(base) [beggsa@bear-pg-login06 54a1ddabf59b1bc07224e116ce2616]$ cat .command.err
INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
/usr/local/bin/redux: line 6: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
12:02:04.927 [main] [INFO ] Redux version 1.1.2
12:02:05.075 [main] [INFO ] output(./)
12:02:05.195 [main] [INFO ] loaded 80309 unmapping regions from unmap_regions.38.tsv
12:02:05.195 [main] [INFO ] duplicate logic: consensus
12:02:05.197 [main] [INFO ] sample(KN-01_TUMOUR) starting duplicate marking
12:02:05.419 [main] [DEBUG] BAM sampled max read-length(126)
12:02:06.289 [main] [INFO ] loaded 1544309 microsatellites regions
12:02:15.234 [main] [DEBUG] splitting 78190 unmapping regions across 12 threads
12:02:23.640 [Thread-6] [DEBUG] processed 10000 unmap regions, remaining(68190)
12:02:29.958 [Thread-11] [DEBUG] processed 20000 unmap regions, remaining(58190)
12:02:34.909 [Thread-5] [DEBUG] processed 30000 unmap regions, remaining(48190)
12:02:39.551 [Thread-4] [DEBUG] processed 40000 unmap regions, remaining(38190)
12:02:43.843 [Thread-7] [DEBUG] processed 50000 unmap regions, remaining(28190)
12:02:47.842 [Thread-3] [DEBUG] processed 60000 unmap regions, remaining(18190)
12:02:52.556 [Thread-1] [DEBUG] processed 70000 unmap regions, remaining(8190)
12:03:00.388 [Thread-1] [DEBUG] extracted 173916 fully-unmapped reads
12:03:01.016 [main] [DEBUG] initial unmapping complete
12:03:01.026 [main] [INFO ] readsProcessed(1367107) unmapped stats: reads(203966) mates(0) both(429116 existing=173916) supps(read=100662 align=2) seconds(0) reasons(depth=643178 softClip=78412 chimeric=8126)
12:03:01.026 [main] [DEBUG] unsorted-writer records written(203966) to BAM(KN-01_TUMOUR.redux.unmapping.bam)
12:03:01.824 [main] [DEBUG] splitting 24 partition regions across 12 threads
12:03:01.924 [main] [DEBUG] adding partition regions(1) totalLength(128678601): chr1:1-128678601
12:03:02.407 [main] [DEBUG] adding partition regions(2) totalLength(128678601): chr1:128678602-248956422;chr2:1-8400780
12:03:02.845 [main] [DEBUG] adding partition regions(1) totalLength(128678601): chr2:8400781-137079381
12:03:03.297 [main] [DEBUG] adding partition regions(2) totalLength(128678601): chr2:137079382-242193529;chr3:1-23564453
12:03:03.716 [main] [DEBUG] adding partition regions(1) totalLength(128678601): chr3:23564454-152243054
12:03:04.131 [main] [DEBUG] adding partition regions(2) totalLength(128678601): chr3:152243055-198295559;chr4:1-82626096
12:03:04.538 [main] [DEBUG] adding partition regions(2) totalLength(128678601): chr4:82626097-190214555;chr5:1-21090142
12:03:04.944 [main] [DEBUG] adding partition regions(1) totalLength(128678601): chr5:21090143-149768743
12:03:05.352 [main] [DEBUG] adding partition regions(2) totalLength(128678601): chr5:149768744-181538259;chr6:1-96909085
12:03:05.764 [main] [DEBUG] adding partition regions(2) totalLength(128678601): chr6:96909086-170805979;chr7:1-54781707
12:03:06.182 [main] [DEBUG] adding partition regions(2) totalLength(128678601): chr7:54781708-159345973;chr8:1-24114335
12:03:06.597 [main] [DEBUG] adding partition regions(2) totalLength(128678601): chr8:24114336-145138636;chr9:1-7654300
12:03:07.007 [main] [DEBUG] adding partition regions(1) totalLength(130740417): chr9:7654301-138394717
12:03:07.419 [main] [DEBUG] adding partition regions(1) totalLength(133797422): chr10:1-133797422
12:03:07.844 [main] [DEBUG] adding partition regions(1) totalLength(135086622): chr11:1-135086622
12:03:08.271 [main] [DEBUG] adding partition regions(1) totalLength(133275309): chr12:1-133275309
12:03:08.698 [main] [DEBUG] adding partition regions(2) totalLength(128678601): chr13:1-114364328;chr14:1-14314273
12:03:09.111 [main] [DEBUG] adding partition regions(2) totalLength(128678601): chr14:14314274-107043718;chr15:1-35949156
12:03:09.519 [main] [DEBUG] adding partition regions(2) totalLength(128678601): chr15:35949157-101991189;chr16:1-62636568
12:03:09.923 [main] [DEBUG] adding partition regions(3) totalLength(128678601): chr16:62636569-90338345;chr17:1-83257441;chr18:1-17719383
12:03:10.334 [main] [DEBUG] adding partition regions(3) totalLength(128678601): chr18:17719384-80373285;chr19:1-58617616;chr20:1-7407083
12:03:10.748 [main] [DEBUG] adding partition regions(3) totalLength(128678601): chr20:7407084-64444167;chr21:1-46709983;chr22:1-24931534
12:03:11.154 [main] [DEBUG] adding partition regions(2) totalLength(128678601): chr22:24931535-50818468;chrX:1-102791667
12:03:11.555 [main] [DEBUG] adding partition regions(3345) totalLength(239559114): chrX:102791668-156040895;chrY:1-57227415;multiple
12:03:33.331 [Thread-13] [DEBUG] region(chr1:128678602-248956422) position(150082709) processed 1M reads, cache(coords=204 reads=283)
12:03:33.661 [Thread-15] [DEBUG] region(chr2:137079382-242193529) position(161179606) processed 1M reads, cache(coords=87 reads=120)
12:03:33.703 [Thread-21] [DEBUG] region(chr6:96909086-170805979) position(117336998) processed 1M reads, cache(coords=364 reads=612)
12:03:33.808 [Thread-17] [DEBUG] region(chr3:152243055-198295559) position(179756948) processed 1M reads, cache(coords=72 reads=104)
12:03:33.825 [Thread-14] [DEBUG] region(chr2:8400781-137079381) position(26149340) processed 1M reads, cache(coords=30 reads=47)
12:03:33.978 [Thread-12] [DEBUG] region(chr1:1-128678601) position(6496445) processed 1M reads, cache(coords=163 reads=256)
12:03:33.998 [Thread-22] [DEBUG] region(chr7:54781708-159345973) position(74519410) processed 1M reads, cache(coords=511 reads=929)
12:03:34.100 [Thread-23] [DEBUG] region(chr8:24114336-145138636) position(38423047) processed 1M reads, cache(coords=187 reads=257)
12:03:34.262 [Thread-18] [DEBUG] region(chr4:82626097-190214555) position(103148859) processed 1M reads, cache(coords=201 reads=310)
