{"action":"closed","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/844","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/844/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/844/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/844/events","html_url":"https://github.com/marbl/canu/issues/844","id":309632222,"number":844,"title":"v1.7 - Segmentation fault, bogart failed","user":{"login":"ovidp","id":37553436,"avatar_url":"https://avatars2.githubusercontent.com/u/37553436?v=4","gravatar_id":"","url":"https://api.github.com/users/ovidp","html_url":"https://github.com/ovidp","followers_url":"https://api.github.com/users/ovidp/followers","following_url":"https://api.github.com/users/ovidp/following{/other_user}","gists_url":"https://api.github.com/users/ovidp/gists{/gist_id}","starred_url":"https://api.github.com/users/ovidp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ovidp/subscriptions","organizations_url":"https://api.github.com/users/ovidp/orgs","repos_url":"https://api.github.com/users/ovidp/repos","events_url":"https://api.github.com/users/ovidp/events{/privacy}","received_events_url":"https://api.github.com/users/ovidp/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":13,"created_at":"2018-03-29T06:17:42Z","updated_at":"2018-04-16T10:38:08Z","closed_at":"2018-04-16T10:38:08Z","author_association":"NONE","body":"Hi\r\nI am running a canu (1.7) assembly of a plant genome (1.3gb) based on 11x PacBio reads. It all goes well till unitigging, when bogart fails with a segmentation fault.\r\nI tried restarting and then I start the entire process fresh, but I am getting the same error.\r\nI would greatly appreaciate some help.\r\n\r\nI am running canu in a Linux cluster. The canu command used: '/canu/Linux-amd64/bin/canu -assemble -d /PacBio/ useGrid=false correctedErrorRate=0.105 -pacbio-corrected /PacBio/all_corr_pacbio.fasta  genomeSize=1.3g -p HEcanuCorrLo'\r\n\r\nThe contents of `unitigging/4-unitigger/unitigger.err`:\r\n```\r\n==> PARAMETERS.\r\n\r\nResources:\r\n  Memory                189 GB\r\n  Compute Threads       16 (command line)\r\n\r\nLengths:\r\n  Minimum read          0 bases\r\n  Minimum overlap       500 bases\r\n\r\nOverlap Error Rates:\r\n  Graph                 0.105 (10.500%)\r\n  Max                   0.105 (10.500%)\r\n\r\nDeviations:\r\n  Graph                 6.000\r\n  Bubble                6.000\r\n  Repeat                3.000\r\n\r\nEdge Confusion:\r\n  Absolute              2100\r\n  Percent               200.0000\r\n\r\nUnitig Construction:\r\n  Minimum intersection  500 bases\r\n  Maxiumum placements   2 positions\r\n\r\nDebugging Enabled:\r\n  (none)\r\n\r\n==> LOADING AND FILTERING OVERLAPS.\r\n\r\nReadInfo()-- Using 2138563 reads, no minimum read length used.\r\n\r\nOverlapCache()-- limited to 193536MB memory (user supplied).\r\n\r\nOverlapCache()--      16MB for read data.\r\nOverlapCache()--      81MB for best edges.\r\nOverlapCache()--     212MB for tigs.\r\nOverlapCache()--      57MB for tigs - read layouts.\r\nOverlapCache()--      81MB for tigs - error profiles.\r\nOverlapCache()--   48384MB for tigs - error profile overlaps.\r\nOverlapCache()--   19355MB for other processes.\r\nOverlapCache()-- ---------\r\nOverlapCache()--   68229MB for data structures (sum of above).\r\nOverlapCache()-- ---------\r\nOverlapCache()--      40MB for overlap store structure.\r\nOverlapCache()--  125266MB for overlap data.\r\nOverlapCache()-- ---------\r\nOverlapCache()--  193536MB allowed.\r\nOverlapCache()--\r\nOverlapCache()-- Retain at least 22 overlaps/read, based on 11.28x coverage.\r\nOverlapCache()-- Initial guess at 3838 overlaps/read.\r\nOverlapCache()--\r\nOverlapCache()-- Adjusting for sparse overlaps.\r\nOverlapCache()--\r\nOverlapCache()--               reads loading olaps          olaps               memory\r\nOverlapCache()--   olaps/read       all      some          loaded                 free\r\nOverlapCache()--   ----------   -------   -------     ----------- -------     --------\r\nOverlapCache()--         3838   2126932     11631       134145428  85.20%     123219 MB\r\nOverlapCache()--       698128   2138563         0       157439780 100.00%     122863 MB\r\nOverlapCache()--\r\nOverlapCache()-- Loading overlaps.