGroups Processed 81,000,000 records. Elapsed time: 00:26:02s. Time for last 1,000,000: 18s. Last read position: 19:10,230,330
[2014-10-31 23:40] INFO 2014-10-31 23:40:05 AddOrReplaceReadGroups Processed 82,000,000 records. Elapsed time: 00:26:21s. Time for last 1,000,000: 19s. Last read position: 19:14,574,910
[2014-10-31 23:40] INFO 2014-10-31 23:40:25 AddOrReplaceReadGroups Processed 83,000,000 records. Elapsed time: 00:26:40s. Time for last 1,000,000: 19s. Last read position: 19:21,329,910
[2014-10-31 23:40] INFO 2014-10-31 23:40:44 AddOrReplaceReadGroups Processed 84,000,000 records. Elapsed time: 00:27:00s. Time for last 1,000,000: 19s. Last read position: 19:39,329,210
[2014-10-31 23:41] INFO 2014-10-31 23:41:03 AddOrReplaceReadGroups Processed 85,000,000 records. Elapsed time: 00:27:19s. Time for last 1,000,000: 19s. Last read position: 19:46,880,970
[2014-10-31 23:41] INFO 2014-10-31 23:41:22 AddOrReplaceReadGroups Processed 86,000,000 records. Elapsed time: 00:27:38s. Time for last 1,000,000: 18s. Last read position: 19:49,994,712
[2014-10-31 23:41] INFO 2014-10-31 23:41:41 AddOrReplaceReadGroups Processed 87,000,000 records. Elapsed time: 00:27:57s. Time for last 1,000,000: 19s. Last read position: 19:56,180,074
[2014-10-31 23:42] INFO 2014-10-31 23:42:00 AddOrReplaceReadGroups Processed 88,000,000 records. Elapsed time: 00:28:16s. Time for last 1,000,000: 18s. Last read position: 2:10,924,232
[2014-10-31 23:42] INFO 2014-10-31 23:42:19 AddOrReplaceReadGroups Processed 89,000,000 records. Elapsed time: 00:28:35s. Time for last 1,000,000: 19s. Last read position: 2:28,003,471
[2014-10-31 23:42] INFO 2014-10-31 23:42:39 AddOrReplaceReadGroups Processed 90,000,000 records. Elapsed time: 00:28:55s. Time for last 1,000,000: 19s. Last read position: 2:54,856,833
[2014-10-31 23:42] INFO 2014-10-31 23:42:59 AddOrReplaceReadGroups Processed 91,000,000 records. Elapsed time: 00:29:14s. Time for last 1,000,000: 19s. Last read position: 2:70,515,246
[2014-10-31 23:43] INFO 2014-10-31 23:43:18 AddOrReplaceReadGroups Processed 92,000,000 records. Elapsed time: 00:29:34s. Time for last 1,000,000: 19s. Last read position: 2:88,895,055
[2014-10-31 23:43] INFO 2014-10-31 23:43:38 AddOrReplaceReadGroups Processed 93,000,000 records. Elapsed time: 00:29:54s. Time for last 1,000,000: 19s. Last read position: 2:112,630,902
[2014-10-31 23:43] INFO 2014-10-31 23:43:58 AddOrReplaceReadGroups Processed 94,000,000 records. Elapsed time: 00:30:14s. Time for last 1,000,000: 19s. Last read position: 2:159,396,562
[2014-10-31 23:44] INFO 2014-10-31 23:44:17 AddOrReplaceReadGroups Processed 95,000,000 records. Elapsed time: 00:30:33s. Time for last 1,000,000: 19s. Last read position: 2:188,407,687
[2014-10-31 23:44] INFO 2014-10-31 23:44:36 AddOrReplaceReadGroups Processed 96,000,000 records. Elapsed time: 00:30:52s. Time for last 1,000,000: 19s. Last read position: 2:209,221,700
[2014-10-31 23:44] INFO 2014-10-31 23:44:55 AddOrReplaceReadGroups Processed 97,000,000 records. Elapsed time: 00:31:11s. Time for last 1,000,000: 18s. Last read position: 2:219,139,832
[2014-10-31 23:45] INFO 2014-10-31 23:45:14 AddOrReplaceReadGroups Processed 98,000,000 records. Elapsed time: 00:31:29s. Time for last 1,000,000: 18s. Last read position: 2:234,379,899
[2014-10-31 23:45] INFO 2014-10-31 23:45:34 AddOrReplaceReadGroups Processed 99,000,000 records. Elapsed time: 00:31:49s. Time for last 1,000,000: 19s. Last read position: 20:3,911,618
[2014-10-31 23:45] INFO 2014-10-31 23:45:53 AddOrReplaceReadGroups Processed 100,000,000 records. Elapsed time: 00:32:08s. Time for last 1,000,000: 19s. Last read position: 20:31,437,026
[2014-10-31 23:46] INFO 2014-10-31 23:46:12 AddOrReplaceReadGroups Processed 101,000,000 records. Elapsed time: 00:32:28s. Time for last 1,000,000: 19s. Last read position: 20:39,752,923
[2014-10-31 23:46] INFO 2014-10-31 23:46:32 AddOrReplaceReadGroups Processed 102,000,000 records. Elapsed time: 00:32:47s. Time for last 1,000,000: 19s. Last read position: 20:54,945,004
[2014-10-31 23:46] INFO 2014-10-31 23:46:51 AddOrReplaceReadGroups Processed 103,000,000 records. Elapsed time: 00:33:07s. Time for last 1,000,000: 19s. Last read position: 21:18,985,925
[2014-10-31 23:47] INFO 2014-10-31 23:47:11 AddOrReplaceReadGroups Processed 104,000,000 records. Elapsed time: 00:33:27s. Time for last 1,000,000: 19s. Last read position: 21:44,289,283
[2014-10-31 23:47] INFO 2014-10-31 23:47:31 AddOrReplaceReadGroups Processed 105,000,000 records. Elapsed time: 00:33:47s. Time for last 1,000,000: 19s. Last read position: 22:21,141,489
[2014-10-31 23:47] INFO 2014-10-31 23:47:49 AddOrReplaceReadGroups Processed 106,000,000 records. Elapsed time: 00:34:05s. Time for last 1,000,000: 18s. Last read position: 22:26,895,541
[2014-10-31 23:48] INFO 2014-10-31 23:48:09 AddOrReplaceReadGroups Processed 107,000,000 records. Elapsed time: 00:34:25s. Time for last 1,000,000: 19s. Last read position: 22:38,692,401
[2014-10-31 23:48] INFO 2014-10-31 23:48:28 AddOrReplaceReadGroups Processed 108,000,000 records. Elapsed time: 00:34:44s. Time for last 1,000,000: 19s. Last read position: 22:42,904,708
[2014-10-31 23:48] INFO 2014-10-31 23:48:48 AddOrReplaceReadGroups Processed 109,000,000 records. Elapsed time: 00:35:04s. Time for last 1,000,000: 19s. Last read position: 3:12,880,976
[2014-10-31 23:49] INFO 2014-10-31 23:49:07 AddOrReplaceReadGroups Processed 110,000,000 records. Elapsed time: 00:35:23s. Time for last 1,000,000: 19s. Last read position: 3:33,908,236
[2014-10-31 23:49] INFO 2014-10-31 23:49:26 AddOrReplaceReadGroups Processed 111,000,000 records. Elapsed time: 00:35:42s. Time for last 1,000,000: 19s. Last read position: 3:47,049,532
[2014-10-31 23:49] INFO 2014-10-31 23:49:46 AddOrReplaceReadGroups Processed 112,000,000 records. Elapsed time: 00:36:02s. Time for last 1,000,000: 19s. Last read position: 3:52,029,058
[2014-10-31 23:50] INFO 2014-10-31 23:50:06 AddOrReplaceReadGroups Processed 113,000,000 records. Elapsed time: 00:36:21s. Time for last 1,000,000: 19s. Last read position: 3:100,292,102
[2014-10-31 23:50] INFO 2014-10-31 23:50:26 AddOrReplaceReadGroups Processed 114,000,000 records. Elapsed time: 00:36:41s. Time for last 1,000,000: 19s. Last read position: 3:128,200,671
[2014-10-31 23:50] INFO 2014-10-31 23:50:45 AddOrReplaceReadGroups Processed 115,000,000 records. Elapsed time: 00:37:00s. Time for last 1,000,000: 19s. Last read position: 3:149,093,320
[2014-10-31 23:51] INFO 2014-10-31 23:51:04 AddOrReplaceReadGroups Processed 116,000,000 records. Elapsed time: 00:37:20s. Time for last 1,000,000: 19s. Last read position: 3:183,898,667
[2014-10-31 23:51] INFO 2014-10-31 23:51:23 AddOrReplaceReadGroups Processed 117,000,000 records. Elapsed time: 00:37:39s. Time for last 1,000,000: 18s. Last read position: 3:196,731,002
[2014-10-31 23:51] INFO 2014-10-31 23:51:43 AddOrReplaceReadGroups Processed 118,000,000 records. Elapsed time: 00:37:59s. Time for last 1,000,000: 19s. Last read position: 4:25,363,554
[2014-10-31 23:52] INFO 2014-10-31 23:52:03 AddOrReplaceReadGroups Processed 119,000,000 records. Elapsed time: 00:38:18s. Time for last 1,000,000: 19s. Last read position: 4:71,846,530