12:03:34.343 [Thread-16] [DEBUG] region(chr3:23564454-152243054) position(39644502) processed 1M reads, cache(coords=29 reads=46)
12:03:34.425 [Thread-19] [DEBUG] region(chr5:21090143-149768743) position(42801054) processed 1M reads, cache(coords=387 reads=640)
12:03:34.441 [Thread-20] [DEBUG] region(chr5:149768744-181538259) position(168248289) processed 1M reads, cache(coords=391 reads=615)
12:03:48.643 [Thread-14] [DEBUG] region(chr2:8400781-137079381) position(32916244) processed 2M reads, cache(coords=2 reads=2)
12:03:49.016 [Thread-15] [DEBUG] region(chr2:137079382-242193529) position(173955350) processed 2M reads, cache(coords=562 reads=887)
12:03:49.117 [Thread-21] [DEBUG] region(chr6:96909086-170805979) position(137203566) processed 2M reads, cache(coords=380 reads=575)
12:03:49.244 [Thread-17] [DEBUG] region(chr3:152243055-198295559) position(193322547) processed 2M reads, cache(coords=386 reads=558)
12:03:49.281 [Thread-12] [DEBUG] region(chr1:1-128678601) position(12861684) processed 2M reads, cache(coords=918 reads=1686)
12:03:49.416 [Thread-13] [DEBUG] region(chr1:128678602-248956422) position(153968702) processed 2M reads, cache(coords=292 reads=458)
12:03:49.688 [Thread-22] [DEBUG] region(chr7:54781708-159345973) position(88208448) processed 2M reads, cache(coords=319 reads=557)
12:03:49.768 [Thread-23] [DEBUG] region(chr8:24114336-145138636) position(60828676) processed 2M reads, cache(coords=587 reads=985)
12:03:50.068 [Thread-18] [DEBUG] region(chr4:82626097-190214555) position(123401929) processed 2M reads, cache(coords=351 reads=517)
12:03:50.101 [Thread-16] [DEBUG] region(chr3:23564454-152243054) position(48247588) processed 2M reads, cache(coords=102 reads=152)
12:03:50.272 [Thread-20] [DEBUG] region(chr5:149768744-181538259) position(179616739) processed 2M reads, cache(coords=7 reads=12)
12:03:50.303 [Thread-19] [DEBUG] region(chr5:21090143-149768743) position(70900856) processed 2M reads, cache(coords=340 reads=460)
12:03:54.953 [Thread-20] [DEBUG] region(chr5:149768744-181538259) complete, processed 2300434 reads
12:03:58.608 [Thread-17] [DEBUG] region(chr3:152243055-198295559) complete, processed 2581657 reads
12:04:02.279 [Thread-14] [DEBUG] region(chr2:8400781-137079381) position(47482869) processed 3M reads, cache(coords=666 reads=1135)
12:04:04.435 [Thread-15] [DEBUG] region(chr2:137079382-242193529) position(181902103) processed 3M reads, cache(coords=444 reads=735)
12:04:04.454 [Thread-21] [DEBUG] region(chr6:96909086-170805979) position(152433709) processed 3M reads, cache(coords=78 reads=112)
12:04:04.811 [Thread-13] [DEBUG] region(chr1:128678602-248956422) position(156873386) processed 3M reads, cache(coords=535 reads=882)
12:04:04.856 [Thread-12] [DEBUG] region(chr1:1-128678601) position(18854370) processed 3M reads, cache(coords=287 reads=492)
12:04:05.257 [Thread-17] [DEBUG] region(chr4:1-82626096) position(2238793) processed 3M reads, cache(coords=320 reads=517)
12:04:05.610 [Thread-22] [DEBUG] region(chr7:54781708-159345973) position(100166564) processed 3M reads, cache(coords=273 reads=435)
12:04:05.762 [Thread-23] [DEBUG] region(chr8:24114336-145138636) position(89762849) processed 3M reads, cache(coords=184 reads=268)
12:04:05.988 [Thread-16] [DEBUG] region(chr3:23564454-152243054) position(52300765) processed 3M reads, cache(coords=20 reads=27)
12:04:06.021 [Thread-20] [DEBUG] region(chr6:1-96909085) position(16130661) processed 3M reads, cache(coords=433 reads=700)
12:04:06.231 [Thread-19] [DEBUG] region(chr5:21090143-149768743) position(93585273) processed 3M reads, cache(coords=216 reads=391)
12:04:06.233 [Thread-18] [DEBUG] region(chr4:82626097-190214555) position(153659031) processed 3M reads, cache(coords=341 reads=540)
12:04:18.193 [Thread-14] [DEBUG] region(chr2:8400781-137079381) position(69329654) processed 4M reads, cache(coords=322 reads=543)
12:04:19.784 [Thread-21] [DEBUG] region(chr6:96909086-170805979) position(169237041) processed 4M reads, cache(coords=80 reads=129)
12:04:19.910 [Thread-15] [DEBUG] region(chr2:137079382-242193529) position(200822037) processed 4M reads, cache(coords=20 reads=35)
12:04:20.030 [Thread-13] [DEBUG] region(chr1:128678602-248956422) position(162375324) processed 4M reads, cache(coords=207 reads=335)
12:04:20.420 [Thread-12] [DEBUG] region(chr1:1-128678601) position(26344718) processed 4M reads, cache(coords=211 reads=360)
12:04:20.450 [Thread-17] [DEBUG] region(chr4:1-82626096) position(9253390) processed 4M reads, cache(coords=125 reads=141)
12:04:21.440 [Thread-23] [DEBUG] region(chr8:24114336-145138636) position(111156003) processed 4M reads, cache(coords=2 reads=2)
12:04:21.527 [Thread-16] [DEBUG] region(chr3:23564454-152243054) position(68988839) processed 4M reads, cache(coords=44 reads=63)
12:04:21.742 [Thread-21] [DEBUG] region(chr6:96909086-170805979) complete, processed 4131611 reads
12:04:21.779 [Thread-22] [DEBUG] region(chr7:54781708-159345973) position(102656286) processed 4M reads, cache(coords=1181 reads=1640)
12:04:21.780 [Thread-20] [DEBUG] region(chr6:1-96909085) position(30073179) processed 4M reads, cache(coords=396 reads=656)
12:04:21.963 [Thread-19] [DEBUG] region(chr5:21090143-149768743) position(128263512) processed 4M reads, cache(coords=289 reads=410)
12:04:22.085 [Thread-18] [DEBUG] region(chr4:82626097-190214555) position(185175963) processed 4M reads, cache(coords=633 reads=1076)
12:04:27.512 [Thread-18] [DEBUG] region(chr4:82626097-190214555) complete, processed 4351259 reads
12:04:33.835 [Thread-14] [DEBUG] region(chr2:8400781-137079381) position(85395450) processed 5M reads, cache(coords=52 reads=87)
12:04:34.780 [Thread-17] [DEBUG] region(chr4:1-82626096) position(25312822) processed 5M reads, cache(coords=353 reads=596)
