Found perl:
   /home/jwn2291/.conda/envs/plus/bin/perl
   This is perl 5, version 26, subversion 2 (v5.26.2) built for x86_64-linux-thread-multi

Found java:
   /home/jwn2291/.conda/envs/plus/bin/java
   openjdk version "11.0.1" 2018-10-16 LTS

Found canu:
   /projects/b1100/jwn2291/software/canu/build/bin/canu
   canu snapshot v2.2-development +69 changes (r10178 fcd7f964c882d3a346e6c0c227bab18dc5c97577)

-- canu snapshot v2.2-development +69 changes (r10178 fcd7f964c882d3a346e6c0c227bab18dc5c97577)
--
-- CITATIONS
--
-- For 'standard' assemblies of PacBio or Nanopore reads:
--   Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM.
--   Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
--   Genome Res. 2017 May;27(5):722-736.
--   http://doi.org/10.1101/gr.215087.116
-- 
-- Read and contig alignments during correction and consensus use:
--   Šošic M, Šikic M.
--   Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.
--   Bioinformatics. 2017 May 1;33(9):1394-1395.
--   http://doi.org/10.1093/bioinformatics/btw753
-- 
-- Overlaps are generated using:
--   Berlin K, et al.
--   Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.
--   Nat Biotechnol. 2015 Jun;33(6):623-30.
--   http://doi.org/10.1038/nbt.3238
-- 
--   Myers EW, et al.
--   A Whole-Genome Assembly of Drosophila.
--   Science. 2000 Mar 24;287(5461):2196-204.
--   http://doi.org/10.1126/science.287.5461.2196
-- 
-- Corrected read consensus sequences are generated using an algorithm derived from FALCON-sense:
--   Chin CS, et al.
--   Phased diploid genome assembly with single-molecule real-time sequencing.
--   Nat Methods. 2016 Dec;13(12):1050-1054.
--   http://doi.org/10.1038/nmeth.4035
-- 
-- Contig consensus sequences are generated using an algorithm derived from pbdagcon:
--   Chin CS, et al.
--   Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
--   Nat Methods. 2013 Jun;10(6):563-9
--   http://doi.org/10.1038/nmeth.2474
-- 
-- CONFIGURE CANU
--
-- Detected Java(TM) Runtime Environment '11.0.1' (from '/home/jwn2291/.conda/envs/plus/bin/java') without -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 28 CPUs and 1007 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Detected Slurm with task IDs up to 19999 allowed.
-- 
-- Found   4 hosts with  32 cores and  187 GB memory under Slurm control.
-- Found  72 hosts with  28 cores and   92 GB memory under Slurm control.
-- Found  11 hosts with  52 cores and  187 GB memory under Slurm control.
-- Found   4 hosts with  24 cores and  125 GB memory under Slurm control.
-- Found 198 hosts with  24 cores and  124 GB memory under Slurm control.
-- Found   3 hosts with  28 cores and  502 GB memory under Slurm control.
-- Found   1 host  with  28 cores and  123 GB memory under Slurm control.
-- Found  44 hosts with  40 cores and  187 GB memory under Slurm control.
-- Found 324 hosts with  28 cores and  124 GB memory under Slurm control.
-- Found  49 hosts with  28 cores and  187 GB memory under Slurm control.
-- Found   2 hosts with  28 cores and 1006 GB memory under Slurm control.
--
--                         (tag)Threads
--                (tag)Memory         |
--        (tag)             |         |  algorithm
--        -------  ----------  --------  -----------------------------
-- Grid:  meryl     26.000 GB    7 CPUs  (k-mer counting)
-- Grid:  hap       16.000 GB   24 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   17.000 GB    4 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    24.000 GB    7 CPUs  (overlap detection)
-- Grid:  utgovl    24.000 GB    7 CPUs  (overlap detection)
-- Grid:  cor       24.000 GB    4 CPUs  (read correction)
-- Grid:  ovb        4.000 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       32.000 GB    1 CPU   (overlap store sorting)
-- Grid:  red       37.000 GB    8 CPUs  (read error detection)
-- Grid:  oea        8.000 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      187.000 GB   32 CPUs  (contig construction with bogart)
-- Grid:  cns        -.--- GB    8 CPUs  (consensus)
--
-- Found Nanopore reads in 'outRes.seqStore':
--   Libraries:
--     Nanopore:              1
--   Reads:
--     Raw:                   119833157302
--     Corrected:             89535458442
--     Corrected and Trimmed: 87792316061
--
--
-- Generating assembly 'outRes' in '/projects/jwn2291/WGS/':
--   genomeSize:
--     3500000000
--
--   Overlap Generation Limits:
--     corOvlErrorRate 0.3200 ( 32.00%)
--     obtOvlErrorRate 0.1200 ( 12.00%)
--     utgOvlErrorRate 0.1200 ( 12.00%)
--
--   Overlap Processing Limits:
--     corErrorRate    0.5000 ( 50.00%)
--     obtErrorRate    0.1200 ( 12.00%)
--     utgErrorRate    0.1200 ( 12.00%)
--     cnsErrorRate    0.2000 ( 20.00%)
--
--   Stages to run:
--     assemble corrected and trimmed reads.
--
--
-- Corrected reads exist in outRes.seqStore.
--
-- Trimmed reads exist in outRes.seqStore.
--
-- BEGIN ASSEMBLY
--
-- Bogart failed, tried 2 times, giving up.
--