[2014-10-31 23:52] INFO 2014-10-31 23:52:22 AddOrReplaceReadGroups Processed 120,000,000 records. Elapsed time: 00:38:38s. Time for last 1,000,000: 19s. Last read position: 4:89,688,725
[2014-10-31 23:52] INFO 2014-10-31 23:52:42 AddOrReplaceReadGroups Processed 121,000,000 records. Elapsed time: 00:38:57s. Time for last 1,000,000: 19s. Last read position: 4:140,281,017
[2014-10-31 23:53] INFO 2014-10-31 23:53:01 AddOrReplaceReadGroups Processed 122,000,000 records. Elapsed time: 00:39:17s. Time for last 1,000,000: 19s. Last read position: 4:187,519,216
[2014-10-31 23:53] INFO 2014-10-31 23:53:21 AddOrReplaceReadGroups Processed 123,000,000 records. Elapsed time: 00:39:37s. Time for last 1,000,000: 19s. Last read position: 5:36,871,831
[2014-10-31 23:53] INFO 2014-10-31 23:53:40 AddOrReplaceReadGroups Processed 124,000,000 records. Elapsed time: 00:39:56s. Time for last 1,000,000: 19s. Last read position: 5:61,684,730
[2014-10-31 23:54] INFO 2014-10-31 23:54:00 AddOrReplaceReadGroups Processed 125,000,000 records. Elapsed time: 00:40:15s. Time for last 1,000,000: 19s. Last read position: 5:78,622,906
[2014-10-31 23:54] INFO 2014-10-31 23:54:19 AddOrReplaceReadGroups Processed 126,000,000 records. Elapsed time: 00:40:35s. Time for last 1,000,000: 19s. Last read position: 5:118,175,443
[2014-10-31 23:54] INFO 2014-10-31 23:54:39 AddOrReplaceReadGroups Processed 127,000,000 records. Elapsed time: 00:40:55s. Time for last 1,000,000: 19s. Last read position: 5:137,894,318
[2014-10-31 23:54] INFO 2014-10-31 23:54:59 AddOrReplaceReadGroups Processed 128,000,000 records. Elapsed time: 00:41:14s. Time for last 1,000,000: 19s. Last read position: 5:151,041,225
[2014-10-31 23:55] INFO 2014-10-31 23:55:18 AddOrReplaceReadGroups Processed 129,000,000 records. Elapsed time: 00:41:34s. Time for last 1,000,000: 19s. Last read position: 5:175,824,645
[2014-10-31 23:55] INFO 2014-10-31 23:55:37 AddOrReplaceReadGroups Processed 130,000,000 records. Elapsed time: 00:41:53s. Time for last 1,000,000: 19s. Last read position: 6:2,949,231
[2014-10-31 23:55] INFO 2014-10-31 23:55:57 AddOrReplaceReadGroups Processed 131,000,000 records. Elapsed time: 00:42:12s. Time for last 1,000,000: 19s. Last read position: 6:26,546,267
[2014-10-31 23:56] INFO 2014-10-31 23:56:16 AddOrReplaceReadGroups Processed 132,000,000 records. Elapsed time: 00:42:32s. Time for last 1,000,000: 19s. Last read position: 6:31,601,287
[2014-10-31 23:56] INFO 2014-10-31 23:56:35 AddOrReplaceReadGroups Processed 133,000,000 records. Elapsed time: 00:42:50s. Time for last 1,000,000: 18s. Last read position: 6:33,258,798
[2014-10-31 23:56] INFO 2014-10-31 23:56:54 AddOrReplaceReadGroups Processed 134,000,000 records. Elapsed time: 00:43:09s. Time for last 1,000,000: 19s. Last read position: 6:41,566,808
[2014-10-31 23:57] INFO 2014-10-31 23:57:13 AddOrReplaceReadGroups Processed 135,000,000 records. Elapsed time: 00:43:29s. Time for last 1,000,000: 19s. Last read position: 6:52,366,708
[2014-10-31 23:57] INFO 2014-10-31 23:57:30 AddOrReplaceReadGroups Processed 136,000,000 records. Elapsed time: 00:43:45s. Time for last 1,000,000: 16s. Last read position: 6:74,227,769
[2014-10-31 23:57] INFO 2014-10-31 23:57:47 AddOrReplaceReadGroups Processed 137,000,000 records. Elapsed time: 00:44:02s. Time for last 1,000,000: 17s. Last read position: 6:74,228,490
[2014-10-31 23:58] INFO 2014-10-31 23:58:04 AddOrReplaceReadGroups Processed 138,000,000 records. Elapsed time: 00:44:20s. Time for last 1,000,000: 17s. Last read position: 6:75,796,188
[2014-10-31 23:58] INFO 2014-10-31 23:58:24 AddOrReplaceReadGroups Processed 139,000,000 records. Elapsed time: 00:44:40s. Time for last 1,000,000: 19s. Last read position: 6:119,509,363
[2014-10-31 23:58] INFO 2014-10-31 23:58:44 AddOrReplaceReadGroups Processed 140,000,000 records. Elapsed time: 00:45:00s. Time for last 1,000,000: 19s. Last read position: 6:157,527,495
[2014-10-31 23:59] INFO 2014-10-31 23:59:04 AddOrReplaceReadGroups Processed 141,000,000 records. Elapsed time: 00:45:20s. Time for last 1,000,000: 19s. Last read position: 7:5,567,076
[2014-10-31 23:59] INFO 2014-10-31 23:59:23 AddOrReplaceReadGroups Processed 142,000,000 records. Elapsed time: 00:45:38s. Time for last 1,000,000: 18s. Last read position: 7:22,550,482
[2014-10-31 23:59] INFO 2014-10-31 23:59:42 AddOrReplaceReadGroups Processed 143,000,000 records. Elapsed time: 00:45:57s. Time for last 1,000,000: 19s. Last read position: 7:33,045,603
[2014-11-01 00:00] INFO 2014-11-01 00:00:01 AddOrReplaceReadGroups Processed 144,000,000 records. Elapsed time: 00:46:17s. Time for last 1,000,000: 19s. Last read position: 7:50,470,657
[2014-11-01 00:00] INFO 2014-11-01 00:00:21 AddOrReplaceReadGroups Processed 145,000,000 records. Elapsed time: 00:46:36s. Time for last 1,000,000: 19s. Last read position: 7:74,608,692
[2014-11-01 00:00] INFO 2014-11-01 00:00:40 AddOrReplaceReadGroups Processed 146,000,000 records. Elapsed time: 00:46:56s. Time for last 1,000,000: 19s. Last read position: 7:98,652,276
[2014-11-01 00:01] INFO 2014-11-01 00:01:00 AddOrReplaceReadGroups Processed 147,000,000 records. Elapsed time: 00:47:16s. Time for last 1,000,000: 19s. Last read position: 7:105,738,211
[2014-11-01 00:01] INFO 2014-11-01 00:01:20 AddOrReplaceReadGroups Processed 148,000,000 records. Elapsed time: 00:47:35s. Time for last 1,000,000: 19s. Last read position: 7:134,132,108
[2014-11-01 00:01] INFO 2014-11-01 00:01:38 AddOrReplaceReadGroups Processed 149,000,000 records. Elapsed time: 00:47:53s. Time for last 1,000,000: 18s. Last read position: 7:155,098,838
[2014-11-01 00:01] INFO 2014-11-01 00:01:58 AddOrReplaceReadGroups Processed 150,000,000 records. Elapsed time: 00:48:13s. Time for last 1,000,000: 19s. Last read position: 8:26,224,243
[2014-11-01 00:02] INFO 2014-11-01 00:02:17 AddOrReplaceReadGroups Processed 151,000,000 records. Elapsed time: 00:48:33s. Time for last 1,000,000: 19s. Last read position: 8:54,692,580
[2014-11-01 00:02] INFO 2014-11-01 00:02:36 AddOrReplaceReadGroups Processed 152,000,000 records. Elapsed time: 00:48:52s. Time for last 1,000,000: 19s. Last read position: 8:90,731,341
[2014-11-01 00:02] INFO 2014-11-01 00:02:55 AddOrReplaceReadGroups Processed 153,000,000 records. Elapsed time: 00:49:11s. Time for last 1,000,000: 19s. Last read position: 8:103,855,924
[2014-11-01 00:03] INFO 2014-11-01 00:03:15 AddOrReplaceReadGroups Processed 154,000,000 records. Elapsed time: 00:49:31s. Time for last 1,000,000: 19s. Last read position: 8:144,806,730
[2014-11-01 00:03] INFO 2014-11-01 00:03:34 AddOrReplaceReadGroups Processed 155,000,000 records. Elapsed time: 00:49:50s. Time for last 1,000,000: 19s. Last read position: 9:19,378,707
[2014-11-01 00:03] INFO 2014-11-01 00:03:54 AddOrReplaceReadGroups Processed 156,000,000 records. Elapsed time: 00:50:10s. Time for last 1,000,000: 19s. Last read position: 9:69,231,082
[2014-11-01 00:04] INFO 2014-11-01 00:04:14 AddOrReplaceReadGroups Processed 157,000,000 records. Elapsed time: 00:50:30s. Time for last 1,000,000: 19s. Last read position: 9:100,767,284
[2014-11-01 00:04] INFO 2014-11-01 00:04:34 AddOrReplaceReadGroups Processed 158,000,000 records. Elapsed time: 00:50:50s. Time for last 1,000,000: 19s. Last read position: 9:125,086,095