12:04:35.087 [Thread-21] [DEBUG] region(chr7:1-54781707) position(6918501) processed 5M reads, cache(coords=90 reads=123)
12:04:35.522 [Thread-13] [DEBUG] region(chr1:128678602-248956422) position(177940512) processed 5M reads, cache(coords=94 reads=146)
12:04:35.528 [Thread-15] [DEBUG] region(chr2:137079382-242193529) position(214809369) processed 5M reads, cache(coords=208 reads=399)
12:04:35.821 [Thread-12] [DEBUG] region(chr1:1-128678601) position(34885458) processed 5M reads, cache(coords=127 reads=196)
12:04:37.218 [Thread-23] [DEBUG] region(chr8:24114336-145138636) position(138613756) processed 5M reads, cache(coords=52 reads=82)
12:04:37.335 [Thread-16] [DEBUG] region(chr3:23564454-152243054) position(105853519) processed 5M reads, cache(coords=582 reads=999)
12:04:37.381 [Thread-19] [DEBUG] region(chr5:21090143-149768743) position(140486963) processed 5M reads, cache(coords=330 reads=487)
12:04:37.530 [Thread-22] [DEBUG] region(chr7:54781708-159345973) position(122012237) processed 5M reads, cache(coords=312 reads=501)
12:04:37.713 [Thread-18] [DEBUG] region(chr5:1-21090142) position(13718967) processed 5M reads, cache(coords=527 reads=879)
12:04:37.733 [Thread-20] [DEBUG] region(chr6:1-96909085) position(32116452) processed 5M reads, cache(coords=178 reads=334)
12:04:42.024 [Thread-18] [DEBUG] region(chr5:1-21090142) complete, processed 5266942 reads
12:04:42.027 [Thread-18] [DEBUG] partition(6: 2 regions: chr4:82626097-190214555;chr5:1-21090142) reader complete, total reads(5266942)
12:04:42.027 [Thread-18] [DEBUG] completed 1 partition readers
12:04:42.028 [Thread-18] [DEBUG] sorted-writer records written(6516124 writes=32712 avg=199 max=3122) maxCache(3618) to BAM(KN-01_TUMOUR.redux.6.sorted.bam)
12:04:49.162 [Thread-14] [DEBUG] region(chr2:8400781-137079381) position(96265259) processed 6M reads, cache(coords=574 reads=981)
12:04:50.109 [Thread-17] [DEBUG] region(chr4:1-82626096) position(53452998) processed 6M reads, cache(coords=411 reads=605)
12:04:50.459 [Thread-21] [DEBUG] region(chr7:1-54781707) position(30452127) processed 6M reads, cache(coords=325 reads=527)
12:04:51.155 [Thread-12] [DEBUG] region(chr1:1-128678601) position(42642454) processed 6M reads, cache(coords=146 reads=220)
12:04:51.279 [Thread-15] [DEBUG] region(chr2:137079382-242193529) position(224796304) processed 6M reads, cache(coords=290 reads=553)
12:04:51.430 [Thread-13] [DEBUG] region(chr1:128678602-248956422) position(196258185) processed 6M reads, cache(coords=162 reads=265)
12:04:52.566 [Thread-19] [DEBUG] region(chr5:21090143-149768743) position(146049131) processed 6M reads, cache(coords=501 reads=827)
12:04:52.617 [Thread-23] [DEBUG] region(chr8:24114336-145138636) position(144514215) processed 6M reads, cache(coords=545 reads=1075)
12:04:53.214 [Thread-16] [DEBUG] region(chr3:23564454-152243054) position(122461216) processed 6M reads, cache(coords=211 reads=340)
12:04:53.491 [Thread-22] [DEBUG] region(chr7:54781708-159345973) position(135929900) processed 6M reads, cache(coords=249 reads=408)
12:04:53.662 [Thread-20] [DEBUG] region(chr6:1-96909085) position(36425952) processed 6M reads, cache(coords=322 reads=474)
12:04:53.976 [Thread-18] [DEBUG] region(chr9:7654301-138394717) position(33332469) processed 6M reads, cache(coords=192 reads=297)
12:04:54.644 [Thread-23] [DEBUG] region(chr8:24114336-145138636) complete, processed 6132511 reads
12:04:57.541 [Thread-19] [DEBUG] region(chr5:21090143-149768743) complete, processed 6332824 reads
12:04:57.541 [Thread-19] [DEBUG] partition(7: 1 regions: chr5:21090143-149768743) reader complete, total reads(6332824)
12:04:57.541 [Thread-19] [DEBUG] completed 2 partition readers
12:04:57.542 [Thread-19] [DEBUG] sorted-writer records written(7835448 writes=37193 avg=210 max=3216) maxCache(4241) to BAM(KN-01_TUMOUR.redux.7.sorted.bam)
12:05:01.176 [Thread-23] [DEBUG] region(chr9:1-7654300) complete, processed 6562919 reads
12:05:01.176 [Thread-23] [DEBUG] partition(11: 2 regions: chr8:24114336-145138636;chr9:1-7654300) reader complete, total reads(6562919)
12:05:01.176 [Thread-23] [DEBUG] completed 3 partition readers
12:05:01.177 [Thread-23] [DEBUG] sorted-writer records written(8128776 writes=38957 avg=208 max=2620) maxCache(2940) to BAM(KN-01_TUMOUR.redux.11.sorted.bam)
12:05:04.288 [Thread-14] [DEBUG] region(chr2:8400781-137079381) position(106423452) processed 7M reads, cache(coords=935 reads=1230)
12:05:05.293 [Thread-17] [DEBUG] region(chr4:1-82626096) position(73981190) processed 7M reads, cache(coords=313 reads=518)
12:05:05.557 [Thread-21] [DEBUG] region(chr7:1-54781707) position(47437151) processed 7M reads, cache(coords=56 reads=87)
12:05:06.189 [Thread-12] [DEBUG] region(chr1:1-128678601) position(48239380) processed 7M reads, cache(coords=350 reads=614)
12:05:07.409 [Thread-15] [DEBUG] region(chr2:137079382-242193529) position(237089856) processed 7M reads, cache(coords=242 reads=405)
12:05:07.480 [Thread-13] [DEBUG] region(chr1:128678602-248956422) position(204444098) processed 7M reads, cache(coords=756 reads=1297)
12:05:07.991 [Thread-19] [DEBUG] region(chr10:1-133797422) position(14819803) processed 7M reads, cache(coords=7 reads=13)
12:05:08.066 [Thread-23] [DEBUG] region(chr11:1-135086622) position(1164367) processed 7M reads, cache(coords=270 reads=436)
12:05:09.195 [Thread-22] [DEBUG] region(chr7:54781708-159345973) position(144318619) processed 7M reads, cache(coords=589 reads=807)
12:05:09.262 [Thread-16] [DEBUG] region(chr3:23564454-152243054) position(130997713) processed 7M reads, cache(coords=465 reads=701)
12:05:09.669 [Thread-20] [DEBUG] region(chr6:1-96909085) position(43636502) processed 7M reads, cache(coords=452 reads=785)
12:05:10.276 [Thread-21] [DEBUG] region(chr7:1-54781707) complete, processed 7317768 reads