ABORT:
ABORT: canu snapshot v2.2-development +69 changes (r10178 fcd7f964c882d3a346e6c0c227bab18dc5c97577)
ABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.
ABORT: Try restarting.  If that doesn't work, ask for help.
ABORT:
ABORT: Disk space available:  39405.75 GB
ABORT:
ABORT: Last 50 lines of the relevant log file (unitigging/4-unitigger/unitigger.err):
ABORT:
ABORT:   optimizePositions()--     changed:   1834133 reads
ABORT:   optimizePositions()--   Recomputing positions, iteration 4, with 32 threads.
ABORT:   optimizePositions()--     Reset zero.
ABORT:   optimizePositions()--     Checking convergence.
ABORT:   optimizePositions()--     converged: 1881632 reads
ABORT:   optimizePositions()--     changed:   1821626 reads
ABORT:   optimizePositions()--   Recomputing positions, iteration 5, with 32 threads.
ABORT:   optimizePositions()--     Reset zero.
ABORT:   optimizePositions()--     Checking convergence.
ABORT:   optimizePositions()--     converged: 1901495 reads
ABORT:   optimizePositions()--     changed:   1801763 reads
ABORT:   optimizePositions()--   Expanding short reads with 32 threads.
ABORT:   optimizePositions()--   Updating positions.
ABORT:   optimizePositions()--   Finished.
ABORT:   splitDiscontinuous()-- Tested 2789 tigs, split 9 tigs into 21 new tigs.
ABORT:   
ABORT:   ==> MERGE ORPHANS.
ABORT:   
ABORT:   computeErrorProfiles()-- Computing error profiles for 2819 tigs, with 32 threads.
ABORT:   computeErrorProfiles()-- Finished.
ABORT:   
ABORT:   findPotentialOrphans()-- working on 2819 tigs.
ABORT:   findPotentialOrphans()-- found 1223 potential orphans.
ABORT:   mergeOrphans()-- flagged     412        bubble tigs with 41679 reads
ABORT:   mergeOrphans()-- placed      133 unique orphan tigs with 5604 reads
ABORT:   mergeOrphans()-- shattered    56 repeat orphan tigs with 3244 reads
ABORT:   mergeOrphans()-- ignored      22               tigs with 3559 reads; failed to place
ABORT:   mergeOrphans()--
ABORT:   
ABORT:   ==> MARK SIMPLE BUBBLES.
ABORT:       using 0.010000 user-specified threshold
ABORT:   
ABORT:   
ABORT:   findPotentialOrphans()-- working on 2819 tigs.
ABORT:   read 2466988 at 1456192 1522940 olap to read 3177577 hangs 66862 66762 -> coords 1523054 1522940
ABORT:   bogart: bogart/AS_BAT_MergeOrphans.C:258: void findPotentialOrphans(TigVector&, BubTargetList&, bool): Assertion `mincoord < maxcoord' failed.
ABORT:   
ABORT:   Failed with 'Aborted'; backtrace (libbacktrace):
ABORT:   utility/src/utility/system-stackTrace.C::83 in _Z17AS_UTL_catchCrashiP9siginfo_tPv()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:   bogart/AS_BAT_MergeOrphans.C::258 in _Z20findPotentialOrphansR9TigVectorRSt3mapIjSt6vectorIjSaIjEESt4lessIjESaISt4pairIKjS4_EEEb()
ABORT:   bogart/AS_BAT_MergeOrphans.C::896 in _Z12mergeOrphansR9TigVectorddb()
ABORT:   bogart/bogart.C::572 in main()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:

==> PARAMETERS.