[2014-11-01 00:04] INFO 2014-11-01 00:04:53 AddOrReplaceReadGroups Processed 159,000,000 records. Elapsed time: 00:51:09s. Time for last 1,000,000: 18s. Last read position: 9:131,582,667
[2014-11-01 00:05] INFO 2014-11-01 00:05:11 AddOrReplaceReadGroups Processed 160,000,000 records. Elapsed time: 00:51:27s. Time for last 1,000,000: 18s. Last read position: 9:135,896,182
[2014-11-01 00:05] INFO 2014-11-01 00:05:30 AddOrReplaceReadGroups Processed 161,000,000 records. Elapsed time: 00:51:45s. Time for last 1,000,000: 18s. Last read position: 9:139,757,774
[2014-11-01 00:05] INFO 2014-11-01 00:05:48 AddOrReplaceReadGroups Processed 162,000,000 records. Elapsed time: 00:52:03s. Time for last 1,000,000: 17s. Last read position: GL000220.1:109,603
[2014-11-01 00:06] INFO 2014-11-01 00:06:05 AddOrReplaceReadGroups Processed 163,000,000 records. Elapsed time: 00:52:20s. Time for last 1,000,000: 16s. Last read position: GL000220.1:110,377
[2014-11-01 00:06] INFO 2014-11-01 00:06:22 AddOrReplaceReadGroups Processed 164,000,000 records. Elapsed time: 00:52:37s. Time for last 1,000,000: 17s. Last read position: GL000220.1:114,995
[2014-11-01 00:06] INFO 2014-11-01 00:06:39 AddOrReplaceReadGroups Processed 165,000,000 records. Elapsed time: 00:52:55s. Time for last 1,000,000: 17s. Last read position: GL000220.1:117,056
[2014-11-01 00:06] INFO 2014-11-01 00:06:57 AddOrReplaceReadGroups Processed 166,000,000 records. Elapsed time: 00:53:12s. Time for last 1,000,000: 17s. Last read position: GL000220.1:117,702
[2014-11-01 00:07] INFO 2014-11-01 00:07:14 AddOrReplaceReadGroups Processed 167,000,000 records. Elapsed time: 00:53:30s. Time for last 1,000,000: 17s. Last read position: MT:933
[2014-11-01 00:07] INFO 2014-11-01 00:07:32 AddOrReplaceReadGroups Processed 168,000,000 records. Elapsed time: 00:53:48s. Time for last 1,000,000: 17s. Last read position: MT:2,408
[2014-11-01 00:07] INFO 2014-11-01 00:07:50 AddOrReplaceReadGroups Processed 169,000,000 records. Elapsed time: 00:54:06s. Time for last 1,000,000: 18s. Last read position: MT:3,909
[2014-11-01 00:08] INFO 2014-11-01 00:08:08 AddOrReplaceReadGroups Processed 170,000,000 records. Elapsed time: 00:54:24s. Time for last 1,000,000: 17s. Last read position: MT:6,024
[2014-11-01 00:08] INFO 2014-11-01 00:08:23 AddOrReplaceReadGroups Processed 171,000,000 records. Elapsed time: 00:54:39s. Time for last 1,000,000: 15s. Last read position: MT:6,568
[2014-11-01 00:08] INFO 2014-11-01 00:08:41 AddOrReplaceReadGroups Processed 172,000,000 records. Elapsed time: 00:54:56s. Time for last 1,000,000: 17s. Last read position: MT:6,971
[2014-11-01 00:08] INFO 2014-11-01 00:08:58 AddOrReplaceReadGroups Processed 173,000,000 records. Elapsed time: 00:55:14s. Time for last 1,000,000: 17s. Last read position: MT:7,673
[2014-11-01 00:09] INFO 2014-11-01 00:09:16 AddOrReplaceReadGroups Processed 174,000,000 records. Elapsed time: 00:55:32s. Time for last 1,000,000: 17s. Last read position: MT:8,165
[2014-11-01 00:09] INFO 2014-11-01 00:09:34 AddOrReplaceReadGroups Processed 175,000,000 records. Elapsed time: 00:55:50s. Time for last 1,000,000: 17s. Last read position: MT:9,237
[2014-11-01 00:09] INFO 2014-11-01 00:09:52 AddOrReplaceReadGroups Processed 176,000,000 records. Elapsed time: 00:56:08s. Time for last 1,000,000: 17s. Last read position: MT:10,152
[2014-11-01 00:10] INFO 2014-11-01 00:10:10 AddOrReplaceReadGroups Processed 177,000,000 records. Elapsed time: 00:56:26s. Time for last 1,000,000: 18s. Last read position: MT:11,477
[2014-11-01 00:10] INFO 2014-11-01 00:10:28 AddOrReplaceReadGroups Processed 178,000,000 records. Elapsed time: 00:56:44s. Time for last 1,000,000: 18s. Last read position: MT:12,789
[2014-11-01 00:10] INFO 2014-11-01 00:10:46 AddOrReplaceReadGroups Processed 179,000,000 records. Elapsed time: 00:57:02s. Time for last 1,000,000: 18s. Last read position: MT:15,234
[2014-11-01 00:11] INFO 2014-11-01 00:11:05 AddOrReplaceReadGroups Processed 180,000,000 records. Elapsed time: 00:57:20s. Time for last 1,000,000: 18s. Last read position: X:18,651,952
[2014-11-01 00:11] INFO 2014-11-01 00:11:24 AddOrReplaceReadGroups Processed 181,000,000 records. Elapsed time: 00:57:40s. Time for last 1,000,000: 19s. Last read position: X:49,104,942
[2014-11-01 00:11] INFO 2014-11-01 00:11:42 AddOrReplaceReadGroups Processed 182,000,000 records. Elapsed time: 00:57:57s. Time for last 1,000,000: 17s. Last read position: X:70,767,688
[2014-11-01 00:12] INFO 2014-11-01 00:12:00 AddOrReplaceReadGroups Processed 183,000,000 records. Elapsed time: 00:58:16s. Time for last 1,000,000: 18s. Last read position: X:100,654,704
[2014-11-01 00:12] INFO 2014-11-01 00:12:19 AddOrReplaceReadGroups Processed 184,000,000 records. Elapsed time: 00:58:35s. Time for last 1,000,000: 18s. Last read position: X:131,209,757
[2014-11-01 00:12] INFO 2014-11-01 00:12:38 AddOrReplaceReadGroups Processed 185,000,000 records. Elapsed time: 00:58:53s. Time for last 1,000,000: 18s. Last read position: X:153,628,809
[2014-11-01 00:12] INFO 2014-11-01 00:12:57 AddOrReplaceReadGroups Processed 186,000,000 records. Elapsed time: 00:59:12s. Time for last 1,000,000: 18s. Last read position: */*
[2014-11-01 00:13] INFO 2014-11-01 00:13:16 AddOrReplaceReadGroups Processed 187,000,000 records. Elapsed time: 00:59:31s. Time for last 1,000,000: 19s. Last read position: */*
[2014-11-01 00:13] INFO 2014-11-01 00:13:35 AddOrReplaceReadGroups Processed 188,000,000 records. Elapsed time: 00:59:50s. Time for last 1,000,000: 18s. Last read position: */*
[2014-11-01 00:13] INFO 2014-11-01 00:13:54 AddOrReplaceReadGroups Processed 189,000,000 records. Elapsed time: 01:00:10s. Time for last 1,000,000: 19s. Last read position: */*
[2014-11-01 00:14] INFO 2014-11-01 00:14:13 AddOrReplaceReadGroups Processed 190,000,000 records. Elapsed time: 01:00:29s. Time for last 1,000,000: 19s. Last read position: */*
[2014-11-01 00:14] INFO 2014-11-01 00:14:32 AddOrReplaceReadGroups Processed 191,000,000 records. Elapsed time: 01:00:48s. Time for last 1,000,000: 18s. Last read position: */*
[2014-11-01 00:14] INFO 2014-11-01 00:14:51 AddOrReplaceReadGroups Processed 192,000,000 records. Elapsed time: 01:01:07s. Time for last 1,000,000: 19s. Last read position: */*
[2014-11-01 00:15] INFO 2014-11-01 00:15:10 AddOrReplaceReadGroups Processed 193,000,000 records. Elapsed time: 01:01:25s. Time for last 1,000,000: 18s. Last read position: */*
[2014-11-01 00:15] INFO 2014-11-01 00:15:28 AddOrReplaceReadGroups Processed 194,000,000 records. Elapsed time: 01:01:44s. Time for last 1,000,000: 18s. Last read position: */*
[2014-11-01 00:15] INFO 2014-11-01 00:15:48 AddOrReplaceReadGroups Processed 195,000,000 records. Elapsed time: 01:02:03s. Time for last 1,000,000: 19s. Last read position: */*
[2014-11-01 00:16] INFO 2014-11-01 00:16:07 AddOrReplaceReadGroups Processed 196,000,000 records. Elapsed time: 01:02:22s. Time for last 1,000,000: 19s. Last read position: */*
[2014-11-01 00:16] INFO 2014-11-01 00:16:26 AddOrReplaceReadGroups Processed 197,000,000 records. Elapsed time: 01:02:42s. Time for last 1,000,000: 19s. Last read position: */*