12:05:10.277 [Thread-21] [DEBUG] partition(9: 2 regions: chr6:96909086-170805979;chr7:1-54781707) reader complete, total reads(7317768)
12:05:10.277 [Thread-21] [DEBUG] completed 4 partition readers
12:05:10.277 [Thread-21] [DEBUG] sorted-writer records written(9064859 writes=40365 avg=224 max=2760) maxCache(4012) to BAM(KN-01_TUMOUR.redux.9.sorted.bam)
12:05:10.327 [Thread-18] [DEBUG] region(chr9:7654301-138394717) position(42893833) processed 7M reads, cache(coords=243 reads=321)
12:05:13.146 [Thread-17] [DEBUG] region(chr4:1-82626096) complete, processed 7524553 reads
12:05:13.146 [Thread-17] [DEBUG] partition(5: 2 regions: chr3:152243055-198295559;chr4:1-82626096) reader complete, total reads(7524553)
12:05:13.146 [Thread-17] [DEBUG] completed 5 partition readers
12:05:13.148 [Thread-17] [DEBUG] sorted-writer records written(9244395 writes=39653 avg=233 max=32562) maxCache(38675) to BAM(KN-01_TUMOUR.redux.5.sorted.bam)
12:05:18.428 [Thread-15] [DEBUG] region(chr2:137079382-242193529) complete, processed 7685700 reads
12:05:19.150 [Thread-14] [DEBUG] region(chr2:8400781-137079381) position(113225283) processed 8M reads, cache(coords=308 reads=465)
12:05:20.499 [Thread-17] [DEBUG] region(chr13:1-114364328) position(24321721) processed 8M reads, cache(coords=639 reads=1093)
12:05:20.545 [Thread-21] [DEBUG] region(chr12:1-133275309) position(6452993) processed 8M reads, cache(coords=47 reads=61)
12:05:21.437 [Thread-12] [DEBUG] region(chr1:1-128678601) position(63454371) processed 8M reads, cache(coords=270 reads=418)
12:05:22.519 [Thread-13] [DEBUG] region(chr1:128678602-248956422) position(214645488) processed 8M reads, cache(coords=721 reads=1159)
12:05:23.371 [Thread-15] [DEBUG] region(chr3:1-23564453) position(9704884) processed 8M reads, cache(coords=381 reads=670)
12:05:23.580 [Thread-23] [DEBUG] region(chr11:1-135086622) position(6557733) processed 8M reads, cache(coords=265 reads=404)
12:05:23.917 [Thread-19] [DEBUG] region(chr10:1-133797422) position(32378382) processed 8M reads, cache(coords=56 reads=89)
12:05:25.046 [Thread-16] [DEBUG] region(chr3:23564454-152243054) position(148741941) processed 8M reads, cache(coords=495 reads=860)
12:05:25.304 [Thread-22] [DEBUG] region(chr7:54781708-159345973) position(156962189) processed 8M reads, cache(coords=389 reads=637)
12:05:25.415 [Thread-20] [DEBUG] region(chr6:1-96909085) position(60281309) processed 8M reads, cache(coords=5 reads=7)
12:05:26.502 [Thread-18] [DEBUG] region(chr9:7654301-138394717) position(81992870) processed 8M reads, cache(coords=515 reads=843)
12:05:27.673 [Thread-22] [DEBUG] region(chr7:54781708-159345973) complete, processed 8149553 reads
12:05:30.038 [Thread-16] [DEBUG] region(chr3:23564454-152243054) complete, processed 8313275 reads
12:05:30.038 [Thread-16] [DEBUG] partition(4: 1 regions: chr3:23564454-152243054) reader complete, total reads(8313275)
12:05:30.038 [Thread-16] [DEBUG] completed 6 partition readers
12:05:30.038 [Thread-16] [DEBUG] sorted-writer records written(10294580 writes=44724 avg=230 max=1992) maxCache(2599) to BAM(KN-01_TUMOUR.redux.4.sorted.bam)
12:05:34.770 [Thread-14] [DEBUG] region(chr2:8400781-137079381) position(130465490) processed 9M reads, cache(coords=3 reads=4)
12:05:35.758 [Thread-17] [DEBUG] region(chr13:1-114364328) position(39665072) processed 9M reads, cache(coords=120 reads=169)
12:05:36.321 [Thread-21] [DEBUG] region(chr12:1-133275309) position(11854543) processed 9M reads, cache(coords=245 reads=350)
12:05:36.796 [Thread-12] [DEBUG] region(chr1:1-128678601) position(86125007) processed 9M reads, cache(coords=249 reads=382)
12:05:37.836 [Thread-13] [DEBUG] region(chr1:128678602-248956422) position(228308207) processed 9M reads, cache(coords=326 reads=553)
12:05:38.636 [Thread-15] [DEBUG] region(chr3:1-23564453) complete, processed 8985520 reads
12:05:38.636 [Thread-15] [DEBUG] partition(3: 2 regions: chr2:137079382-242193529;chr3:1-23564453) reader complete, total reads(8985520)
12:05:38.637 [Thread-15] [DEBUG] completed 7 partition readers
12:05:38.637 [Thread-15] [DEBUG] sorted-writer records written(11135556 writes=45668 avg=243 max=4721) maxCache(5191) to BAM(KN-01_TUMOUR.redux.3.sorted.bam)
12:05:39.001 [Thread-15] [DEBUG] region(chr15:35949157-101991189) position(36892397) processed 9M reads, cache(coords=480 reads=749)
12:05:39.039 [Thread-23] [DEBUG] region(chr11:1-135086622) position(18247864) processed 9M reads, cache(coords=213 reads=367)
12:05:39.462 [Thread-19] [DEBUG] region(chr10:1-133797422) position(48719981) processed 9M reads, cache(coords=192 reads=306)
12:05:40.548 [Thread-22] [DEBUG] region(chr8:1-24114335) position(12400272) processed 9M reads, cache(coords=166 reads=234)
12:05:41.026 [Thread-16] [DEBUG] region(chr14:14314274-107043718) position(23103722) processed 9M reads, cache(coords=452 reads=757)
12:05:41.131 [Thread-20] [DEBUG] region(chr6:1-96909085) position(87258965) processed 9M reads, cache(coords=381 reads=565)
12:05:42.181 [Thread-18] [DEBUG] region(chr9:7654301-138394717) position(93247424) processed 9M reads, cache(coords=10 reads=12)
12:05:43.462 [Thread-14] [DEBUG] region(chr2:8400781-137079381) complete, processed 9557785 reads
12:05:43.462 [Thread-14] [DEBUG] partition(2: 1 regions: chr2:8400781-137079381) reader complete, total reads(9557785)
12:05:43.463 [Thread-14] [DEBUG] completed 8 partition readers
12:05:43.463 [Thread-14] [DEBUG] sorted-writer records written(11588744 writes=46531 avg=249 max=6345) maxCache(9163) to BAM(KN-01_TUMOUR.redux.2.sorted.bam)
12:05:47.346 [Thread-20] [DEBUG] region(chr6:1-96909085) complete, processed 9395808 reads
12:05:47.346 [Thread-20] [DEBUG] partition(8: 2 regions: chr5:149768744-181538259;chr6:1-96909085) reader complete, total reads(9395808)