\r\nOverlapCache()--\r\nOverlapCache()--          read from store           saved in cache\r\nOverlapCache()--   ------------ ---------   ------------ ---------\r\nOverlapCache()--       29347933 (018.64%)       28982507 (018.41%)\r\nOverlapCache()--       58686018 (037.28%)       57964060 (036.82%)\r\nOverlapCache()--       86967419 (055.24%)       85908451 (054.57%)\r\nOverlapCache()--      114979131 (073.03%)      113584331 (072.14%)\r\nOverlapCache()--      143507013 (091.15%)      141800857 (090.07%)\r\nOverlapCache()--   ------------ ---------   ------------ ---------\r\nOverlapCache()--      157439780 (100.00%)      155583954 (098.82%)\r\nOverlapCache()--\r\nOverlapCache()-- Ignored 1191848 duplicate overlaps.\r\nOverlapCache()--\r\nOverlapCache()-- Symmetrizing overlaps.\r\nOverlapCache()--   Finding missing twins.\r\nOverlapCache()--   Found 119302 missing twins in 155583954 overlaps, 1620 are strong.\r\nOverlapCache()--   Dropping weak non-twin overlaps; allocated 0 MB scratch space.\r\nOverlapCache()--   Dropped 3422 overlaps; scratch space released.\r\nOverlapCache()--   Adding 115880 missing twin overlaps.\r\nOverlapCache()--   Finished.\r\n\r\nBestOverlapGraph()-- allocating best edges (65MB)\r\n\r\nBestOverlapGraph()-- finding initial best edges.\r\n\r\nBestOverlapGraph()-- filtering suspicious reads.\r\nBestOverlapGraph()-- marked 1626591 reads as suspicious.\r\n\r\nBestOverlapGraph()-- filtering high error edges.\r\n\r\nBestOverlapGraph()-- filtering reads with lopsided best edges.\r\n\r\nBestOverlapGraph()-- filtering spur reads.\r\nBestOverlapGraph()-- detected 276777 spur reads and 1704959 singleton reads.\r\n\r\nFailed with 'Segmentation fault'; backtrace (libbacktrace):\r\nAS_UTL/AS_UTL_stackTrace.C::97 in _Z17AS_UTL_catchCrashiP9siginfo_tPv()\r\n(null)::0 in (null)()\r\n../../../../../libstdc++-v3/src/c++98/tree.cc::138 in local_Rb_tree_rotate_left()\r\n../../../../../libstdc++-v3/src/c++98/tree.cc::278 in _ZSt29_Rb_tree_insert_and_rebalancebPSt18_Rb_tree_node_baseS0_RS_()\r\n/usr/include/c++/4.8/bits/stl_tree.h::1025 in _ZNSt8_Rb_treeIjjSt9_IdentityIjESt4lessIjESaIjEE10_M_insert_EPSt18_Rb_tree_node_baseS7_RKj()\r\n/usr/include/c++/4.8/bits/stl_tree.h::1382 in _ZNSt8_Rb_treeIjjSt9_IdentityIjESt4lessIjESaIjEE16_M_insert_uniqueERKj()\r\n/usr/include/c++/4.8/bits/stl_set.h::463 in _ZNSt3setIjSt4lessIjESaIjEE6insertERKj()\r\nbogart/AS_BAT_BestOverlapGraph.C::417 in _ZN16BestOverlapGraph11findZombiesEPKc._omp_fn.3()\r\n../../../libgomp/team.c::116 in gomp_thread_start()\r\n(null)::0 in (null)()\r\n(null)::0 in (null)()\r\n(null)::0 in (null)()\r\n```\r\nThe contents of the 'log file':\r\n```\r\n-- Canu snapshot v1.7 +23 changes (r8715 967fcea3c70699eaccc92ff5bfe36d9d10e65a55)\r\n--\r\n-- CITATIONS\r\n--\r\n-- Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM.\r\n-- Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.\r\n-- Genome Res. 2017 May;27(5):722-736.\r\n-- http://doi.org/10.1101/gr.215087.116\r\n-- \r\n-- Read and contig alignments during correction, consensus and GFA building use:\r\n--   Šošic M, Šikic M.\r\n--   Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.\r\n--   Bioinformatics. 2017 May 1;33(9):1394-1395.\r\n--   http://doi.org/10.1093/bioinformatics/btw753\r\n-- \r\n-- Overlaps are generated using:\r\n--   Berlin K, et al.\r\n--   Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.\r\n--   Nat Biotechnol. 2015 Jun;33(6):623-30.\r\n--   http://doi.org/10.1038/nbt.3238\r\n-- \r\n--   Myers EW, et al.\r\n--   A Whole-Genome Assembly of Drosophila.\r\n--   Science. 2000 Mar 24;287(5461):2196-204.\r\n--   http://doi.org/10.1126/science.287.5461.2196\r\n-- \r\n--   Li H.\r\n--   Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.\r\n--   Bioinformatics. 2016 Jul 15;32(14):2103-10.\r\n--   http://doi.org/10.1093/bioinformatics/btw152\r\n-- \r\n-- Corrected read consensus sequences are generated using an algorithm derived from FALCON-sense:\r\n--   Chin CS, et al.\r\n--   Phased diploid genome assembly with single-molecule real-time sequencing.\r\n--   Nat Methods. 2016 Dec;13(12):1050-1054.