[2014-11-01 00:16] [Sat Nov 01 00:16:34 UTC 2014] net.sf.picard.sam.AddOrReplaceReadGroups done. Elapsed time: 62.84 minutes.
[2014-11-01 00:16] Runtime.totalMemory()=760217600
[2014-11-01 00:16] Sort BAM file (multi core, queryname): merged-fixrgs.bam to merged-fixrgs.nsorted.bam
[2014-11-01 00:49] [bam_sort_core] merging from 85 files...
[2014-11-01 02:47] Sort BAM file (multi core, coordinate): merged_fixed.bam to merged_fixed.sorted.bam
[2014-11-01 03:10] [bam_sort_core] merging from 83 files...
[2014-11-01 03:59] Picard ReorderSam
[2014-11-01 03:59] [Sat Nov 01 03:59:45 UTC 2014] net.sf.picard.sam.ReorderSam INPUT=/vagrant_data/seqc-test/seqc/work/align/UHRR_rep1/1_2014-10-08_seqc_tophat/accepted_hits.sam OUTPUT=/vagrant_data/seqc-test/seqc/work/align/UHRR_rep1/1_2014-10-08_seqc_tophat/tx/tmp4mz83f/accepted_hits.picard.bam REFERENCE=/usr/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa ALLOW_INCOMPLETE_DICT_CONCORDANCE=true TMP_DIR=[/vagrant_data/seqc-test/seqc/work/tx/tmpg1yfkW] VALIDATION_STRINGENCY=SILENT ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[2014-11-01 03:59] [Sat Nov 01 03:59:45 UTC 2014] Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_67-b01; Picard version: 1.96(1510)
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SAM/BAM file
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n1249250621
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n10135534747
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n11135006516
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n12133851895
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n13115169878
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n14107349540
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n15102531392
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n1690354753
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n1781195210
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n1878077248
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n1959128983
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n2243199373
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n2063025520
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n2148129895
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n2251304566
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n3198022430
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n4191154276
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n5180915260
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n6171115067
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n7159138663
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n8146364022
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n9141213431
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000191.1106433
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000192.1547496
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000193.1189789
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000194.1191469
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000195.1182896
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000196.138914
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000197.137175
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000198.190085
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000199.1169874
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000200.1187035
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000201.136148
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000202.140103
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000203.137498
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000204.181310
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000205.1174588
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000206.141001
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000207.14262
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000208.192689
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000209.1159169
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000210.127682
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000211.1166566
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000212.1186858
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000213.1164239
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000214.1137718
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000215.1172545
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000216.1172294
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000217.1172149
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000218.1161147
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000219.1179198
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000220.1161802
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000221.1155397
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000222.1186861
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000223.1180455
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000224.1179693
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000225.1211173
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000226.115008
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000227.1128374
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000228.1129120
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000229.119913
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000230.143691
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000231.127386
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000232.140652
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000233.145941
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000234.140531
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000235.134474
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000236.141934
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000237.145867
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000238.139939
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000239.133824
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000240.141933
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000241.142152
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000242.143523
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000243.143341
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000244.139929
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000245.136651
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000246.138154
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000247.136422
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000248.139786
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000249.138502
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nMT16569
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nX155270560
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nY59373566
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reference
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n1249250621
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n2243199373
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n3198022430
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n4191154276
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n5180915260
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n6171115067
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n7159138663
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n8146364022
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n9141213431
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n10135534747
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n11135006516
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n12133851895
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n13115169878
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n14107349540
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n15102531392
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n1690354753
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n1781195210
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n1878077248
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n1959128983
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n2063025520
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n2148129895
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%n2251304566
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nX155270560
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nY59373566
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nMT16569
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000207.14262
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000226.115008
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000229.119913
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000231.127386
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000210.127682
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000239.133824
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000235.134474
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000201.136148
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000247.136422
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000245.136651
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000197.137175
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000203.137498
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000246.138154
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000249.138502
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000196.138914
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000248.139786
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000244.139929
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000238.139939
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000202.140103
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000234.140531
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000232.140652
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000206.141001
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000240.141933
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000236.141934
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000241.142152
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000243.143341
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000242.143523
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000230.143691
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000237.145867
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000233.145941
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000204.181310
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000198.190085
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000208.192689
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000191.1106433
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000227.1128374
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000228.1129120
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000214.1137718
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000221.1155397
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000209.1159169
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000218.1161147
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000220.1161802
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000213.1164239
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000211.1166566
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000199.1169874
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000217.1172149
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000216.1172294
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000215.1172545
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000205.1174588
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000219.1179198
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000224.1179693
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000223.1180455
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000195.1182896
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000212.1186858
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000222.1186861
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000200.1187035
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000193.1189789
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000194.1191469
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000225.1211173
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam SN=%s LN=%d%nGL000192.1547496
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering SAM/BAM file:
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 1 [index=0] to => ref contig 1 [index=0]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 2 [index=11] to => ref contig 2 [index=1]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 3 [index=15] to => ref contig 3 [index=2]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 4 [index=16] to => ref contig 4 [index=3]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 5 [index=17] to => ref contig 5 [index=4]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 6 [index=18] to => ref contig 6 [index=5]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 7 [index=19] to => ref contig 7 [index=6]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 8 [index=20] to => ref contig 8 [index=7]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 9 [index=21] to => ref contig 9 [index=8]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 10 [index=1] to => ref contig 10 [index=9]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 11 [index=2] to => ref contig 11 [index=10]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 12 [index=3] to => ref contig 12 [index=11]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 13 [index=4] to => ref contig 13 [index=12]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 14 [index=5] to => ref contig 14 [index=13]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 15 [index=6] to => ref contig 15 [index=14]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 16 [index=7] to => ref contig 16 [index=15]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 17 [index=8] to => ref contig 17 [index=16]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 18 [index=9] to => ref contig 18 [index=17]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 19 [index=10] to => ref contig 19 [index=18]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 20 [index=12] to => ref contig 20 [index=19]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 21 [index=13] to => ref contig 21 [index=20]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig 22 [index=14] to => ref contig 22 [index=21]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig X [index=82] to => ref contig X [index=22]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig Y [index=83] to => ref contig Y [index=23]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig MT [index=81] to => ref contig MT [index=24]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000207.1 [index=38] to => ref contig GL000207.1 [index=25]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000226.1 [index=57] to => ref contig GL000226.1 [index=26]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000229.1 [index=60] to => ref contig GL000229.1 [index=27]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000231.1 [index=62] to => ref contig GL000231.1 [index=28]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000210.1 [index=41] to => ref contig GL000210.1 [index=29]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000239.1 [index=70] to => ref contig GL000239.1 [index=30]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000235.1 [index=66] to => ref contig GL000235.1 [index=31]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000201.1 [index=32] to => ref contig GL000201.1 [index=32]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000247.1 [index=78] to => ref contig GL000247.1 [index=33]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000245.1 [index=76] to => ref contig GL000245.1 [index=34]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000197.1 [index=28] to => ref contig GL000197.1 [index=35]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000203.1 [index=34] to => ref contig GL000203.1 [index=36]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000246.1 [index=77] to => ref contig GL000246.1 [index=37]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000249.1 [index=80] to => ref contig GL000249.1 [index=38]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000196.1 [index=27] to => ref contig GL000196.1 [index=39]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000248.1 [index=79] to => ref contig GL000248.1 [index=40]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000244.1 [index=75] to => ref contig GL000244.1 [index=41]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000238.1 [index=69] to => ref contig GL000238.1 [index=42]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000202.1 [index=33] to => ref contig GL000202.1 [index=43]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000234.1 [index=65] to => ref contig GL000234.1 [index=44]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000232.1 [index=63] to => ref contig GL000232.1 [index=45]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000206.1 [index=37] to => ref contig GL000206.1 [index=46]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000240.1 [index=71] to => ref contig GL000240.1 [index=47]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000236.1 [index=67] to => ref contig GL000236.1 [index=48]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000241.1 [index=72] to => ref contig GL000241.1 [index=49]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000243.1 [index=74] to => ref contig GL000243.1 [index=50]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000242.1 [index=73] to => ref contig GL000242.1 [index=51]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000230.1 [index=61] to => ref contig GL000230.1 [index=52]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000237.1 [index=68] to => ref contig GL000237.1 [index=53]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000233.1 [index=64] to => ref contig GL000233.1 [index=54]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000204.1 [index=35] to => ref contig GL000204.1 [index=55]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000198.1 [index=29] to => ref contig GL000198.1 [index=56]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000208.1 [index=39] to => ref contig GL000208.1 [index=57]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000191.1 [index=22] to => ref contig GL000191.1 [index=58]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000227.1 [index=58] to => ref contig GL000227.1 [index=59]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000228.1 [index=59] to => ref contig GL000228.1 [index=60]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000214.1 [index=45] to => ref contig GL000214.1 [index=61]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000221.1 [index=52] to => ref contig GL000221.1 [index=62]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000209.1 [index=40] to => ref contig GL000209.1 [index=63]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000218.1 [index=49] to => ref contig GL000218.1 [index=64]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000220.1 [index=51] to => ref contig GL000220.1 [index=65]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000213.1 [index=44] to => ref contig GL000213.1 [index=66]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000211.1 [index=42] to => ref contig GL000211.1 [index=67]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000199.1 [index=30] to => ref contig GL000199.1 [index=68]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000217.1 [index=48] to => ref contig GL000217.1 [index=69]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000216.1 [index=47] to => ref contig GL000216.1 [index=70]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000215.1 [index=46] to => ref contig GL000215.1 [index=71]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000205.1 [index=36] to => ref contig GL000205.1 [index=72]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000219.1 [index=50] to => ref contig GL000219.1 [index=73]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000224.1 [index=55] to => ref contig GL000224.1 [index=74]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000223.1 [index=54] to => ref contig GL000223.1 [index=75]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000195.1 [index=26] to => ref contig GL000195.1 [index=76]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000212.1 [index=43] to => ref contig GL000212.1 [index=77]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000222.1 [index=53] to => ref contig GL000222.1 [index=78]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000200.1 [index=31] to => ref contig GL000200.1 [index=79]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000193.1 [index=24] to => ref contig GL000193.1 [index=80]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000194.1 [index=25] to => ref contig GL000194.1 [index=81]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000225.1 [index=56] to => ref contig GL000225.1 [index=82]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000192.1 [index=23] to => ref contig GL000192.1 [index=83]
[2014-11-01 03:59]
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Writing reads...
[2014-11-01 03:59] INFO 2014-11-01 03:59:45 ReorderSam Processing All reads
[2014-11-01 04:07] [Sat Nov 01 04:07:06 UTC 2014] net.sf.picard.sam.ReorderSam done. Elapsed time: 7.35 minutes.
[2014-11-01 04:07] Runtime.totalMemory()=1468911616
[2014-11-01 04:07] To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
[2014-11-01 04:07] Exception in thread "main" java.lang.RuntimeException: Mismatch between read length and quals length writing read SRR950078.72351183; read length: 55; quals length: 101
[2014-11-01 04:07] at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:143)
[2014-11-01 04:07] at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:37)
[2014-11-01 04:07] at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:210)
[2014-11-01 04:07] at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:150)
[2014-11-01 04:07] at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:170)
[2014-11-01 04:07] at net.sf.picard.sam.ReorderSam.writeReads(ReorderSam.java:172)
[2014-11-01 04:07] at net.sf.picard.sam.ReorderSam.doWork(ReorderSam.java:119)
[2014-11-01 04:07] at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
[2014-11-01 04:07] at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
[2014-11-01 04:07] at net.sf.picard.sam.ReorderSam.main(ReorderSam.java:77)
[2014-11-01 04:07] Uncaught exception occurred
Traceback (most recent call last):
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 20, in run
_do_run(cmd, checks, log_stdout)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 93, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'java -Xms750m -Xmx3500m -XX:+UseSerialGC -jar /usr/local/share/java/picard/ReorderSam.jar INPUT=/vagrant_data/seqc-test/seqc/work/align/UHRR_rep1/1_2014-10-08_seqc_tophat/accepted_hits.sam OUTPUT=/vagrant_data/seqc-test/seqc/work/align/UHRR_rep1/1_2014-10-08_seqc_tophat/tx/tmp4mz83f/accepted_hits.picard.bam REFERENCE=/usr/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa ALLOW_INCOMPLETE_DICT_CONCORDANCE=true TMP_DIR=/vagrant_data/seqc-test/seqc/work/tx/tmpg1yfkW VALIDATION_STRINGENCY=SILENT
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000238.1 [index=69] to => ref contig GL000238.1 [index=42]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000202.1 [index=33] to => ref contig GL000202.1 [index=43]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000234.1 [index=65] to => ref contig GL000234.1 [index=44]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000232.1 [index=63] to => ref contig GL000232.1 [index=45]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000206.1 [index=37] to => ref contig GL000206.1 [index=46]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000240.1 [index=71] to => ref contig GL000240.1 [index=47]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000236.1 [index=67] to => ref contig GL000236.1 [index=48]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000241.1 [index=72] to => ref contig GL000241.1 [index=49]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000243.1 [index=74] to => ref contig GL000243.1 [index=50]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000242.1 [index=73] to => ref contig GL000242.1 [index=51]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000230.1 [index=61] to => ref contig GL000230.1 [index=52]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000237.1 [index=68] to => ref contig GL000237.1 [index=53]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000233.1 [index=64] to => ref contig GL000233.1 [index=54]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000204.1 [index=35] to => ref contig GL000204.1 [index=55]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000198.1 [index=29] to => ref contig GL000198.1 [index=56]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000208.1 [index=39] to => ref contig GL000208.1 [index=57]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000191.1 [index=22] to => ref contig GL000191.1 [index=58]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000227.1 [index=58] to => ref contig GL000227.1 [index=59]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000228.1 [index=59] to => ref contig GL000228.1 [index=60]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000214.1 [index=45] to => ref contig GL000214.1 [index=61]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000221.1 [index=52] to => ref contig GL000221.1 [index=62]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000209.1 [index=40] to => ref contig GL000209.1 [index=63]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000218.1 [index=49] to => ref contig GL000218.1 [index=64]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000220.1 [index=51] to => ref contig GL000220.1 [index=65]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000213.1 [index=44] to => ref contig GL000213.1 [index=66]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000211.1 [index=42] to => ref contig GL000211.1 [index=67]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000199.1 [index=30] to => ref contig GL000199.1 [index=68]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000217.1 [index=48] to => ref contig GL000217.1 [index=69]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000216.1 [index=47] to => ref contig GL000216.1 [index=70]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000215.1 [index=46] to => ref contig GL000215.1 [index=71]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000205.1 [index=36] to => ref contig GL000205.1 [index=72]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000219.1 [index=50] to => ref contig GL000219.1 [index=73]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000224.1 [index=55] to => ref contig GL000224.1 [index=74]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000223.1 [index=54] to => ref contig GL000223.1 [index=75]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000195.1 [index=26] to => ref contig GL000195.1 [index=76]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000212.1 [index=43] to => ref contig GL000212.1 [index=77]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000222.1 [index=53] to => ref contig GL000222.1 [index=78]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000200.1 [index=31] to => ref contig GL000200.1 [index=79]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000193.1 [index=24] to => ref contig GL000193.1 [index=80]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000194.1 [index=25] to => ref contig GL000194.1 [index=81]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000225.1 [index=56] to => ref contig GL000225.1 [index=82]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000192.1 [index=23] to => ref contig GL000192.1 [index=83]
INFO 2014-11-01 03:59:45 ReorderSam Writing reads...
INFO 2014-11-01 03:59:45 ReorderSam Processing All reads
[Sat Nov 01 04:07:06 UTC 2014] net.sf.picard.sam.ReorderSam done. Elapsed time: 7.35 minutes.
Runtime.totalMemory()=1468911616
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.RuntimeException: Mismatch between read length and quals length writing read SRR950078.72351183; read length: 55; quals length: 101
at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:143)
at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:37)
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:210)
at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:150)
at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:170)
at net.sf.picard.sam.ReorderSam.writeReads(ReorderSam.java:172)
at net.sf.picard.sam.ReorderSam.doWork(ReorderSam.java:119)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
at net.sf.picard.sam.ReorderSam.main(ReorderSam.java:77)
' returned non-zero exit status 1
Traceback (most recent call last):
File "/usr/local/bin/bcbio_nextgen.py", line 216, in <module>
main(**kwargs)
File "/usr/local/bin/bcbio_nextgen.py", line 42, in main
run_main(**kwargs)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 36, in run_main
fc_dir, run_info_yaml)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 82, in _run_toplevel
for xs in pipeline.run(config, config_file, parallel, dirs, pipeline_items):
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 304, in run
samples = run_parallel("process_alignment", samples)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 84, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 653, in __call__
self.dispatch(function, args, kwargs)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 400, in dispatch
job = ImmediateApply(func, args, kwargs)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 138, in __init__
self.results = func(*args, **kwargs)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 63, in wrapper
return apply(f, *args, **kwargs)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 27, in process_alignment
return sample.process_alignment(*args)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 104, in process_alignment
data = align_to_sort_bam(fastq1, fastq2, aligner, data)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 64, in align_to_sort_bam
names, align_dir, data)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 98, in _align_from_fastq
out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py", line 260, in align
align_dir, data, names)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py", line 162, in tophat_align
os.path.splitext(out_file)[0] + ".picard.bam")
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/broad/__init__.py", line 164, in run_fn
return fn(self, *args, **kwds)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/broad/picardrun.py", line 109, in picard_reorder
picard.run("ReorderSam", opts)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/broad/__init__.py", line 186, in run
do.run(cl, "Picard {0}".format(command), None)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 20, in run
_do_run(cmd, checks, log_stdout)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 93, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'java -Xms750m -Xmx3500m -XX:+UseSerialGC -jar /usr/local/share/java/picard/ReorderSam.jar INPUT=/vagrant_data/seqc-test/seqc/work/align/UHRR_rep1/1_2014-10-08_seqc_tophat/accepted_hits.sam OUTPUT=/vagrant_data/seqc-test/seqc/work/align/UHRR_rep1/1_2014-10-08_seqc_tophat/tx/tmp4mz83f/accepted_hits.picard.bam REFERENCE=/usr/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa ALLOW_INCOMPLETE_DICT_CONCORDANCE=true TMP_DIR=/vagrant_data/seqc-test/seqc/work/tx/tmpg1yfkW VALIDATION_STRINGENCY=SILENT
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000238.1 [index=69] to => ref contig GL000238.1 [index=42]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000202.1 [index=33] to => ref contig GL000202.1 [index=43]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000234.1 [index=65] to => ref contig GL000234.1 [index=44]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000232.1 [index=63] to => ref contig GL000232.1 [index=45]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000206.1 [index=37] to => ref contig GL000206.1 [index=46]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000240.1 [index=71] to => ref contig GL000240.1 [index=47]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000236.1 [index=67] to => ref contig GL000236.1 [index=48]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000241.1 [index=72] to => ref contig GL000241.1 [index=49]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000243.1 [index=74] to => ref contig GL000243.1 [index=50]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000242.1 [index=73] to => ref contig GL000242.1 [index=51]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000230.1 [index=61] to => ref contig GL000230.1 [index=52]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000237.1 [index=68] to => ref contig GL000237.1 [index=53]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000233.1 [index=64] to => ref contig GL000233.1 [index=54]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000204.1 [index=35] to => ref contig GL000204.1 [index=55]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000198.1 [index=29] to => ref contig GL000198.1 [index=56]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000208.1 [index=39] to => ref contig GL000208.1 [index=57]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000191.1 [index=22] to => ref contig GL000191.1 [index=58]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000227.1 [index=58] to => ref contig GL000227.1 [index=59]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000228.1 [index=59] to => ref contig GL000228.1 [index=60]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000214.1 [index=45] to => ref contig GL000214.1 [index=61]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000221.1 [index=52] to => ref contig GL000221.1 [index=62]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000209.1 [index=40] to => ref contig GL000209.1 [index=63]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000218.1 [index=49] to => ref contig GL000218.1 [index=64]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000220.1 [index=51] to => ref contig GL000220.1 [index=65]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000213.1 [index=44] to => ref contig GL000213.1 [index=66]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000211.1 [index=42] to => ref contig GL000211.1 [index=67]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000199.1 [index=30] to => ref contig GL000199.1 [index=68]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000217.1 [index=48] to => ref contig GL000217.1 [index=69]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000216.1 [index=47] to => ref contig GL000216.1 [index=70]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000215.1 [index=46] to => ref contig GL000215.1 [index=71]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000205.1 [index=36] to => ref contig GL000205.1 [index=72]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000219.1 [index=50] to => ref contig GL000219.1 [index=73]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000224.1 [index=55] to => ref contig GL000224.1 [index=74]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000223.1 [index=54] to => ref contig GL000223.1 [index=75]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000195.1 [index=26] to => ref contig GL000195.1 [index=76]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000212.1 [index=43] to => ref contig GL000212.1 [index=77]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000222.1 [index=53] to => ref contig GL000222.1 [index=78]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000200.1 [index=31] to => ref contig GL000200.1 [index=79]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000193.1 [index=24] to => ref contig GL000193.1 [index=80]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000194.1 [index=25] to => ref contig GL000194.1 [index=81]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000225.1 [index=56] to => ref contig GL000225.1 [index=82]
INFO 2014-11-01 03:59:45 ReorderSam Reordering read contig GL000192.1 [index=23] to => ref contig GL000192.1 [index=83]
INFO 2014-11-01 03:59:45 ReorderSam Writing reads...
INFO 2014-11-01 03:59:45 ReorderSam Processing All reads
[Sat Nov 01 04:07:06 UTC 2014] net.sf.picard.sam.ReorderSam done. Elapsed time: 7.35 minutes.
Runtime.totalMemory()=1468911616
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.RuntimeException: Mismatch between read length and quals length writing read SRR950078.72351183; read length: 55; quals length: 101
at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:143)
at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:37)
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:210)
at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:150)
at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:170)
at net.sf.picard.sam.ReorderSam.writeReads(ReorderSam.java:172)
at net.sf.picard.sam.ReorderSam.doWork(ReorderSam.java:119)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
at net.sf.picard.sam.ReorderSam.main(ReorderSam.java:77)
' returned non-zero exit status 1
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