12:05:47.346 [Thread-20] [DEBUG] completed 9 partition readers
12:05:47.346 [Thread-20] [DEBUG] sorted-writer records written(11642551 writes=48608 avg=239 max=4556) maxCache(5337) to BAM(KN-01_TUMOUR.redux.8.sorted.bam)
12:05:50.184 [Thread-22] [DEBUG] region(chr8:1-24114335) complete, processed 9618297 reads
12:05:50.184 [Thread-22] [DEBUG] partition(10: 2 regions: chr7:54781708-159345973;chr8:1-24114335) reader complete, total reads(9618297)
12:05:50.184 [Thread-22] [DEBUG] completed 10 partition readers
12:05:50.184 [Thread-22] [DEBUG] sorted-writer records written(11843356 writes=47778 avg=247 max=9032) maxCache(12250) to BAM(KN-01_TUMOUR.redux.10.sorted.bam)
12:05:50.473 [Thread-14] [DEBUG] region(chr16:62636569-90338345) position(67654511) processed 10M reads, cache(coords=391 reads=659)
12:05:51.042 [Thread-17] [DEBUG] region(chr13:1-114364328) position(65788002) processed 10M reads, cache(coords=505 reads=806)
12:05:51.625 [Thread-21] [DEBUG] region(chr12:1-133275309) position(29487693) processed 10M reads, cache(coords=217 reads=380)
12:05:52.532 [Thread-12] [DEBUG] region(chr1:1-128678601) position(103432843) processed 10M reads, cache(coords=85 reads=123)
12:05:53.217 [Thread-13] [DEBUG] region(chr1:128678602-248956422) position(241796251) processed 10M reads, cache(coords=277 reads=440)
12:05:54.511 [Thread-23] [DEBUG] region(chr11:1-135086622) position(45926810) processed 10M reads, cache(coords=508 reads=918)
12:05:54.540 [Thread-15] [DEBUG] region(chr15:35949157-101991189) position(43526793) processed 10M reads, cache(coords=500 reads=770)
12:05:55.181 [Thread-19] [DEBUG] region(chr10:1-133797422) position(69389200) processed 10M reads, cache(coords=375 reads=642)
12:05:56.169 [Thread-22] [DEBUG] region(chr20:7407084-64444167) position(18162187) processed 10M reads, cache(coords=566 reads=925)
12:05:56.670 [Thread-16] [DEBUG] region(chr14:14314274-107043718) position(39348809) processed 10M reads, cache(coords=271 reads=422)
12:05:56.974 [Thread-20] [DEBUG] region(chr18:17719384-80373285) position(35569683) processed 10M reads, cache(coords=15 reads=22)
12:05:57.964 [Thread-18] [DEBUG] region(chr9:7654301-138394717) position(110329145) processed 10M reads, cache(coords=44 reads=69)
12:06:02.817 [Thread-13] [DEBUG] region(chr1:128678602-248956422) complete, processed 10615494 reads
12:06:06.137 [Thread-13] [DEBUG] region(chr2:1-8400780) complete, processed 10826504 reads
12:06:06.137 [Thread-13] [DEBUG] partition(1: 2 regions: chr1:128678602-248956422;chr2:1-8400780) reader complete, total reads(10826504)
12:06:06.138 [Thread-13] [DEBUG] completed 11 partition readers
12:06:06.138 [Thread-13] [DEBUG] sorted-writer records written(13353311 writes=50511 avg=264 max=5302) maxCache(5347) to BAM(KN-01_TUMOUR.redux.1.sorted.bam)
12:06:06.185 [Thread-14] [DEBUG] region(chr16:62636569-90338345) position(71986187) processed 11M reads, cache(coords=126 reads=213)
12:06:06.397 [Thread-17] [DEBUG] region(chr13:1-114364328) position(107865696) processed 11M reads, cache(coords=341 reads=548)
12:06:06.811 [Thread-21] [DEBUG] region(chr12:1-133275309) position(48654900) processed 11M reads, cache(coords=179 reads=283)
12:06:08.492 [Thread-12] [DEBUG] region(chr1:1-128678601) position(113854853) processed 11M reads, cache(coords=154 reads=255)
12:06:09.006 [Thread-13] [DEBUG] region(chr22:24931535-50818468) position(27189058) processed 11M reads, cache(coords=282 reads=438)
12:06:10.018 [Thread-23] [DEBUG] region(chr11:1-135086622) position(58403096) processed 11M reads, cache(coords=585 reads=897)
12:06:10.090 [Thread-15] [DEBUG] region(chr15:35949157-101991189) position(55230346) processed 11M reads, cache(coords=162 reads=257)
12:06:10.925 [Thread-19] [DEBUG] region(chr10:1-133797422) position(80274554) processed 11M reads, cache(coords=334 reads=527)
12:06:11.353 [Thread-22] [DEBUG] region(chr20:7407084-64444167) position(33788730) processed 11M reads, cache(coords=3 reads=4)
12:06:12.071 [Thread-16] [DEBUG] region(chr14:14314274-107043718) position(63942061) processed 11M reads, cache(coords=312 reads=478)
12:06:12.950 [Thread-20] [DEBUG] region(chr18:17719384-80373285) position(63723114) processed 11M reads, cache(coords=206 reads=309)
12:06:13.799 [Thread-18] [DEBUG] region(chr9:7654301-138394717) position(126395630) processed 11M reads, cache(coords=305 reads=551)
12:06:14.015 [Thread-17] [DEBUG] region(chr13:1-114364328) complete, processed 11495150 reads
12:06:14.029 [Thread-17] [DEBUG] region(chr14:1-14314273) complete, processed 11495150 reads
12:06:14.030 [Thread-17] [DEBUG] partition(16: 2 regions: chr13:1-114364328;chr14:1-14314273) reader complete, total reads(3970597)
12:06:14.030 [Thread-17] [DEBUG] completed 12 partition readers
12:06:14.030 [Thread-17] [DEBUG] sorted-writer records written(4900076 writes=26472 avg=185 max=3530) maxCache(5021) to BAM(KN-01_TUMOUR.redux.16.sorted.bam)
12:06:18.165 [Thread-20] [DEBUG] region(chr18:17719384-80373285) complete, processed 11333694 reads
12:06:20.999 [Thread-12] [DEBUG] region(chr1:1-128678601) complete, processed 11813609 reads
12:06:20.999 [Thread-12] [DEBUG] partition(0: 1 regions: chr1:1-128678601) reader complete, total reads(11813609)
12:06:20.999 [Thread-12] [DEBUG] completed 13 partition readers
12:06:20.999 [Thread-12] [DEBUG] sorted-writer records written(14615786 writes=57148 avg=255 max=4560) maxCache(5650) to BAM(KN-01_TUMOUR.redux.0.sorted.bam)
12:06:21.855 [Thread-14] [DEBUG] region(chr16:62636569-90338345) position(85678168) processed 12M reads, cache(coords=79 reads=133)
12:06:22.006 [Thread-17] [DEBUG] region(chrX:102791668-156040895) position(108696355) processed 12M reads, cache(coords=411 reads=665)
12:06:22.201 [Thread-21] [DEBUG] region(chr12:1-133275309) position(52489912) processed 12M reads, cache(coords=218 reads=385)