\r\n--   http://doi.org/10.1038/nmeth.4035\r\n-- \r\n-- Contig consensus sequences are generated using an algorithm derived from pbdagcon:\r\n--   Chin CS, et al.\r\n--   Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.\r\n--   Nat Methods. 2013 Jun;10(6):563-9\r\n--   http://doi.org/10.1038/nmeth.2474\r\n-- \r\n-- CONFIGURE CANU\r\n--\r\n-- Detected Java(TM) Runtime Environment '1.8.0_92' (from '/net/gmi.oeaw.ac.at/software/mendel/intel-x86_64-sandybridge-avx/software/Java/1.8.0_92/bin/java').\r\n-- Detected gnuplot version '4.6 patchlevel 0' (from 'gnuplot') and image format 'svg'.\r\n-- Detected 16 CPUs and 189 gigabytes of memory.\r\n-- No grid engine detected, grid disabled.\r\n--\r\n--                            (tag)Concurrency\r\n--                     (tag)Threads          |\r\n--            (tag)Memory         |          |\r\n--        (tag)         |         |          |     total usage     algorithm\r\n--        -------  ------  --------   --------  -----------------  -----------------------------\r\n-- Local: meryl    189 GB   16 CPUs x   1 job    189 GB   16 CPUs  (k-mer counting)\r\n-- Local: cormhap   32 GB   16 CPUs x   1 job     32 GB   16 CPUs  (overlap detection with mhap)\r\n-- Local: obtovl    16 GB   16 CPUs x   1 job     16 GB   16 CPUs  (overlap detection)\r\n-- Local: utgovl    16 GB   16 CPUs x   1 job     16 GB   16 CPUs  (overlap detection)\r\n-- Local: ovb        4 GB    1 CPU  x  16 jobs    64 GB   16 CPUs  (overlap store bucketizer)\r\n-- Local: ovs       32 GB    1 CPU  x   5 jobs   160 GB    5 CPUs  (overlap store sorting)\r\n-- Local: red        8 GB    4 CPUs x   4 jobs    32 GB   16 CPUs  (read error detection)\r\n-- Local: oea        4 GB    1 CPU  x  16 jobs    64 GB   16 CPUs  (overlap error adjustment)\r\n-- Local: bat      189 GB   16 CPUs x   1 job    189 GB   16 CPUs  (contig construction)\r\n-- Local: gfa       16 GB   16 CPUs x   1 job     16 GB   16 CPUs  (GFA alignment and processing)\r\n--\r\n-- In 'HEcanuCorrLo.gkpStore', found PacBio reads:\r\n--   Raw:        0\r\n--   Corrected:  2138563\r\n--   Trimmed:    2138563\r\n--\r\n-- Generating assembly 'HEcanuCorrLo' in '/lustre/scratch/users/ovidiu.paun/PacBio'\r\n--\r\n-- Parameters:\r\n--\r\n--  genomeSize        1300000000\r\n--\r\n--  Overlap Generation Limits:\r\n--    corOvlErrorRate 0.2400 ( 24.00%)\r\n--    obtOvlErrorRate 0.1050 ( 10.50%)\r\n--    utgOvlErrorRate 0.1050 ( 10.50%)\r\n--\r\n--  Overlap Processing Limits:\r\n--    corErrorRate    0.3000 ( 30.00%)\r\n--    obtErrorRate    0.1050 ( 10.50%)\r\n--    utgErrorRate    0.1050 ( 10.50%)\r\n--    cnsErrorRate    0.1050 ( 10.50%)\r\n--\r\n--\r\n-- BEGIN ASSEMBLY\r\n--\r\n--\r\n-- Running jobs.  First attempt out of 2.\r\n----------------------------------------\r\n-- Starting 'utgovl' concurrent execution on Sun Mar 25 23:09:59 2018 with 15192.636 GB free disk space (16 processes; 1 concurrently)\r\n\r\n    cd unitigging/1-overlapper\r\n    ./overlap.sh 28 > ./overlap.000028.out 2>&1\r\n    ./overlap.sh 29 > ./overlap.000029.out 2>&1\r\n    ./overlap.sh 30 > ./overlap.000030.out 2>&1\r\n    ./overlap.sh 31 > ./overlap.000031.out 2>&1\r\n    ./overlap.sh 32 > ./overlap.000032.out 2>&1\r\n    ./overlap.sh 33 > ./overlap.000033.out 2>&1\r\n    ./overlap.sh 34 > ./overlap.000034.out 2>&1\r\n    ./overlap.sh 35 > ./overlap.000035.out 2>&1\r\n    ./overlap.sh 36 > ./overlap.000036.out 2>&1\r\n    ./overlap.sh 37 > ./overlap.000037.out 2>&1\r\n    ./overlap.sh 38 > ./overlap.000038.out 2>&1\r\n    ./overlap.sh 39 > ./overlap.000039.out 2>&1\r\n    ./overlap.sh 40 > ./overlap.000040.out 2>&1\r\n    ./overlap.sh 41 > ./overlap.000041.out 2>&1\r\n    ./overlap.sh 42 > ./overlap.000042.out 2>&1\r\n    ./overlap.sh 43 > ./overlap.000043.out 2>&1\r\n\r\n-- Finished on Wed Mar 28 18:12:47 2018 (241368 seconds) with 14171.596 GB free disk space\r\n----------------------------------------\r\n-- Found 43 overlapInCore output files.\r\n--\r\n-- overlapInCore compute 'unitigging/1-overlapper':\r\n--   kmer hits\r\n--     with no overlap      45501570067  6048.06977 +- 620223540.657\r\n--     with an overlap         78719890  5.11627907 +- 1063541.313\r\n--\r\n--   overlaps                  78719890  5.11627907 +- 1063541.313\r\n--     contained               26906585  .534883721 +- 377754.298\r\n--     dovetail                51813305  0.58139535 +- 686550.596\r\n--\r\n--   overlaps rejected\r\n--     multiple per pair              0           0 +- 0\r\n--     bad short window               0           0 +- 0\r\n--     bad long window                0           0 +- 0\r\n----------------------------------------\r\n-- Starting command on Wed Mar 28 18:12:47 2018 with 14171.596 GB free disk space\r\n\r\n    cd unitigging\r\n   /canu/Linux-amd64/bin/ovStoreBuild \\\r\n     -O ./HEcanuCorrLo.ovlStore.BUILDING \\\r\n     -G ./HEcanuCorrLo.gkpStore \\\r\n     -M 4-32 \\\r\n     -L ./1-overlapper/ovljob.files \\\r\n     > ./HEcanuCorrLo.ovlStore.err 2>&1\r\n\r\n-- Finished on Wed Mar 28 18:15:10 2018 (143 seconds) with 14152.947 GB free disk space\r\n----------------------------------------\r\n-- Checking store.\r\n----------------------------------------\r\n-- Starting command on Wed Mar 28 18:15:10 2018 with 14152.947 GB free disk space\r\n\r\n    cd unitigging\r\n   /canu/Linux-amd64/bin/ovStoreDump \\\r\n     -G ./HEcanuCorrLo.gkpStore \\\r\n     -O ./HEcanuCorrLo.ovlStore \\\r\n     -d -counts \\\r\n     > ./HEcanuCorrLo.ovlStore/counts.dat 2> ./HEcanuCorrLo.ovlStore/counts.err\r\n\r\n-- Finished on Wed Mar 28 18:15:11 2018 (1 second) with 14152.947 GB free disk space\r\n----------------------------------------\r\n--\r\n-- Overlap store 'unitigging/HEcanuCorrLo.ovlStore' successfully constructed.\r\n-- Found 157439780 overlaps for 550391 reads; 1588172 reads have no overlaps.\r\n--\r\n--\r\n-- Purged 1.572 GB in 129 overlap output files.\r\n----------------------------------------\r\n-- Starting command on Wed Mar 28 18:15:14 2018 with 14152.39 GB free disk space\r\n\r\n    cd unitigging\r\n   /canu/Linux-amd64/bin/ovStoreStats \\\r\n     -G ./HEcanuCorrLo.gkpStore \\\r\n     -O ./HEcanuCorrLo.ovlStore \\\r\n     -C 11 \\\r\n     -o ./HEcanuCorrLo.ovlStore \\\r\n     > ./HEcanuCorrLo.ovlStore.summary.err 2>&1\r\n\r\n-- Finished on Wed Mar 28 18:16:05 2018 (51 seconds) with 14148.996 GB free disk space\r\n----------------------------------------\r\n--\r\n-- Overlap store 'unitigging/HEcanuCorrLo.ovlStore' contains:\r\n--\r\n--   category            reads     %          read length        feature size or coverage  analysis\r\n--   ----------------  -------  -------  ----------------------  ------------------------  --------------------\r\n--   middle-missing      77125    3.61    11221.40 +- 6346.65       3338.89 +- 3694.25    (bad trimming)\r\n--   middle-hump         61626    2.88    11920.87 +- 6178.76       9550.08 +- 6039.32    (bad trimming)\r\n--   no-5-prime         180664    8.45     7729.42 +- 4847.88       5592.58 +- 4630.36    (bad trimming)\r\n--   no-3-prime          99962    4.67     7417.30 +- 4463.44       5276.57 +- 4241.36    (bad trimming)\r\n--   \r\n--   low-coverage        16160    0.76     3561.37 +- 2421.01          1.75 +- 0.76       (easy to assemble, potential for lower quality consensus)\r\n--   unique              16974    0.79     3741.52 +- 2491.78          8.00 +- 2.99       (easy to assemble, perfect, yay)\r\n--   repeat-cont         61443    2.87     5770.34 +- 3660.59        929.18 +- 1259.15    (potential for consensus errors, no impact on assembly)\r\n--   repeat-dove           632    0.03    15601.24 +- 7152.88        453.37 +- 581.10     (hard to assemble, likely won't assemble correctly or even at all)\r\n--   \r\n--   span-repeat          5299    0.25     6810.68 +- 3631.66       2594.70 +- 2564.25    (read spans a large repeat, usually easy to assemble)\r\n--   uniq-repeat-cont    20664    0.97     5177.34 +- 3198.95                             (should be uniquely placed, low potential for consensus errors, no impact on assembly)\r\n--   uniq-repeat-dove     4807    0.22     8171.09 +- 4468.72                             (will end contigs, potential to misassemble)\r\n--   uniq-anchor          5035    0.24     9108.13 +- 4910.64       1420.18 +- 1816.33    (repeat read, with unique section, probable bad read)\r\n--\r\n-- Loading read lengths.\r\n-- Loading number of overlaps per read.\r\n--\r\n-- Configure RED for 8gb memory.\r\n--                   Batches of at most (unlimited) reads.\r\n--                                      500000000 bases.\r\n--                   Expecting evidence of at most 751708149 bases per iteration.\r\n--\r\n--           Total                                               Reads                 Olaps Evidence\r\n--    Job   Memory      Read Range         Reads        Bases   Memory        Olaps   Memory   Memory  (Memory in MB)\r\n--   ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------\r\n--      1  8192.02         1-53236         53236    406751735  4656.58      4690102    53.67  1433.77\r\n--      2  8192.03     53237-108640        55404    407058176  4660.15      4378311    50.11  1433.77\r\n--      3  8192.06    108641-165681        57041    407060655  4660.23      4373937    50.06  1433.77\r\n--      4  8192.20    165682-223579        57898    406926469  4658.73      4517802    51.70  1433.77\r\n--      5  8192.02    223580-281937        58358    406768637  4656.93      4658623    53.31  1433.77\r\n--      6  8192.02    281938-340027        58090    407147650  4661.26      4280241    48.98  1433.77\r\n--      7  8192.03    340028-398170        58143    406903129  4658.47      4525458    51.79  1433.77\r\n--      8  8192.02    398171-456141        57971    406961128  4659.12      4467801    51.13  1433.77\r\n--      9  8192.06    456142-514312        58171    407007916  4659.67      4423468    50.62  1433.77\r\n--     10  8192.02    514313-572003        57691    407213170  4662.00      4215923    48.25  1433.77\r\n--     11  8192.03    572004-628990        56987    407220443  4662.06      4211870    48.20  1433.77\r\n--     12  8192.01    628991-684956        55966    407046114  4660.03      4386794    50.20  1433.77\r\n--     13  8192.11    684957-743122        58166    406875055  4658.15      4560387    52.19  1433.77\r\n--     14  8192.07    743123-801973        58851    407168672  4661.53      4261673    48.77  1433.77\r\n--     15  8192.12    801974-860697        58724    407244086  4662.39      4191514    47.97  1433.77\r\n--     16  8192.01    860698-919443        58746    406938801  4658.89      4486500    51.34  1433.77\r\n--     17  8192.08    919444-977503        58060    407058542  4660.24      4374867    50.07  1433.77\r\n--     18  8192.04    977504-1034412       56909    407141746  4661.16      4291247    49.11  1433.77\r\n--     19  8192.23   1034413-1090958       56546    407051103  4660.11      4399832    50.35  1433.77\r\n--     20  8192.02   1090959-1150102       59144    407180421  4661.67      4244928    48.58  1433.77\r\n--     21  8192.05   1150103-1210676       60574    407327615  4663.40      4096032    46.88  1433.77\r\n--     22  8192.10   1210677-1271576       60900    407364754  4663.84      4062336    46.49  1433.77\r\n--     23  8192.29   1271577-1332469       60893    407401180  4664.25      4042686    46.26  1433.77\r\n--     24  8192.01   1332470-1392863       60394    407183726  4661.75      4237685    48.50  1433.77\r\n--     25  8192.06   1392864-1453334       60471    407245779  4662.46      4179038    47.83  1433.77\r\n--     26  8192.08   1453335-1513091       59757    407093086  4660.69      4335507    49.62  1433.77\r\n--     27  8192.01   1513092-1572596       59505    406820379  4657.56      4603248    52.68  1433.77\r\n--     28  8192.17   1572597-1631900       59304    406782920  4657.13      4655267    53.28  1433.77\r\n--     29  8192.00   1631901-1691702       59802    406834482  4657.73      4587501    52.50  1433.77\r\n--     30  8192.05   1691703-1753446       61744    406920733  4658.78      4499911    51.50  1433.77\r\n--     31  8192.08   1753447-1817396       63950    406924947  4658.90      4492130    51.41  1433.77\r\n--     32  8192.09   1817397-1881863       64467    407192994  4661.98      4223568    48.33  1433.77\r\n--     33  8192.10   1881864-1946497       64634    407068661  4660.57      4348615    49.77  1433.77\r\n--     34  8192.10   1946498-2011054       64557    407341488  4663.69      4076124    46.65  1433.77\r\n--     35  8192.11   2011055-2074416       63362    406965302  4659.34      4456528    51.00  1433.77\r\n--     36  8192.02   2074417-2136642       62226    406949112  4659.12      4467353    51.12  1433.77\r\n--     37  3633.09   2136643-2138563        1921     13082253   149.77       134973     1.54  1433.77\r\n--   ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------\r\n--                                                14667223059             157439780\r\n--\r\n-- Running jobs.  First attempt out of 2.\r\n----------------------------------------\r\n-- Starting 'red' concurrent execution on Wed Mar 28 18:16:32 2018 with 14147.134 GB free disk space (37 processes; 4 concurrently)\r\n\r\n    cd unitigging/3-overlapErrorAdjustment\r\n    ./red.sh 1 > ./red.000001.out 2>&1\r\n    ./red.sh 2 > ./red.000002.out 2>&1\r\n    ./red.sh 3 > ./red.000003.out 2>&1\r\n    ./red.sh 4 > ./red.000004.out 2>&1\r\n    ./red.sh 5 > ./red.000005.out 2>&1\r\n    ./red.sh 6 > ./red.000006.out 2>&1\r\n    ./red.sh 7 > ./red.000007.out 2>&1\r\n    ./red.sh 8 > ./red.000008.out 2>&1\r\n    ./red.sh 9 > ./red.000009.out 2>&1\r\n    ./red.sh 10 > ./red.000010.out 2>&1\r\n    ./red.sh 11 > ./red.000011.out 2>&1\r\n    ./red.sh 12 > ./red.000012.out 2>&1\r\n    ./red.sh 13 > ./red.000013.out 2>&1\r\n    ./red.sh 14 > ./red.000014.out 2>&1\r\n    ./red.sh 15 > ./red.000015.out 2>&1\r\n    ./red.sh 16 > ./red.000016.out 2>&1\r\n    ./red.sh 17 > ./red.000017.out 2>&1\r\n    ./red.sh 18 > ./red.000018.out 2>&1\r\n    ./red.sh 19 > ./red.000019.out 2>&1\r\n    ./red.sh 20 > ./red.000020.out 2>&1\r\n    ./red.sh 21 > ./red.000021.out 2>&1\r\n    ./red.sh 22 > ./red.000022.out 2>&1\r\n    ./red.sh 23 > ./red.000023.out 2>&1\r\n    ./red.sh 24 > ./red.000024.out 2>&1\r\n    ./red.sh 25 > ./red.000025.out 2>&1\r\n    ./red.sh 26 > ./red.000026.out 2>&1\r\n    ./red.sh 27 > ./red.000027.out 2>&1\r\n    ./red.sh 28 > ./red.000028.out 2>&1\r\n    ./red.sh 29 > ./red.000029.out 2>&1\r\n    ./red.sh 30 > ./red.000030.out 2>&1\r\n    ./red.sh 31 > ./red.000031.out 2>&1\r\n    ./red.sh 32 > ./red.000032.out 2>&1\r\n    ./red.sh 33 > ./red.000033.out 2>&1\r\n    ./red.sh 34 > ./red.000034.out 2>&1\r\n    ./red.sh 35 > ./red.000035.out 2>&1\r\n    ./red.sh 36 > ./red.000036.out 2>&1\r\n    ./red.sh 37 > ./red.000037.out 2>&1\r\n\r\n-- Finished on Wed Mar 28 19:43:48 2018 (5236 seconds) with 13822.363 GB free disk space\r\n----------------------------------------\r\n-- Found 37 read error detection output files.\r\n--\r\n-- Loading read lengths.\r\n-- Loading number of overlaps per read.\r\n--\r\n-- Configure OEA for 4gb memory.\r\n--                   Batches of at most (unlimited) reads.\r\n--                                      300000000 bases.\r\n--\r\n--           Total                                               Reads                 Olaps  Adjusts\r\n--    Job   Memory      Read Range         Reads        Bases   Memory        Olaps   Memory   Memory  (Memory in MB)\r\n--   ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------\r\n--      1  3022.12         1-39387         39387    300001809   295.31      3405530   103.93   574.88\r\n--      2  3019.34     39388-78986         39599    300001730   295.31      3314228   101.14   574.88\r\n--      3  3013.92     78987-120511        41525    300005698   295.37      3134633    95.66   574.88\r\n--      4  3021.27    120512-162713        42202    300006623   295.40      3374914   102.99   574.88\r\n--      5  3015.90    162714-205447        42734    300005738   295.41      3198499    97.61   574.88\r\n--      6  3025.96    205448-248391        42944    300001634   295.41      3527889   107.66   574.88\r\n--      7  3018.78    248392-291146        42755    300000693   295.41      3292801   100.49   574.88\r\n--      8  3015.79    291147-334159        43013    300006775   295.42      3194383    97.48   574.88\r\n--      9  3017.60    334160-376856        42697    300006630   295.41      3254191    99.31   574.88\r\n--     10  3022.95    376857-419505        42649    300003122   295.41      3429569   104.66   574.88\r\n--     11  3017.35    419506-462579        43074    300003180   295.42      3245520    99.05   574.88\r\n--     12  3018.38    462580-505406        42827    300022708   295.43      3278936   100.07   574.88\r\n--     13  3013.41    