Resources:
  Memory                50 GB
  Compute Threads       20 (command line)

Lengths:
  Minimum read          0 bases
  Maximum read          4294967295 bases
  Minimum overlap       500 bases

Overlap Error Rates:
  Graph                 0.120 (12.000%)
  Max                   0.120 (12.000%)

Deviations:
  Graph                 12.000
  Bubble                1.000
  Repeat                1.000

Similarity Thresholds:
  Graph                 0.000
  Bubble                0.010
  Repeat                0.010

Edge Confusion:
  Absolute              2500
  Percent               15.0000

Unitig Construction:
  Minimum intersection  500 bases
  Maxiumum placements   2 positions

Debugging Enabled:
  (none)

==> LOADING AND FILTERING OVERLAPS.

ReadInfo()-- Found     2255634 reads.

OverlapCache()-- limited to 51200MB memory (user supplied).

OverlapCache()--      28MB for read data.
OverlapCache()--     113MB for best edges.
OverlapCache()--     367MB for tigs.
OverlapCache()--      98MB for tigs - read layouts.
OverlapCache()--     141MB for tigs - error profiles.
OverlapCache()--   12800MB for tigs - error profile overlaps.
OverlapCache()--       0MB for other processes.
OverlapCache()-- ---------
OverlapCache()--   13619MB for data structures (sum of above).
OverlapCache()-- ---------
OverlapCache()--      70MB for overlap store structure.
OverlapCache()--   37510MB for overlap data.
OverlapCache()-- ---------
OverlapCache()--   51200MB allowed.
OverlapCache()--
OverlapCache()-- Retain at least 50 overlaps/read, based on 25.08x coverage.
OverlapCache()-- Initial guess at 663 overlaps/read.
OverlapCache()--
OverlapCache()-- Adjusting for sparse overlaps.
OverlapCache()--
OverlapCache()--               reads loading olaps          olaps               memory
OverlapCache()--   olaps/read       all      some          loaded                 free
OverlapCache()--   ----------   -------   -------     ----------- -------     --------
OverlapCache()--          663   3427530    275727       420549242  55.54%      31092 MB
OverlapCache()--         8053   3702880       377       756931576  99.96%      25960 MB
OverlapCache()--      4520850   3703257         0       757247030 100.00%      25955 MB
OverlapCache()--
OverlapCache()-- Loading overlaps.
OverlapCache()--
OverlapCache()--          read from store           saved in cache
OverlapCache()--   ------------ ---------   ------------ ---------
OverlapCache()--       14361380 (001.90%)       14317854 (001.89%)
OverlapCache()--       28438923 (003.76%)       28353453 (003.74%)
OverlapCache()--       42483008 (005.61%)       42352424 (005.59%)
OverlapCache()--       82696369 (010.92%)       82482188 (010.89%)
OverlapCache()--      105186365 (013.89%)      104901726 (013.85%)
OverlapCache()--      126035633 (016.64%)      125684348 (016.60%)
OverlapCache()--      154741070 (020.43%)      154329339 (020.38%)
OverlapCache()--      169727901 (022.41%)      169274904 (022.35%)
OverlapCache()--      182688399 (024.13%)      182199416 (024.06%)
OverlapCache()--      197035705 (026.02%)      196501103 (025.95%)
OverlapCache()--      219480679 (028.98%)      218884684 (028.91%)
OverlapCache()--      240180077 (031.72%)      239533812 (031.63%)
OverlapCache()--      262085903 (034.61%)      261375907 (034.52%)
OverlapCache()--      282764695 (037.34%)      281994298 (037.24%)
OverlapCache()--      303043723 (040.02%)      302209678 (039.91%)
OverlapCache()--      323045538 (042.66%)      322154019 (042.54%)
OverlapCache()--      343988533 (045.43%)      343040420 (045.30%)
OverlapCache()--      365895219 (048.32%)      364867615 (048.18%)
OverlapCache()--      386396447 (051.03%)      385299953 (050.88%)
OverlapCache()--      407072282 (053.76%)      405904062 (053.60%)
OverlapCache()--      427654987 (056.47%)      426431384 (056.31%)
OverlapCache()--      447017954 (059.03%)      445729731 (058.86%)
OverlapCache()--      467291293 (061.71%)      465944296 (061.53%)
OverlapCache()--      487903484 (064.43%)      486498873 (064.25%)
OverlapCache()--      509134188 (067.23%)      507664094 (067.04%)
OverlapCache()--      529792366 (069.96%)      528267534 (069.76%)
OverlapCache()--      549822616 (072.61%)      548234784 (072.40%)
OverlapCache()--      571028533 (075.41%)      569362466 (075.19%)
OverlapCache()--      591717466 (078.14%)      589990417 (077.91%)
OverlapCache()--      612761514 (080.92%)      610980694 (080.68%)
OverlapCache()--      633950053 (083.72%)      632109565 (083.47%)
OverlapCache()--      655697485 (086.59%)      653795504 (086.34%)
OverlapCache()--      674893327 (089.12%)      672931803 (088.87%)
OverlapCache()--      694320297 (091.69%)      692296243 (091.42%)
OverlapCache()--      714728615 (094.39%)      712639352 (094.11%)
OverlapCache()--      735946769 (097.19%)      733787946 (096.90%)
OverlapCache()--      756588565 (099.91%)      754369338 (099.62%)
OverlapCache()--   ------------ ---------   ------------ ---------
OverlapCache()--      757247030 (100.00%)      755025624 (099.71%)
OverlapCache()--
OverlapCache()-- Ignored 1791242 duplicate overlaps.
OverlapCache()--
OverlapCache()-- Symmetrizing overlaps.
OverlapCache()--   Finding missing twins.
OverlapCache()--   In 755025624 overlaps:
OverlapCache()--     Found 116121601 overlaps with non-symmetric error rates.
OverlapCache()--     Found 108438 overlaps with missing twins.
OverlapCache()--     Dropped 0 weak missing-twin overlaps.
OverlapCache()--   Shifting overlaps.
OverlapCache()--   Adding missing twins.
OverlapCache()--   Sorting overlaps.
OverlapCache()--   Checking overlap symmetry.
OverlapCache()--   Finished.

BestOverlapGraph()-- Computing Best Overlap Graph.
BestOverlapGraph()-- Allocating best edges (113MB).
BestOverlapGraph()-- Filtering high error edges.
BestOverlapGraph()--   Ignore overlaps with more than 2.881350% error.
BestOverlapGraph()-- Filtering reads with a gap in overlap coverage.
BestOverlapGraph()--   89720 reads removed.
BestOverlapGraph()-- Filtering reads with lopsided best edges (more than 25.00% different).
BestOverlapGraph()--   1815 reads have lopsided edges.
BestOverlapGraph()-- Filtering spur reads.
BestOverlapGraph()--   Initial          51565 terminal  spur reads -    53357/52880    5'/3' spur path reads.
BestOverlapGraph()--   Iteration 1 -    51565 terminal  spur reads -    53230/52759    5'/3' spur path reads -      449/449      edges changed to avoid spur path.
BestOverlapGraph()--   Iteration 2 -    51565 terminal  spur reads -    53201/52723    5'/3' spur path reads -       28/29       edges changed to avoid spur path.
BestOverlapGraph()--   Iteration 3 -    51565 terminal  spur reads -    53195/52720    5'/3' spur path reads -        3/2        edges changed to avoid spur path.
BestOverlapGraph()--   Iteration 4 -    51565 terminal  spur reads -    53195/52720    5'/3' spur path reads -        0/0        edges changed to avoid spur path.
BestOverlapGraph()--   Final            57416 confirmed spur reads -    53195/52720    5'/3' spur path reads.

==> BUILDING GREEDY TIGS.

breakSingletonTigs()-- Removed 20 singleton tigs; reads are now unplaced.
optimizePositions()-- Optimizing read positions for 3703258 reads in 2798 tigs, with 20 threads.
optimizePositions()--   Allocating scratch space for 3703258 reads (115726 KB).
optimizePositions()--   Initializing positions with 20 threads.
optimizePositions()--   Recomputing positions, iteration 1, with 20 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 2245351 reads
optimizePositions()--     changed:   1457907 reads
optimizePositions()--   Recomputing positions, iteration 2, with 20 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 2247763 reads
optimizePositions()--     changed:   1455495 reads
optimizePositions()--   Recomputing positions, iteration 3, with 20 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 2255102 reads
optimizePositions()--     changed:   1448156 reads
optimizePositions()--   Recomputing positions, iteration 4, with 20 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 2255407 reads
optimizePositions()--     changed:   1447851 reads
optimizePositions()--   Recomputing positions, iteration 5, with 20 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 2255487 reads
optimizePositions()--     changed:   1447771 reads
optimizePositions()--   Expanding short reads with 20 threads.
optimizePositions()--   Updating positions.
optimizePositions()--   Finished.
splitDiscontinuous()-- Tested 2777 tigs, split none.
detectSpur() done.
tested         1312
nEdges      5'  433   3'  438
nPotential       55        64
nVerified         0         0

==> PLACE CONTAINED READS.

computeErrorProfiles()-- Computing error profiles for 2798 tigs, with 20 threads.
computeErrorProfiles()-- Finished.

placeContains()-- placing 1934373 contained and 1590376 unplaced reads, with 20 threads.
placeContains()-- Placed 1920072 contained reads and 84672 unplaced reads.
placeContains()-- Failed to place 14301 contained reads (too high error suspected) and 1505704 unplaced reads (lack of overlaps suspected).
optimizePositions()-- Optimizing read positions for 3703258 reads in 2798 tigs, with 20 threads.
optimizePositions()--   Allocating scratch space for 3703258 reads (115726 KB).
optimizePositions()--   Initializing positions with 20 threads.
optimizePositions()--   Recomputing positions, iteration 1, with 20 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 1232244 reads
optimizePositions()--     changed:   2471014 reads
optimizePositions()--   Recomputing positions, iteration 2, with 20 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 1848999 reads
optimizePositions()--     changed:   1854259 reads
optimizePositions()--   Recomputing positions, iteration 3, with 20 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 1869125 reads
optimizePositions()--     changed:   1834133 reads
optimizePositions()--   Recomputing positions, iteration 4, with 20 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 1881632 reads
optimizePositions()--     changed:   1821626 reads
optimizePositions()--   Recomputing positions, iteration 5, with 20 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 1901495 reads
optimizePositions()--     changed:   1801763 reads
optimizePositions()--   Expanding short reads with 20 threads.
optimizePositions()--   Updating positions.
optimizePositions()--   Finished.
splitDiscontinuous()-- Tested 2789 tigs, split 9 tigs into 21 new tigs.

==> MERGE ORPHANS.

computeErrorProfiles()-- Computing error profiles for 2819 tigs, with 20 threads.
computeErrorProfiles()-- Finished.

findPotentialOrphans()-- working on 2819 tigs.
findPotentialOrphans()-- found 1223 potential orphans.
mergeOrphans()-- flagged     412        bubble tigs with 41679 reads
mergeOrphans()-- placed      133 unique orphan tigs with 5604 reads
mergeOrphans()-- shattered    56 repeat orphan tigs with 3244 reads
mergeOrphans()-- ignored      22               tigs with 3559 reads; failed to place
mergeOrphans()--

==> MARK SIMPLE BUBBLES.
    using 0.010000 user-specified threshold


findPotentialOrphans()-- working on 2819 tigs.
read 2466988 at 1456192 1522940 olap to read 3177577 hangs 66862 66762 -> coords 1523054 1522940
bogart: bogart/AS_BAT_MergeOrphans.C:258: void findPotentialOrphans(TigVector&, BubTargetList&, bool): Assertion `mincoord < maxcoord' failed.

Failed with 'Aborted'; backtrace (libbacktrace):
utility/src/utility/system-stackTrace.C::83 in _Z17AS_UTL_catchCrashiP9siginfo_tPv()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
bogart/AS_BAT_MergeOrphans.C::258 in _Z20findPotentialOrphansR9TigVectorRSt3mapIjSt6vectorIjSaIjEESt4lessIjESaISt4pairIKjS4_EEEb()
bogart/AS_BAT_MergeOrphans.C::896 in _Z12mergeOrphansR9TigVectorddb()
bogart/bogart.C::572 in main()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()