12:06:24.701 [Thread-13] [DEBUG] region(chr22:24931535-50818468) position(37060872) processed 12M reads, cache(coords=274 reads=484)
12:06:25.095 [Thread-23] [DEBUG] region(chr11:1-135086622) position(63658933) processed 12M reads, cache(coords=226 reads=356)
12:06:25.758 [Thread-15] [DEBUG] region(chr15:35949157-101991189) position(67822061) processed 12M reads, cache(coords=295 reads=486)
12:06:26.103 [Thread-22] [DEBUG] region(chr20:7407084-64444167) position(42677946) processed 12M reads, cache(coords=891 reads=1628)
12:06:26.170 [Thread-19] [DEBUG] region(chr10:1-133797422) position(95354880) processed 12M reads, cache(coords=243 reads=335)
12:06:27.197 [Thread-16] [DEBUG] region(chr14:14314274-107043718) position(75017042) processed 12M reads, cache(coords=177 reads=278)
12:06:28.800 [Thread-20] [DEBUG] region(chr19:1-58617616) position(2477532) processed 12M reads, cache(coords=394 reads=654)
12:06:28.969 [Thread-18] [DEBUG] region(chr9:7654301-138394717) position(132648357) processed 12M reads, cache(coords=271 reads=418)
12:06:32.475 [Thread-14] [DEBUG] region(chr16:62636569-90338345) complete, processed 12654612 reads
12:06:36.970 [Thread-21] [DEBUG] region(chr12:1-133275309) position(56599789) processed 13M reads, cache(coords=462 reads=706)
12:06:37.753 [Thread-17] [DEBUG] region(chrX:102791668-156040895) position(124062842) processed 13M reads, cache(coords=136 reads=206)
12:06:38.044 [Thread-14] [DEBUG] region(chr17:1-83257441) position(2065000) processed 13M reads, cache(coords=46 reads=62)
12:06:40.186 [Thread-23] [DEBUG] region(chr11:1-135086622) position(66551247) processed 13M reads, cache(coords=375 reads=607)
12:06:40.680 [Thread-13] [DEBUG] region(chr22:24931535-50818468) position(42213268) processed 13M reads, cache(coords=534 reads=830)
12:06:40.855 [Thread-22] [DEBUG] region(chr20:7407084-64444167) position(51784616) processed 13M reads, cache(coords=400 reads=619)
12:06:40.962 [Thread-19] [DEBUG] region(chr10:1-133797422) position(102425159) processed 13M reads, cache(coords=375 reads=601)
12:06:41.680 [Thread-15] [DEBUG] region(chr15:35949157-101991189) position(77919963) processed 13M reads, cache(coords=403 reads=591)
12:06:42.020 [Thread-16] [DEBUG] region(chr14:14314274-107043718) position(95103545) processed 13M reads, cache(coords=578 reads=965)
12:06:43.947 [Thread-18] [DEBUG] region(chr9:7654301-138394717) position(138078069) processed 13M reads, cache(coords=131 reads=217)
12:06:44.583 [Thread-18] [DEBUG] region(chr9:7654301-138394717) complete, processed 13042961 reads
12:06:44.583 [Thread-18] [DEBUG] partition(12: 1 regions: chr9:7654301-138394717) reader complete, total reads(7776019)
12:06:44.583 [Thread-18] [DEBUG] completed 14 partition readers
12:06:44.583 [Thread-18] [DEBUG] sorted-writer records written(9611878 writes=43544 avg=220 max=3599) maxCache(4292) to BAM(KN-01_TUMOUR.redux.12.sorted.bam)
12:06:44.892 [Thread-20] [DEBUG] region(chr19:1-58617616) position(7558879) processed 13M reads, cache(coords=198 reads=311)
12:06:51.787 [Thread-21] [DEBUG] region(chr12:1-133275309) position(69572128) processed 14M reads, cache(coords=263 reads=431)
12:06:53.576 [Thread-17] [DEBUG] region(chrX:102791668-156040895) position(136346075) processed 14M reads, cache(coords=473 reads=740)
12:06:53.955 [Thread-14] [DEBUG] region(chr17:1-83257441) position(7226299) processed 14M reads, cache(coords=308 reads=497)
12:06:54.793 [Thread-16] [DEBUG] region(chr14:14314274-107043718) complete, processed 13863221 reads
12:06:55.054 [Thread-23] [DEBUG] region(chr11:1-135086622) position(72829347) processed 14M reads, cache(coords=284 reads=455)
12:06:55.497 [Thread-22] [DEBUG] region(chr20:7407084-64444167) position(63735480) processed 14M reads, cache(coords=493 reads=884)
12:06:55.840 [Thread-19] [DEBUG] region(chr10:1-133797422) position(118335134) processed 14M reads, cache(coords=395 reads=647)
12:06:56.241 [Thread-13] [DEBUG] region(chr22:24931535-50818468) complete, processed 13981830 reads
12:06:56.517 [Thread-13] [DEBUG] region(chrX:1-102791667) position(312682) processed 14M reads, cache(coords=190 reads=378)
12:06:56.844 [Thread-16] [DEBUG] region(chr15:1-35949156) position(20845860) processed 14M reads, cache(coords=1090 reads=1718)
12:06:57.327 [Thread-15] [DEBUG] region(chr15:35949157-101991189) position(87999667) processed 14M reads, cache(coords=432 reads=658)
12:06:57.578 [Thread-22] [DEBUG] region(chr20:7407084-64444167) complete, processed 14145163 reads
12:07:00.697 [Thread-20] [DEBUG] region(chr19:1-58617616) position(11222062) processed 14M reads, cache(coords=400 reads=668)
12:07:06.651 [Thread-21] [DEBUG] region(chr12:1-133275309) position(95485887) processed 15M reads, cache(coords=283 reads=437)
12:07:09.502 [Thread-17] [DEBUG] region(chrX:102791668-156040895) position(153580261) processed 15M reads, cache(coords=667 reads=1210)
12:07:09.580 [Thread-22] [DEBUG] region(chr21:1-46709983) position(32695080) processed 15M reads, cache(coords=279 reads=436)
12:07:09.623 [Thread-23] [DEBUG] region(chr11:1-135086622) position(89799760) processed 15M reads, cache(coords=1418 reads=2071)
12:07:10.126 [Thread-14] [DEBUG] region(chr17:1-83257441) position(10644563) processed 15M reads, cache(coords=388 reads=607)
12:07:11.279 [Thread-19] [DEBUG] region(chr10:1-133797422) position(126504074) processed 15M reads, cache(coords=459 reads=651)
12:07:11.800 [Thread-16] [DEBUG] region(chr15:1-35949156) position(30638589) processed 15M reads, cache(coords=2 reads=2)
12:07:12.317 [Thread-13] [DEBUG] region(chrX:1-102791667) position(20024894) processed 15M reads, cache(coords=72 reads=112)
12:07:13.078 [Thread-15] [DEBUG] region(chr15:35949157-101991189) position(99805767) processed 15M reads, cache(coords=16 reads=24)