505407-547799        42393    300008097   295.40      3117190    95.13   574.88\r\n--     14  3008.12    547800-590464        42665    300007331   295.41      2943476    89.83   574.88\r\n--     15  3018.79    590465-632166        41702    300007048   295.38      3294131   100.53   574.88\r\n--     16  3017.18    632167-673187        41021    300000621   295.35      3242224    98.94   574.88\r\n--     17  3017.94    673188-715932        42745    300004316   295.41      3265342    99.65   574.88\r\n--     18  3023.90    715933-758883        42951    300022712   295.43      3459705   105.58   574.88\r\n--     19  3010.15    758884-802258        43375    300006622   295.43      3009352    91.84   574.88\r\n--     20  3013.10    802259-845562        43304    300004264   295.43      3106071    94.79   574.88\r\n--     21  3018.56    845563-888981        43419    300011068   295.44      3284750   100.24   574.88\r\n--     22  3015.40    888982-932138        43157    300001161   295.42      3181821    97.10   574.88\r\n--     23  3017.36    932139-974885        42747    300002388   295.41      3246240    99.07   574.88\r\n--     24  3014.79    974886-1016930       42045    300003372   295.39      3162788    96.52   574.88\r\n--     25  3012.00   1016931-1058658       41728    300003312   295.38      3071756    93.74   574.88\r\n--     26  3019.50   1058659-1100376       41718    300003579   295.38      3317371   101.24   574.88\r\n--     27  3014.53   1100377-1144201       43825    300005645   295.45      3152457    96.21   574.88\r\n--     28  3010.42   1144202-1188614       44413    300001584   295.46      3017350    92.08   574.88\r\n--     29  3012.34   1188615-1233389       44775    300009590   295.48      3079485    93.98   574.88\r\n--     30  3007.96   1233390-1278361       44972    300011643   295.49      2935869    89.60   574.88\r\n--     31  3009.54   1278362-1323247       44886    300001380   295.47      2988071    91.19   574.88\r\n--     32  3013.02   1323248-1367846       44599    300004461   295.47      3102057    94.67   574.88\r\n--     33  3012.70   1367847-1412070       44224    300014065   295.47      3091839    94.36   574.88\r\n--     34  3012.25   1412071-1456755       44685    300006820   295.47      3076846    93.90   574.88\r\n--     35  3017.97   1456756-1500798       44043    300003167   295.45      3265019    99.64   574.88\r\n--     36  3020.15   1500799-1544662       43864    300009600   295.45      3336422   101.82   574.88\r\n--     37  3020.66   1544663-1588578       43916    300002472   295.44      3353143   102.33   574.88\r\n--     38  3023.31   1588579-1632227       43649    300011383   295.45      3440228   104.99   574.88\r\n--     39  3023.18   1632228-1676299       44072    300006196   295.45      3435557   104.84   574.88\r\n--     40  3023.69   1676300-1721098       44799    300006682   295.48      3451504   105.33   574.88\r\n--     41  3015.36   1721099-1767180       46082    300003784   295.51      3177516    96.97   574.88\r\n--     42  3018.60   1767181-1814386       47206    300007039   295.55      3282206   100.16   574.88\r\n--     43  3015.36   1814387-1861924       47538    300006251   295.56      3175976    96.92   574.88\r\n--     44  3017.75   1861925-1909502       47578    300010111   295.56      3254158    99.31   574.88\r\n--     45  3011.11   1909503-1957203       47701    300007354   295.57      3036325    92.66   574.88\r\n--     46  3007.58   1957204-2004771       47568    300000013   295.55      2920950    89.14   574.88\r\n--     47  3019.55   2004772-2051632       46861    300026111   295.56      3313293   101.11   574.88\r\n--     48  3016.49   2051633-2097750       46118    300007429   295.52      3214236    98.09   574.88\r\n--     49  2977.79   2097751-2138563       40813    266908048   263.79      2985963    91.12   574.88\r\n--   ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------\r\n--                                                14667223059             157439780\r\n--\r\n-- Running jobs.  First attempt out of 2.\r\n----------------------------------------\r\n-- Starting 'oea' concurrent execution on Wed Mar 28 19:44:17 2018 with 13821.989 GB free disk space (49 processes; 16 concurrently)\r\n\r\n    cd unitigging/3-overlapErrorAdjustment\r\n    ./oea.sh 1 > ./oea.000001.out 2>&1\r\n    ./oea.sh 2 > ./oea.000002.out 2>&1\r\n    ./oea.sh 3 > ./oea.000003.out 2>&1\r\n    ./oea.sh 4 > ./oea.000004.out 2>&1\r\n    ./oea.sh 5 > ./oea.000005.out 2>&1\r\n    ./oea.sh 6 > ./oea.000006.out 2>&1\r\n    ./oea.sh 7 > ./oea.000007.out 2>&1\r\n    ./oea.sh 8 > ./oea.000008.out 2>&1\r\n    ./oea.sh 9 > ./oea.000009.out 2>&1\r\n    ./oea.sh 10 > ./oea.000010.out 2>&1\r\n    ./oea.sh 11 > ./oea.000011.out 2>&1\r\n    ./oea.sh 12 > ./oea.000012.out 2>&1\r\n    ./oea.sh 13 > ./oea.000013.out 2>&1\r\n    ./oea.sh 14 > ./oea.000014.out 2>&1\r\n    ./oea.sh 15 > ./oea.000015.out 2>&1\r\n    ./oea.sh 16 > ./oea.000016.out 2>&1\r\n    ./oea.sh 17 > ./oea.000017.out 2>&1\r\n    ./oea.sh 18 > ./oea.000018.out 2>&1\r\n    ./oea.sh 19 > ./oea.000019.out 2>&1\r\n    ./oea.sh 20 > ./oea.000020.out 2>&1\r\n    ./oea.sh 21 > ./oea.000021.out 2>&1\r\n    ./oea.sh 22 > ./oea.000022.out 2>&1\r\n    ./oea.sh 23 > ./oea.000023.out 2>&1\r\n    ./oea.sh 24 > ./oea.000024.out 2>&1\r\n    ./oea.sh 25 > ./oea.000025.out 2>&1\r\n    ./oea.sh 26 > ./oea.000026.out 2>&1\r\n    ./oea.sh 27 > ./oea.000027.out 2>&1\r\n    ./oea.sh 28 > ./oea.000028.out 2>&1\r\n    ./oea.sh 29 > ./oea.000029.out 2>&1\r\n    ./oea.sh 30 > ./oea.000030.out 2>&1\r\n    ./oea.sh 31 > ./oea.000031.out 2>&1\r\n    ./oea.sh 32 > ./oea.000032.out 2>&1\r\n    ./oea.sh 33 > ./oea.000033.out 2>&1\r\n    ./oea.sh 34 > ./oea.000034.out 2>&1\r\n    ./oea.sh 35 > ./oea.000035.out 2>&1\r\n    ./oea.sh 36 > ./oea.000036.out 2>&1\r\n    ./oea.sh 37 > ./oea.000037.out 2>&1\r\n    ./oea.sh 38 > ./oea.000038.out 2>&1\r\n    ./oea.sh 39 > ./oea.000039.out 2>&1\r\n    ./oea.sh 40 > ./oea.000040.out 2>&1\r\n    ./oea.sh 41 > ./oea.000041.out 2>&1\r\n    ./oea.sh 42 > ./oea.000042.out 2>&1\r\n    ./oea.sh 43 > ./oea.000043.out 2>&1\r\n    ./oea.sh 44 > ./oea.000044.out 2>&1\r\n    ./oea.sh 45 > ./oea.000045.out 2>&1\r\n    ./oea.sh 46 > ./oea.000046.out 2>&1\r\n    ./oea.sh 47 > ./oea.000047.out 2>&1\r\n    ./oea.sh 48 > ./oea.000048.out 2>&1\r\n    ./oea.sh 49 > ./oea.000049.out 2>&1\r\n\r\n-- Finished on Wed Mar 28 21:23:32 2018 (5955 seconds) with 14531.423 GB free disk space\r\n----------------------------------------\r\n-- Found 49 overlap error adjustment output files.\r\n----------------------------------------\r\n-- Starting command on Wed Mar 28 21:23:32 2018 with 14531.423 GB free disk space\r\n\r\n    cd unitigging/3-overlapErrorAdjustment\r\n    /canu/Linux-amd64/bin/ovStoreBuild \\\r\n      -G ../HEcanuCorrLo.gkpStore \\\r\n      -O ../HEcanuCorrLo.ovlStore \\\r\n      -evalues \\\r\n      -L ./oea.files \\\r\n    > ./oea.apply.err 2>&1\r\n\r\n-- Finished on Wed Mar 28 21:23:33 2018 (1 second) with 14531.423 GB free disk space\r\n----------------------------------------\r\n-- No report available.\r\n--\r\n-- Running jobs.  First attempt out of 2.\r\n----------------------------------------\r\n-- Starting 'bat' concurrent execution on Wed Mar 28 21:23:33 2018 with 14531.423 GB free disk space (1 processes; 1 concurrently)\r\n\r\n    cd unitigging/4-unitigger\r\n    ./unitigger.sh 1 > ./unitigger.000001.out 2>&1\r\n\r\n-- Finished on Wed Mar 28 21:24:37 2018 (64 seconds) with 14526.822 GB free disk space\r\n----------------------------------------\r\n--\r\n-- Bogart failed, retry\r\n--\r\n--\r\n-- Running jobs.  Second attempt out of 2.\r\n----------------------------------------\r\n-- Starting 'bat' concurrent execution on Wed Mar 28 21:24:37 2018 with 14526.822 GB free disk space (1 processes; 1 concurrently)\r\n\r\n    cd unitigging/4-unitigger\r\n    ./unitigger.sh 1 > ./unitigger.000001.out 2>&1\r\n\r\n-- Finished on Wed Mar 28 21:25:36 2018 (59 seconds) with 14537.416 GB free disk space\r\n----------------------------------------\r\n--\r\n-- Bogart failed, tried 2 times, giving up.\r\n--\r\n\r\nABORT:\r\nABORT: Canu snapshot v1.7 +23 changes (r8715 967fcea3c70699eaccc92ff5bfe36d9d10e65a55)\r\nABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.\r\nABORT: Try restarting.  If that doesn't work, ask for help.\r\nABORT:\r\n```"}}
{"actor":{"display_login":"brianwalenz"}}