12:07:15.850 [Thread-15] [DEBUG] region(chr15:35949157-101991189) complete, processed 15176905 reads
12:07:16.616 [Thread-20] [DEBUG] region(chr19:1-58617616) position(15475725) processed 15M reads, cache(coords=218 reads=358)
12:07:18.957 [Thread-19] [DEBUG] region(chr10:1-133797422) complete, processed 15527712 reads
12:07:18.957 [Thread-19] [DEBUG] partition(13: 1 regions: chr10:1-133797422) reader complete, total reads(9194888)
12:07:18.958 [Thread-19] [DEBUG] completed 15 partition readers
12:07:18.958 [Thread-19] [DEBUG] sorted-writer records written(11362435 writes=48491 avg=234 max=10797) maxCache(16925) to BAM(KN-01_TUMOUR.redux.13.sorted.bam)
12:07:19.630 [Thread-16] [DEBUG] region(chr15:1-35949156) complete, processed 15539171 reads
12:07:19.630 [Thread-16] [DEBUG] partition(17: 2 regions: chr14:14314274-107043718;chr15:1-35949156) reader complete, total reads(7225896)
12:07:19.630 [Thread-16] [DEBUG] completed 16 partition readers
12:07:19.630 [Thread-16] [DEBUG] sorted-writer records written(8876236 writes=41500 avg=213 max=4235) maxCache(4675) to BAM(KN-01_TUMOUR.redux.17.sorted.bam)
12:07:21.470 [Thread-21] [DEBUG] region(chr12:1-133275309) position(109279660) processed 16M reads, cache(coords=131 reads=214)
12:07:24.041 [Thread-22] [DEBUG] region(chr21:1-46709983) position(42760816) processed 16M reads, cache(coords=240 reads=371)
12:07:24.095 [Thread-17] [DEBUG] region(chrX:102791668-156040895) complete, processed 15960333 reads
12:07:24.556 [Thread-23] [DEBUG] region(chr11:1-135086622) position(108510137) processed 16M reads, cache(coords=376 reads=609)
12:07:24.587 [Thread-17] [DEBUG] region(chrY:1-57227415) complete, processed 15984398 reads
12:07:24.622 [Thread-17] [DEBUG] region(chrM:1-16569) position(2528) processed 16M reads, cache(coords=0 reads=0)
12:07:25.093 [Thread-17] [DEBUG] region(chrM:1-16569) complete, processed 16224239 reads
12:07:25.774 [Thread-14] [DEBUG] region(chr17:1-83257441) position(19936242) processed 16M reads, cache(coords=133 reads=223)
12:07:27.967 [Thread-13] [DEBUG] region(chrX:1-102791667) position(47056129) processed 16M reads, cache(coords=362 reads=624)
12:07:28.625 [Thread-15] [DEBUG] region(chr16:1-62636568) position(2207096) processed 16M reads, cache(coords=306 reads=478)
12:07:32.278 [Thread-20] [DEBUG] region(chr19:1-58617616) position(21020771) processed 16M reads, cache(coords=397 reads=702)
12:07:35.581 [Thread-22] [DEBUG] region(chr21:1-46709983) complete, processed 16774631 reads
12:07:36.361 [Thread-21] [DEBUG] region(chr12:1-133275309) position(120144760) processed 17M reads, cache(coords=345 reads=508)
12:07:38.951 [Thread-22] [DEBUG] region(chr22:1-24931534) position(17100262) processed 17M reads, cache(coords=54 reads=84)
12:07:39.111 [Thread-17] [DEBUG] partition(23: 3345 regions: chrX:102791668-156040895;chrY:1-57227415;multiple) reader complete, total reads(5423633)
12:07:39.111 [Thread-17] [DEBUG] completed 17 partition readers
12:07:39.111 [Thread-17] [DEBUG] sorted-writer records written(6365530 writes=27829 avg=228 max=13022) maxCache(17906) to BAM(KN-01_TUMOUR.redux.23.sorted.bam)
12:07:39.787 [Thread-23] [DEBUG] region(chr11:1-135086622) position(121162100) processed 17M reads, cache(coords=294 reads=477)
12:07:41.660 [Thread-14] [DEBUG] region(chr17:1-83257441) position(31261668) processed 17M reads, cache(coords=151 reads=222)
12:07:43.711 [Thread-13] [DEBUG] region(chrX:1-102791667) position(53082625) processed 17M reads, cache(coords=571 reads=1132)
12:07:44.550 [Thread-15] [DEBUG] region(chr16:1-62636568) position(13235220) processed 17M reads, cache(coords=293 reads=482)
12:07:48.300 [Thread-20] [DEBUG] region(chr19:1-58617616) position(37889529) processed 17M reads, cache(coords=386 reads=591)
12:07:50.612 [Thread-23] [DEBUG] region(chr11:1-135086622) complete, processed 17736109 reads
12:07:50.612 [Thread-23] [DEBUG] partition(14: 1 regions: chr11:1-135086622) reader complete, total reads(11173190)
12:07:50.612 [Thread-23] [DEBUG] completed 18 partition readers
12:07:50.612 [Thread-23] [DEBUG] sorted-writer records written(13852671 writes=57566 avg=240 max=5789) maxCache(5814) to BAM(KN-01_TUMOUR.redux.14.sorted.bam)
12:07:51.007 [Thread-21] [DEBUG] region(chr12:1-133275309) position(130441963) processed 18M reads, cache(coords=339 reads=548)
12:07:53.002 [Thread-22] [DEBUG] region(chr22:1-24931534) position(21115828) processed 18M reads, cache(coords=341 reads=415)
12:07:56.524 [Thread-21] [DEBUG] region(chr12:1-133275309) complete, processed 18378899 reads
12:07:56.524 [Thread-21] [DEBUG] partition(15: 1 regions: chr12:1-133275309) reader complete, total reads(11061131)
12:07:56.525 [Thread-21] [DEBUG] completed 19 partition readers
12:07:56.525 [Thread-21] [DEBUG] sorted-writer records written(13700116 writes=57514 avg=238 max=6077) maxCache(8900) to BAM(KN-01_TUMOUR.redux.15.sorted.bam)
12:07:56.874 [Thread-14] [DEBUG] region(chr17:1-83257441) position(38837116) processed 18M reads, cache(coords=184 reads=284)
12:07:59.074 [Thread-13] [DEBUG] region(chrX:1-102791667) position(71118759) processed 18M reads, cache(coords=553 reads=926)
12:07:59.505 [Thread-15] [DEBUG] region(chr16:1-62636568) position(20590700) processed 18M reads, cache(coords=103 reads=156)
12:08:03.693 [Thread-20] [DEBUG] region(chr19:1-58617616) position(41719849) processed 18M reads, cache(coords=39 reads=56)
12:08:07.037 [Thread-22] [DEBUG] region(chr22:1-24931534) position(24611118) processed 19M reads, cache(coords=487 reads=986)
12:08:08.188 [Thread-22] [DEBUG] region(chr22:1-24931534) complete, processed 19078521 reads
12:08:08.188 [Thread-22] [DEBUG] partition(21: 3 regions: chr20:7407084-64444167;chr21:1-46709983;chr22:1-24931534) reader complete, total reads(9460224)
12:08:08.188 [Thread-22] [DEBUG] completed 20 partition readers
12:08:08.188 [Thread-22] [DEBUG] sorted-writer records written(11663874 writes=44557 avg=261 max=8776) maxCache(8777) to BAM(KN-01_TUMOUR.redux.21.sorted.bam)
12:08:12.341 [Thread-14] [DEBUG] region(chr17:1-83257441) position(41873801) processed 19M reads, cache(coords=268 reads=398)
12:08:14.341 [Thread-13] [DEBUG] region(chrX:1-102791667) position(85046367) processed 19M reads, cache(coords=34 reads=45)
12:08:14.416 [Thread-15] [DEBUG] region(chr16:1-62636568) position(28648265) processed 19M reads, cache(coords=446 reads=596)
12:08:19.120 [Thread-20] [DEBUG] region(chr19:1-58617616) position(45830015) processed 19M reads, cache(coords=99 reads=149)
12:08:25.228 [Thread-13] [DEBUG] region(chrX:1-102791667) complete, processed 19719797 reads
12:08:25.229 [Thread-13] [DEBUG] partition(22: 2 regions: chr22:24931535-50818468;chrX:1-102791667) reader complete, total reads(8893293)
12:08:25.229 [Thread-13] [DEBUG] completed 21 partition readers
12:08:25.229 [Thread-13] [DEBUG] sorted-writer records written(11021303 writes=46600 avg=236 max=11045) maxCache(14334) to BAM(KN-01_TUMOUR.redux.22.sorted.bam)
12:08:27.417 [Thread-14] [DEBUG] region(chr17:1-83257441) position(45081633) processed 20M reads, cache(coords=241 reads=385)
12:08:29.387 [Thread-15] [DEBUG] region(chr16:1-62636568) position(31330071) processed 20M reads, cache(coords=174 reads=257)
12:08:34.321 [Thread-20] [DEBUG] region(chr19:1-58617616) position(49960237) processed 20M reads, cache(coords=623 reads=882)
12:08:42.392 [Thread-14] [DEBUG] region(chr17:1-83257441) position(50195260) processed 21M reads, cache(coords=254 reads=388)
12:08:43.700 [Thread-15] [DEBUG] region(chr16:1-62636568) position(56568911) processed 21M reads, cache(coords=338 reads=567)
12:08:49.207 [Thread-20] [DEBUG] region(chr19:1-58617616) position(54634978) processed 21M reads, cache(coords=8 reads=13)
12:08:51.178 [Thread-15] [DEBUG] region(chr16:1-62636568) complete, processed 21510744 reads
12:08:51.178 [Thread-15] [DEBUG] partition(18: 2 regions: chr15:35949157-101991189;chr16:1-62636568) reader complete, total reads(12525224)
12:08:51.178 [Thread-15] [DEBUG] completed 22 partition readers
12:08:51.178 [Thread-15] [DEBUG] sorted-writer records written(15390910 writes=63034 avg=244 max=4820) maxCache(6999) to BAM(KN-01_TUMOUR.redux.18.sorted.bam)
12:08:57.040 [Thread-14] [DEBUG] region(chr17:1-83257441) position(61368457) processed 22M reads, cache(coords=631 reads=1110)
12:09:03.644 [Thread-20] [DEBUG] region(chr19:1-58617616) position(58480565) processed 22M reads, cache(coords=224 reads=388)
12:09:04.250 [Thread-20] [DEBUG] region(chr19:1-58617616) complete, processed 22042924 reads
12:09:11.664 [Thread-14] [DEBUG] region(chr17:1-83257441) position(68524898) processed 23M reads, cache(coords=492 reads=882)
12:09:13.430 [Thread-20] [DEBUG] region(chr20:1-7407083) complete, processed 22681868 reads
12:09:13.430 [Thread-20] [DEBUG] partition(20: 3 regions: chr18:17719384-80373285;chr19:1-58617616;chr20:1-7407083) reader complete, total reads(13286060)
12:09:13.430 [Thread-20] [DEBUG] completed 23 partition readers
12:09:13.430 [Thread-20] [DEBUG] sorted-writer records written(16461688 writes=70476 avg=233 max=6531) maxCache(6532) to BAM(KN-01_TUMOUR.redux.20.sorted.bam)
12:09:26.028 [Thread-14] [DEBUG] region(chr17:1-83257441) position(76155674) processed 24M reads, cache(coords=511 reads=794)
12:09:40.317 [Thread-14] [DEBUG] region(chr17:1-83257441) position(81833670) processed 25M reads, cache(coords=61 reads=90)
12:09:45.047 [Thread-14] [DEBUG] region(chr17:1-83257441) complete, processed 25330794 reads
12:09:54.779 [Thread-14] [DEBUG] region(chr18:1-17719383) position(14538169) processed 26M reads, cache(coords=603 reads=897)
12:09:55.405 [Thread-14] [DEBUG] region(chr18:1-17719383) complete, processed 26041962 reads
12:09:55.405 [Thread-14] [DEBUG] partition(19: 3 regions: chr16:62636569-90338345;chr17:1-83257441;chr18:1-17719383) reader complete, total reads(16484177)
12:09:55.405 [Thread-14] [DEBUG] completed 24 partition readers
12:09:55.405 [Thread-14] [DEBUG] sorted-writer records written(20441950 writes=74163 avg=275 max=6484) maxCache(6806) to BAM(KN-01_TUMOUR.redux.19.sorted.bam)
12:09:55.408 [main] [INFO ] all partition tasks complete
12:09:55.408 [main] [INFO ] analysing microsatellite jitter
12:10:02.289 [main] [DEBUG] unsorted-writer records written(603032) to BAM(KN-01_TUMOUR.redux.full_unmapped.bam)
12:10:02.293 [main] [DEBUG] concatenating 25 BAMs
12:10:09.813 [main] [DEBUG] final concatenate complete: ./KN-01_TUMOUR.redux.bam
12:10:09.813 [main] [DEBUG] indexing BAM: ./KN-01_TUMOUR.redux.bam
12:10:27.988 [main] [DEBUG] final BAM complete: ./KN-01_TUMOUR.redux.bam
12:10:27.998 [main] [INFO ] stats: totalReads(217990136) duplicates(80722205) dupGroups(51704141) umiGroups(0)
12:10:27.998 [main] [INFO ] consensus stats: dualStrandMismatches(groups=2761802 reads=7663428) outcomes(ALIGNMENT_ONLY=50895123, INDEL_MATCH=315254, INDEL_MISMATCH=429486)
12:10:27.999 [main] [DEBUG] duplicate frequency: 1=84781666, 2=33099715, 3=11982976, 4=4240344, 5=1511025, 6=543456, 7=201275, 8=75810, 9=29378, 10=20080, 20=56, 30=6, 50=2, 60=4, 70=2, 80=4, 90=2, 100=4, 300=2
12:10:27.999 [main] [DEBUG] re-unmapped stats: reads(203966) mates(206189) both(429116 existing=0) supps(read=149042 align=82787) seconds(0) reasons(depth=643178 softClip=78412 chimeric=8126)
12:10:28.000 [main] [INFO ] PerfStat(Total) intervals(44) total(3365.263 avg=76.483 max=192.572)
12:10:28.000 [main] [INFO ] PerfStat(ProcessDuplicates) intervals(44) total(2545.846 avg=57.860 max=146.593)
12:10:28.000 [main] [INFO ] Redux complete, mins(8.380)
/usr/local/bin/redux: line 6: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory