Bogart Fail with canu 1.7

[Bessem06]

I have a similar issue like #546 and #718 I installed canu 1.7 on an ubuntu (16.4) workstation. I have a 1G assembly length but with a very low nanopore reads coverage (5X). This is the command I used : canu -p X -d X_canu genomeSize=1g -nanopore-raw X.fastq corMinCoverage=0 useGrid=false maxMemory=64g maxThreads=6

This is the unitigger.err log

==> PARAMETERS.

Resources:
  Memory                64 GB
  Compute Threads       6 (command line)

Lengths:
  Minimum read          0 bases
  Minimum overlap       500 bases

Overlap Error Rates:
  Graph                 0.144 (14.400%)
  Max                   0.144 (14.400%)

Deviations:
  Graph                 6.000
  Bubble                6.000
  Repeat                3.000

Edge Confusion:
  Absolute              2100
  Percent               200.0000

Unitig Construction:
  Minimum intersection  500 bases
  Maxiumum placements   2 positions

Debugging Enabled:
  (none)

==> LOADING AND FILTERING OVERLAPS.

ReadInfo()-- Using 541708 reads, no minimum read length used.

OverlapCache()-- limited to 65536MB memory (user supplied).

OverlapCache()--       4MB for read data.
OverlapCache()--      20MB for best edges.
OverlapCache()--      53MB for tigs.
OverlapCache()--      14MB for tigs - read layouts.
OverlapCache()--      20MB for tigs - error profiles.
OverlapCache()--   16384MB for tigs - error profile overlaps.
OverlapCache()--       0MB for other processes.
OverlapCache()-- ---------
OverlapCache()--   16507MB for data structures (sum of above).
OverlapCache()-- ---------
OverlapCache()--      10MB for overlap store structure.
OverlapCache()--   49017MB for overlap data.
OverlapCache()-- ---------
OverlapCache()--   65536MB allowed.
OverlapCache()--
OverlapCache()-- Retain at least 3 overlaps/read, based on 1.64x coverage.
OverlapCache()-- Initial guess at 5930 overlaps/read.
OverlapCache()--
OverlapCache()-- Adjusting for sparse overlaps.
OverlapCache()--
OverlapCache()--               reads loading olaps          olaps               memory
OverlapCache()--   olaps/read       all      some          loaded                 free
OverlapCache()--   ----------   -------   -------     ----------- -------     --------
OverlapCache()--         5930    541301       407       151305132  99.95%      46708 MB
OverlapCache()--      7527103    541708         0       151386714 100.00%      46707 MB
OverlapCache()--
OverlapCache()-- Loading overlaps.
OverlapCache()--
OverlapCache()--          read from store           saved in cache
OverlapCache()--   ------------ ---------   ------------ ---------
OverlapCache()--       45163057 (029.83%)       45052037 (029.76%)
OverlapCache()--       89462599 (059.10%)       89239694 (058.95%)
OverlapCache()--      128408747 (084.82%)      128092895 (084.61%)
OverlapCache()--   ------------ ---------   ------------ ---------
OverlapCache()--      151386714 (100.00%)      151011835 (099.75%)
OverlapCache()--
OverlapCache()-- Ignored 171306 duplicate overlaps.
OverlapCache()--
OverlapCache()-- Symmetrizing overlaps.
OverlapCache()--   Finding missing twins.
OverlapCache()--   Found 47871 missing twins in 151011835 overlaps, 31 are strong.
OverlapCache()--   Dropping weak non-twin overlaps; allocated 0 MB scratch space.
OverlapCache()--   Dropped 574 overlaps; scratch space released.
OverlapCache()--   Adding 47297 missing twin overlaps.
OverlapCache()--   Finished.

BestOverlapGraph()-- allocating best edges (16MB)

BestOverlapGraph()-- finding initial best edges.

BestOverlapGraph()-- filtering suspicious reads.
BestOverlapGraph()-- marked 186977 reads as suspicious.

BestOverlapGraph()-- filtering high error edges.

BestOverlapGraph()-- filtering reads with lopsided best edges.

BestOverlapGraph()-- filtering spur reads.
BestOverlapGraph()-- detected 44569 spur reads and 210080 singleton reads.

BestOverlapGraph()-- removing best edges for contained reads.

==> BUILDING GREEDY TIGS.

breakSingletonTigs()-- Removed 61406 singleton tigs; reads are now unplaced.
optimizePositions()-- Optimizing read positions for 541709 reads in 67790 tigs, with 6 threads.
optimizePositions()--   Allocating scratch space for 541709 reads (33856 KB).
optimizePositions()--   Initializing positions with 6 threads.
optimizePositions()--   Recomputing positions, iteration 1, with 6 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 354702 reads
optimizePositions()--     changed:   187007 reads
optimizePositions()--   Recomputing positions, iteration 2, with 6 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 356948 reads
optimizePositions()--     changed:   184761 reads
optimizePositions()--   Recomputing positions, iteration 3, with 6 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 358789 reads
optimizePositions()--     changed:   182920 reads
optimizePositions()--   Recomputing positions, iteration 4, with 6 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 359789 reads
optimizePositions()--     changed:   181920 reads
optimizePositions()--   Recomputing positions, iteration 5, with 6 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 360202 reads
optimizePositions()--     changed:   181507 reads
optimizePositions()--   Expanding short reads with 6 threads.
optimizePositions()--   Updating positions.
optimizePositions()--   Finished.

==> PLACE CONTAINED READS.

computeErrorProfiles()-- Computing error profiles for 67790 tigs, with 6 threads.
computeErrorProfiles()-- Finished.

placeContains()-- placing 261725 contained and 261328 unplaced reads, with 6 threads.
placeContains()-- Placed 117228 contained reads and 436 unplaced reads.
placeContains()-- Failed to place 144497 contained reads (too high error suspected) and 260892 unplaced reads (lack of overlaps suspected).
optimizePositions()-- Optimizing read positions for 541709 reads in 67790 tigs, with 6 threads.
optimizePositions()--   Allocating scratch space for 541709 reads (33856 KB).
optimizePositions()--   Initializing positions with 6 threads.
optimizePositions()--   Recomputing positions, iteration 1, with 6 threads.
bogart: bogart/AS_BAT_OptimizePositions.C:210: void Unitig::optimize_recompute(uint32, optPos*, optPos*, bool): Assertion `cnt > 0' failed.

Failed with 'Aborted'; backtrace (libbacktrace):
AS_UTL/AS_UTL_stackTrace.C::97 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_OptimizePositions.C::210 in _ZN6Unitig18optimize_recomputeEjP6optPosS1_b()
bogart/AS_BAT_OptimizePositions.C::414 in _ZN9TigVector17optimizePositionsEPKcS1_._omp_fn.1()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
Aborted (core dumped)

and the log messages

-- Canu 1.7
--
-- CITATIONS
--
-- 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, consensus and GFA building 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
-- 
--   Li H.
--   Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.
--   Bioinformatics. 2016 Jul 15;32(14):2103-10.
--   http://doi.org/10.1093/bioinformatics/btw152
-- 
-- 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 '1.8.0_161' (from '/usr/lib/jvm/java-8-oracle/bin/java').
-- Detected gnuplot version '5.0 patchlevel 3' (from 'gnuplot') and image format 'png'.
-- Detected 12 CPUs and 126 gigabytes of memory.
-- Limited to 64g gigabytes from maxMemory option.
-- Limited to 6 CPUs from maxThreads option.
-- No grid engine detected, grid disabled.
--
--                            (tag)Concurrency
--                     (tag)Threads          |
--            (tag)Memory         |          |
--        (tag)         |         |          |     total usage     algorithm
--        -------  ------  --------   --------  -----------------  -----------------------------
-- Local: meryl     64 GB    6 CPUs x   1 job     64 GB    6 CPUs  (k-mer counting)
-- Local: cormhap   32 GB    6 CPUs x   1 job     32 GB    6 CPUs  (overlap detection with mhap)
-- Local: obtovl    16 GB    6 CPUs x   1 job     16 GB    6 CPUs  (overlap detection)
-- Local: utgovl    16 GB    6 CPUs x   1 job     16 GB    6 CPUs  (overlap detection)
-- Local: ovb        4 GB    1 CPU  x   6 jobs    24 GB    6 CPUs  (overlap store bucketizer)
-- Local: ovs       32 GB    1 CPU  x   2 jobs    64 GB    2 CPUs  (overlap store sorting)
-- Local: red        8 GB    3 CPUs x   2 jobs    16 GB    6 CPUs  (read error detection)
-- Local: oea        4 GB    1 CPU  x   6 jobs    24 GB    6 CPUs  (overlap error adjustment)
-- Local: bat       64 GB    6 CPUs x   1 job     64 GB    6 CPUs  (contig construction)
-- Local: gfa       16 GB    6 CPUs x   1 job     16 GB    6 CPUs  (GFA alignment and processing)
--
-- Found Nanopore uncorrected reads in the input files.
--
-- Generating assembly 'X' in '/media/hal9000/2e96b5f4-d012-482e-a4b5-17a3f95c75061/minion/X/fast5/basecall/assembly/X_canu'
--
-- Parameters:
--
--  genomeSize        1000000000
--
--  Overlap Generation Limits:
--    corOvlErrorRate 0.3200 ( 32.00%)
--    obtOvlErrorRate 0.1440 ( 14.40%)
--    utgOvlErrorRate 0.1440 ( 14.40%)
--
--  Overlap Processing Limits:
--    corErrorRate    0.5000 ( 50.00%)
--    obtErrorRate    0.1440 ( 14.40%)
--    utgErrorRate    0.1440 ( 14.40%)
--    cnsErrorRate    0.1920 ( 19.20%)
--
--
-- BEGIN CORRECTION
--
----------------------------------------
-- Starting command on Thu Apr 12 10:58:38 2018 with 321.307 GB free disk space

    cd .
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/gatekeeperCreate \
      -minlength 1000 \
      -o ./X.gkpStore.BUILDING \
      ./X.gkpStore.gkp \
    > ./X.gkpStore.BUILDING.err 2>&1

-- Finished on Thu Apr 12 11:00:08 2018 (90 seconds) with 319.886 GB free disk space
----------------------------------------
--
-- In gatekeeper store './X.gkpStore':
--   Found 541708 reads.
--   Found 5250323567 bases (5.25 times coverage).
--
--   Read length histogram (one '*' equals 2814.97 reads):
--        0   4999 197048 **********************************************************************
--     5000   9999 142994 **************************************************
--    10000  14999  87150 ******************************
--    15000  19999  52797 ******************
--    20000  24999  29757 **********
--    25000  29999  16401 *****
--    30000  34999   8357 **
--    35000  39999   3884 *
--    40000  44999   1788 
--    45000  49999    803 
--    50000  54999    352 
--    55000  59999    188 
--    60000  64999     90 
--    65000  69999     49 
--    70000  74999     23 
--    75000  79999     10 
--    80000  84999      6 
--    85000  89999      3 
--    90000  94999      5 
--    95000  99999      1 
--   100000 104999      0 
--   105000 109999      0 
--   110000 114999      1 
--   115000 119999      0 
--   120000 124999      0 
--   125000 129999      1 
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Thu Apr 12 11:00:13 2018 with 319.883 GB free disk space (1 processes; 1 concurrently)

    cd correction/0-mercounts
    ./meryl.sh 1 > ./meryl.000001.out 2>&1

-- Finished on Thu Apr 12 11:09:23 2018 (550 seconds) with 314.588 GB free disk space
----------------------------------------
-- Meryl finished successfully.
--
--  16-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1 536105395 *******************************************************************--> 0.4161 0.1023
--       2-     2 281216840 ********************************************************************** 0.6343 0.2096
--       3-     4 242121204 ************************************************************           0.7530 0.2970
--       5-     7 118460611 *****************************                                          0.8656 0.4183
--       8-    11  51998858 ************                                                           0.9287 0.5235
--      12-    16  24489358 ******                                                                 0.9599 0.6018
--      17-    22  12603178 ***                                                                    0.9758 0.6591
--      23-    29   7014713 *                                                                      0.9844 0.7016
--      30-    37   4196580 *                                                                      0.9893 0.7339
--      38-    46   2667898                                                                        0.9923 0.7592
--      47-    56   1781927                                                                        0.9943 0.7797
--      57-    67   1242749                                                                        0.9956 0.7965
--      68-    79    896394                                                                        0.9965 0.8108
--      80-    92    665571                                                                        0.9972 0.8231
--      93-   106    506252                                                                        0.9977 0.8338
--     107-   121    390698                                                                        0.9981 0.8432
--     122-   137    311157                                                                        0.9984 0.8516
--     138-   154    252195                                                                        0.9986 0.8592
--     155-   172    206141                                                                        0.9988 0.8661
--     173-   191    170026                                                                        0.9990 0.8725
--     192-   211    141294                                                                        0.9991 0.8783
--     212-   232    119059                                                                        0.9992 0.8837
--     233-   254    100803                                                                        0.9993 0.8887
--     255-   277     86327                                                                        0.9994 0.8934
--     278-   301     74059                                                                        0.9995 0.8977
--     302-   326     64061                                                                        0.9995 0.9018
--     327-   352     55905                                                                        0.9996 0.9056
--     353-   379     48573                                                                        0.9996 0.9092
--     380-   407     42779                                                                        0.9996 0.9126
--     408-   436     38239                                                                        0.9997 0.9158
--     437-   466     34093                                                                        0.9997 0.9188
--     467-   497     30154                                                                        0.9997 0.9218
--     498-   529     26859                                                                        0.9998 0.9245
--     530-   562     24407                                                                        0.9998 0.9272
--     563-   596     21863                                                                        0.9998 0.9297
--     597-   631     19442                                                                        0.9998 0.9321
--     632-   667     17681                                                                        0.9998 0.9344
--     668-   704     15825                                                                        0.9998 0.9366
--     705-   742     14614                                                                        0.9999 0.9386
--     743-   781     13184                                                                        0.9999 0.9406
--     782-   821     11680                                                                        0.9999 0.9425
--
--      316624 (max occurrences)
--  4706092552 (total mers, non-unique)
--   752347427 (distinct mers, non-unique)
--   536105395 (unique mers)
-- For mhap overlapping, set repeat k-mer threshold to 52421.
--
-- Found 5242197947 16-mers; 1288452822 distinct and 536105395 unique.  Largest count 316624.
--
-- OVERLAPPER (mhap) (correction)
--
-- Set corMhapSensitivity=high based on read coverage of 5.
--
-- PARAMETERS: hashes=768, minMatches=2, threshold=0.78
--
-- Given 32 GB, can fit 48000 reads per block.
-- For 13 blocks, set stride to 2 blocks.
-- Logging partitioning to 'correction/1-overlapper/partitioning.log'.
-- Configured 12 mhap precompute jobs.
-- Configured 37 mhap overlap jobs.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Thu Apr 12 11:09:52 2018 with 319.882 GB free disk space (12 processes; 1 concurrently)

    cd correction/1-overlapper
    ./precompute.sh 1 > ./precompute.000001.out 2>&1
    ./precompute.sh 2 > ./precompute.000002.out 2>&1
    ./precompute.sh 3 > ./precompute.000003.out 2>&1
    ./precompute.sh 4 > ./precompute.000004.out 2>&1
    ./precompute.sh 5 > ./precompute.000005.out 2>&1
    ./precompute.sh 6 > ./precompute.000006.out 2>&1
    ./precompute.sh 7 > ./precompute.000007.out 2>&1
    ./precompute.sh 8 > ./precompute.000008.out 2>&1
    ./precompute.sh 9 > ./precompute.000009.out 2>&1
    ./precompute.sh 10 > ./precompute.000010.out 2>&1
    ./precompute.sh 11 > ./precompute.000011.out 2>&1
    ./precompute.sh 12 > ./precompute.000012.out 2>&1

-- Finished on Thu Apr 12 18:19:51 2018 (25799 seconds) with 304.495 GB free disk space
----------------------------------------
-- All 12 mhap precompute jobs finished successfully.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Thu Apr 12 18:19:51 2018 with 304.495 GB free disk space (37 processes; 1 concurrently)

    cd correction/1-overlapper
    ./mhap.sh 1 > ./mhap.000001.out 2>&1
    ./mhap.sh 2 > ./mhap.000002.out 2>&1
    ./mhap.sh 3 > ./mhap.000003.out 2>&1
    ./mhap.sh 4 > ./mhap.000004.out 2>&1
    ./mhap.sh 5 > ./mhap.000005.out 2>&1
    ./mhap.sh 6 > ./mhap.000006.out 2>&1
    ./mhap.sh 7 > ./mhap.000007.out 2>&1
    ./mhap.sh 8 > ./mhap.000008.out 2>&1
    ./mhap.sh 9 > ./mhap.000009.out 2>&1
    ./mhap.sh 10 > ./mhap.000010.out 2>&1
    ./mhap.sh 11 > ./mhap.000011.out 2>&1
    ./mhap.sh 12 > ./mhap.000012.out 2>&1
    ./mhap.sh 13 > ./mhap.000013.out 2>&1
    ./mhap.sh 14 > ./mhap.000014.out 2>&1
    ./mhap.sh 15 > ./mhap.000015.out 2>&1
    ./mhap.sh 16 > ./mhap.000016.out 2>&1
    ./mhap.sh 17 > ./mhap.000017.out 2>&1
    ./mhap.sh 18 > ./mhap.000018.out 2>&1
    ./mhap.sh 19 > ./mhap.000019.out 2>&1
    ./mhap.sh 20 > ./mhap.000020.out 2>&1
    ./mhap.sh 21 > ./mhap.000021.out 2>&1
    ./mhap.sh 22 > ./mhap.000022.out 2>&1
    ./mhap.sh 23 > ./mhap.000023.out 2>&1
    ./mhap.sh 24 > ./mhap.000024.out 2>&1
    ./mhap.sh 25 > ./mhap.000025.out 2>&1
    ./mhap.sh 26 > ./mhap.000026.out 2>&1
    ./mhap.sh 27 > ./mhap.000027.out 2>&1
    ./mhap.sh 28 > ./mhap.000028.out 2>&1
    ./mhap.sh 29 > ./mhap.000029.out 2>&1
    ./mhap.sh 30 > ./mhap.000030.out 2>&1
    ./mhap.sh 31 > ./mhap.000031.out 2>&1
    ./mhap.sh 32 > ./mhap.000032.out 2>&1
    ./mhap.sh 33 > ./mhap.000033.out 2>&1
    ./mhap.sh 34 > ./mhap.000034.out 2>&1
    ./mhap.sh 35 > ./mhap.000035.out 2>&1
    ./mhap.sh 36 > ./mhap.000036.out 2>&1
    ./mhap.sh 37 > ./mhap.000037.out 2>&1

-- Finished on Fri Apr 13 11:52:12 2018 (63141 seconds) with 263.324 GB free disk space
----------------------------------------
-- Found 37 mhap overlap output files.
----------------------------------------
-- Starting command on Fri Apr 13 11:52:12 2018 with 263.324 GB free disk space

    cd correction
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/ovStoreBuild \
     -O ./X.ovlStore.BUILDING \
     -G ./X.gkpStore \
     -M 4-32 \
     -L ./1-overlapper/ovljob.files \
     > ./X.ovlStore.err 2>&1

-- Finished on Fri Apr 13 12:50:37 2018 (3505 seconds) with 170.359 GB free disk space
----------------------------------------
-- Checking store.
----------------------------------------
-- Starting command on Fri Apr 13 12:50:37 2018 with 170.359 GB free disk space

    cd correction
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/ovStoreDump \
     -G ./X.gkpStore \
     -O ./X.ovlStore \
     -d -counts \
     > ./X.ovlStore/counts.dat 2> ./X.ovlStore/counts.err

-- Finished on Fri Apr 13 12:50:37 2018 (lickety-split) with 170.353 GB free disk space
----------------------------------------
--
-- Overlap store 'correction/X.ovlStore' successfully constructed.
-- Found 4988296752 overlaps for 541682 reads; 26 reads have no overlaps.
--
--
-- Purged 135.787 GB in 152 overlap output files.
-- Global filter scores will be estimated.
-- Computing correction layouts.
----------------------------------------
-- Starting command on Fri Apr 13 12:50:40 2018 with 226.917 GB free disk space

    cd correction
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/generateCorrectionLayouts \
      -G ./X.gkpStore \
      -O ./X.ovlStore \
      -C ./X.corStore.WORKING \
      -ec 0 \
      -eC 80 \
    > ./X.corStore.err 2>&1

-- Finished on Fri Apr 13 13:00:01 2018 (561 seconds) with 226.008 GB free disk space
----------------------------------------
-- Computing correction layouts.
----------------------------------------
-- Starting command on Fri Apr 13 13:00:01 2018 with 226.008 GB free disk space

    cd correction/2-correction
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/filterCorrectionLayouts \
      -G  ../X.gkpStore \
      -C  ../X.corStore \
      -R  ./X.readsToCorrect.WORKING \
      -cc 0 \
      -cl 1000 \
      -g  1000000000 \
      -c  40 \
    > ./X.readsToCorrect.err 2>&1

-- Finished on Fri Apr 13 13:00:06 2018 (5 seconds) with 225.968 GB free disk space
----------------------------------------
--                             original      original
--                            raw reads     raw reads
--   category                w/overlaps  w/o/overlaps
--   -------------------- ------------- -------------
--   Number of Reads             535055          6653
--   Number of Bases         5225314893      24579045
--   Coverage                     5.225         0.025
--   Median                        7362          2442
--   Mean                          9765          3694
--   N50                          14876          5312
--   Minimum                       1000             0
--   Maximum                     126774         54531
--   
--                                        --------corrected---------  ----------rescued----------
--                             evidence                     expected                     expected
--   category                     reads            raw     corrected            raw     corrected
--   -------------------- -------------  ------------- -------------  ------------- -------------
--   Number of Reads             541682         535055        535055              0             0
--   Number of Bases         5249893938     5225314893    4955911548              0             0
--   Coverage                     5.250          5.225         4.956          0.000         0.000
--   Median                        7269           7362          6925              0             0
--   Mean                          9691           9765          9262              0             0
--   N50                          14824          14876         14737              0             0
--   Minimum                       1000           1000             2              0             0
--   Maximum                     126774         126774        120177              0             0
--   
--                        --------uncorrected--------
--                                           expected
--   category                       raw     corrected
--   -------------------- ------------- -------------
--   Number of Reads               6653          6653
--   Number of Bases           24579045             0
--   Coverage                     0.025         0.000
--   Median                        2442             0
--   Mean                          3694             0
--   N50                           5312             0
--   Minimum                          0             0
--   Maximum                      54531             0
--   
--   Maximum Memory          1669058660
--
--                            (tag)Concurrency
--                     (tag)Threads          |
--            (tag)Memory         |          |
--        (tag)         |         |          |     total usage     algorithm
--        -------  ------  --------   --------  -----------------  -----------------------------
-- Local: cor        6 GB    4 CPUs x   1 job      6 GB    4 CPUs  (read correction)
--
-- Using overlaps no worse than 0.5 fraction error for correcting reads (from corErrorRate parameter).
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cor' concurrent execution on Fri Apr 13 13:00:06 2018 with 225.968 GB free disk space (37 processes; 1 concurrently)

    cd correction/2-correction
    ./correctReads.sh 1 > ./correctReads.000001.out 2>&1
    ./correctReads.sh 2 > ./correctReads.000002.out 2>&1
    ./correctReads.sh 3 > ./correctReads.000003.out 2>&1
    ./correctReads.sh 4 > ./correctReads.000004.out 2>&1
    ./correctReads.sh 5 > ./correctReads.000005.out 2>&1
    ./correctReads.sh 6 > ./correctReads.000006.out 2>&1
    ./correctReads.sh 7 > ./correctReads.000007.out 2>&1
    ./correctReads.sh 8 > ./correctReads.000008.out 2>&1
    ./correctReads.sh 9 > ./correctReads.000009.out 2>&1
    ./correctReads.sh 10 > ./correctReads.000010.out 2>&1
    ./correctReads.sh 11 > ./correctReads.000011.out 2>&1
    ./correctReads.sh 12 > ./correctReads.000012.out 2>&1
    ./correctReads.sh 13 > ./correctReads.000013.out 2>&1
    ./correctReads.sh 14 > ./correctReads.000014.out 2>&1
    ./correctReads.sh 15 > ./correctReads.000015.out 2>&1
    ./correctReads.sh 16 > ./correctReads.000016.out 2>&1
    ./correctReads.sh 17 > ./correctReads.000017.out 2>&1
    ./correctReads.sh 18 > ./correctReads.000018.out 2>&1
    ./correctReads.sh 19 > ./correctReads.000019.out 2>&1
    ./correctReads.sh 20 > ./correctReads.000020.out 2>&1
    ./correctReads.sh 21 > ./correctReads.000021.out 2>&1
    ./correctReads.sh 22 > ./correctReads.000022.out 2>&1
    ./correctReads.sh 23 > ./correctReads.000023.out 2>&1
    ./correctReads.sh 24 > ./correctReads.000024.out 2>&1
    ./correctReads.sh 25 > ./correctReads.000025.out 2>&1
    ./correctReads.sh 26 > ./correctReads.000026.out 2>&1
    ./correctReads.sh 27 > ./correctReads.000027.out 2>&1
    ./correctReads.sh 28 > ./correctReads.000028.out 2>&1
    ./correctReads.sh 29 > ./correctReads.000029.out 2>&1
    ./correctReads.sh 30 > ./correctReads.000030.out 2>&1
    ./correctReads.sh 31 > ./correctReads.000031.out 2>&1
    ./correctReads.sh 32 > ./correctReads.000032.out 2>&1
    ./correctReads.sh 33 > ./correctReads.000033.out 2>&1
    ./correctReads.sh 34 > ./correctReads.000034.out 2>&1
    ./correctReads.sh 35 > ./correctReads.000035.out 2>&1
    ./correctReads.sh 36 > ./correctReads.000036.out 2>&1
    ./correctReads.sh 37 > ./correctReads.000037.out 2>&1

-- Finished on Sat Apr 14 07:18:50 2018 (65924 seconds) with 211.161 GB free disk space
----------------------------------------
-- Found 37 read correction output files.
-- Found 37 read correction output files.
--
-- Loading corrected reads into corStore and gkpStore.
----------------------------------------
-- Starting command on Sat Apr 14 07:18:50 2018 with 211.161 GB free disk space

    cd correction
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/loadCorrectedReads \
      -G ./X.gkpStore \
      -C ./X.corStore \
      -L ./2-correction/corjob.files \
    > ./2-correction/corjob.files.load.err 2>&1

-- Finished on Sat Apr 14 07:19:19 2018 (29 seconds) with 199.647 GB free disk space
----------------------------------------
--
-- In gatekeeper store './X.gkpStore':
--   Found 535018 reads.
--   Found 4559772904 bases (4.55 times coverage).
--
--   Read length histogram (one '*' equals 3355.2 reads):
--        0   4999 234864 **********************************************************************
--     5000   9999 136492 ****************************************
--    10000  14999  73343 *********************
--    15000  19999  41969 ************
--    20000  24999  23530 *******
--    25000  29999  12822 ***
--    30000  34999   6533 *
--    35000  39999   2914 
--    40000  44999   1365 
--    45000  49999    609 
--    50000  54999    285 
--    55000  59999    139 
--    60000  64999     74 
--    65000  69999     36 
--    70000  74999     18 
--    75000  79999      9 
--    80000  84999      6 
--    85000  89999      2 
--    90000  94999      5 
--    95000  99999      1 
--   100000 104999      0 
--   105000 109999      0 
--   110000 114999      1 
--   115000 119999      0 
--   120000 124999      0 
--   125000 129999      1 
--
-- Purging correctReads output after loading into stores.
-- Purged 37 .cns outputs.
-- Purged 74 .out job log outputs.
--
-- Purging overlaps used for correction.
----------------------------------------
-- Starting command on Sat Apr 14 07:19:29 2018 with 307.44 GB free disk space

    cd .
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/gatekeeperDumpFASTQ \
      -corrected \
      -G ./X.gkpStore \
      -o ./X.correctedReads.gz \
      -fasta \
      -nolibname \
    > X.correctedReads.fasta.err 2>&1

-- Finished on Sat Apr 14 07:20:33 2018 (64 seconds) with 306.012 GB free disk space
----------------------------------------
--
-- Corrected reads saved in 'X.correctedReads.fasta.gz'.
--
--
-- BEGIN TRIMMING
--
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Sat Apr 14 07:20:33 2018 with 306.012 GB free disk space (1 processes; 1 concurrently)

    cd trimming/0-mercounts
    ./meryl.sh 1 > ./meryl.000001.out 2>&1

-- Finished on Sat Apr 14 07:29:44 2018 (551 seconds) with 290.572 GB free disk space
----------------------------------------
-- Meryl finished successfully.
--
--  22-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1 2582982711 *******************************************************************--> 0.8856 0.5679
--       2-     2 167080701 ********************************************************************** 0.9429 0.6413
--       3-     4  99522783 *****************************************                              0.9659 0.6856
--       5-     7  35286752 **************                                                         0.9831 0.7336
--       8-    11  13201314 *****                                                                  0.9907 0.7666
--      12-    16   6776641 **                                                                     0.9942 0.7897
--      17-    22   3910935 *                                                                      0.9962 0.8085
--      23-    29   2329621                                                                        0.9974 0.8239
--      30-    37   1425759                                                                        0.9982 0.8364
--      38-    46    914097                                                                        0.9986 0.8463
--      47-    56    624079                                                                        0.9989 0.8544
--      57-    67    457920                                                                        0.9991 0.8612
--      68-    79    347886                                                                        0.9993 0.8673
--      80-    92    270279                                                                        0.9994 0.8729
--      93-   106    212779                                                                        0.9995 0.8779
--     107-   121    176969                                                                        0.9995 0.8825
--     122-   137    146670                                                                        0.9996 0.8869
--     138-   154    124392                                                                        0.9996 0.8910
--     155-   172    105280                                                                        0.9997 0.8950
--     173-   191     91464                                                                        0.9997 0.8987
--     192-   211     77325                                                                        0.9998 0.9023
--     212-   232     66610                                                                        0.9998 0.9057
--     233-   254     58141                                                                        0.9998 0.9090
--     255-   277     50711                                                                        0.9998 0.9121
--     278-   301     45460                                                                        0.9998 0.9150
--     302-   326     39630                                                                        0.9999 0.9179
--     327-   352     35278                                                                        0.9999 0.9206
--     353-   379     31436                                                                        0.9999 0.9232
--     380-   407     27950                                                                        0.9999 0.9258
--     408-   436     24953                                                                        0.9999 0.9282
--     437-   466     22278                                                                        0.9999 0.9305
--     467-   497     19286                                                                        0.9999 0.9327
--     498-   529     17334                                                                        0.9999 0.9347
--     530-   562     15607                                                                        0.9999 0.9367
--     563-   596     14064                                                                        0.9999 0.9385
--     597-   631     13320                                                                        0.9999 0.9403
--     632-   667     11878                                                                        0.9999 0.9421
--     668-   704     11401                                                                        0.9999 0.9438
--     705-   742     10340                                                                        1.0000 0.9455
--     743-   781      8713                                                                        1.0000 0.9472
--     782-   821      8034                                                                        1.0000 0.9486
--
--      174679 (max occurrences)
--  1965554828 (total mers, non-unique)
--   333728948 (distinct mers, non-unique)
--  2582982711 (unique mers)
----------------------------------------
-- Starting command on Sat Apr 14 07:29:44 2018 with 290.572 GB free disk space

    cd trimming/0-mercounts
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/meryl \
      -Dt \
      -n 1045 \
      -s ./X.ms22 \
    > ./X.ms22.frequentMers.fasta \
    2> ./X.ms22.frequentMers.fasta.err

-- Finished on Sat Apr 14 07:30:21 2018 (37 seconds) with 290.57 GB free disk space
----------------------------------------
-- Reset obtOvlMerThreshold from auto to 1045.
--
-- Found 4548537539 22-mers; 2916711659 distinct and 2582982711 unique.  Largest count 174679.
--
-- OVERLAPPER (normal) (trimming) erate=0.144
--
----------------------------------------
-- Starting command on Sat Apr 14 07:30:22 2018 with 306.009 GB free disk space

    cd trimming/1-overlapper
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/overlapInCorePartition \
     -G  ../X.gkpStore \
     -hl 341248000 \
     -rl 15000000000 \
     -ol 500 \
     -o  ./X.partition \
    > ./X.partition.err 2>&1

-- Finished on Sat Apr 14 07:30:22 2018 (lickety-split) with 306.009 GB free disk space
----------------------------------------
--
-- Configured 14 overlapInCore jobs.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'obtovl' concurrent execution on Sat Apr 14 07:30:22 2018 with 306.009 GB free disk space (14 processes; 1 concurrently)

    cd trimming/1-overlapper
    ./overlap.sh 1 > ./overlap.000001.out 2>&1
    ./overlap.sh 2 > ./overlap.000002.out 2>&1
    ./overlap.sh 3 > ./overlap.000003.out 2>&1
    ./overlap.sh 4 > ./overlap.000004.out 2>&1
    ./overlap.sh 5 > ./overlap.000005.out 2>&1
    ./overlap.sh 6 > ./overlap.000006.out 2>&1
    ./overlap.sh 7 > ./overlap.000007.out 2>&1
    ./overlap.sh 8 > ./overlap.000008.out 2>&1
    ./overlap.sh 9 > ./overlap.000009.out 2>&1
    ./overlap.sh 10 > ./overlap.000010.out 2>&1
    ./overlap.sh 11 > ./overlap.000011.out 2>&1
    ./overlap.sh 12 > ./overlap.000012.out 2>&1
    ./overlap.sh 13 > ./overlap.000013.out 2>&1
    ./overlap.sh 14 > ./overlap.000014.out 2>&1

-- Finished on Mon Apr 16 10:09:20 2018 (182338 seconds) with 300.914 GB free disk space
----------------------------------------
-- Found 14 overlapInCore output files.
--
-- overlapInCore compute 'trimming/1-overlapper':
--   kmer hits
--     with no overlap       3851224378  455.571429 +- 160476820.9
--     with an overlap        254047958  82.7142857 +- 10075741.865
--
--   overlaps                 254039585  84.6428571 +- 10075394.61
--     contained                      0           0 +- 0
--     dovetail                       0           0 +- 0
--
--   overlaps rejected
--     multiple per pair              0           0 +- 0
--     bad short window               0           0 +- 0
--     bad long window                0           0 +- 0
----------------------------------------
-- Starting command on Mon Apr 16 10:09:20 2018 with 300.914 GB free disk space

    cd trimming
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/ovStoreBuild \
     -O ./X.ovlStore.BUILDING \
     -G ./X.gkpStore \
     -M 4-32 \
     -L ./1-overlapper/ovljob.files \
     > ./X.ovlStore.err 2>&1

-- Finished on Mon Apr 16 10:14:23 2018 (303 seconds) with 291.402 GB free disk space
----------------------------------------
-- Checking store.
----------------------------------------
-- Starting command on Mon Apr 16 10:14:23 2018 with 291.402 GB free disk space

    cd trimming
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/ovStoreDump \
     -G ./X.gkpStore \
     -O ./X.ovlStore \
     -d -counts \
     > ./X.ovlStore/counts.dat 2> ./X.ovlStore/counts.err

-- Finished on Mon Apr 16 10:14:23 2018 (lickety-split) with 291.397 GB free disk space
----------------------------------------
--
-- Overlap store 'trimming/X.ovlStore' successfully constructed.
-- Found 508095916 overlaps for 444950 reads; 96758 reads have no overlaps.
--
--
-- Purged 5.094 GB in 42 overlap output files.
----------------------------------------
-- Starting command on Mon Apr 16 10:14:24 2018 with 296.497 GB free disk space

    cd trimming/3-overlapbasedtrimming
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/trimReads \
      -G  ../X.gkpStore \
      -O  ../X.ovlStore \
      -Co ./X.1.trimReads.clear \
      -e  0.144 \
      -minlength 1000 \
      -ol 1 \
      -oc 1 \
      -o  ./X.1.trimReads \
    >     ./X.1.trimReads.err 2>&1

-- Finished on Mon Apr 16 10:15:53 2018 (89 seconds) with 296.456 GB free disk space
----------------------------------------
--  PARAMETERS:
--  ----------
--     1000    (reads trimmed below this many bases are deleted)
--   0.1440    (use overlaps at or below this fraction error)
--        1    (break region if overlap is less than this long, for 'largest covered' algorithm)
--        1    (break region if overlap coverage is less than this many read, for 'largest covered' algorithm)
--  
--  INPUT READS:
--  -----------
--  541708 reads   4559772904 bases (reads processed)
--       0 reads            0 bases (reads not processed, previously deleted)
--       0 reads            0 bases (reads not processed, in a library where trimming isn't allowed)
--  
--  OUTPUT READS:
--  ------------
--  344659 reads   1561521903 bases (trimmed reads output)
--   23075 reads     80539642 bases (reads with no change, kept as is)
--   96758 reads    346770244 bases (reads with no overlaps, deleted)
--   77216 reads    394900211 bases (reads with short trimmed length, deleted)
--  
--  TRIMMING DETAILS:
--  ----------------
--  306653 reads   1036737604 bases (bases trimmed from the 5' end of a read)
--  332221 reads   1139303300 bases (bases trimmed from the 3' end of a read)
----------------------------------------
-- Starting command on Mon Apr 16 10:15:53 2018 with 296.456 GB free disk space

    cd trimming/3-overlapbasedtrimming
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/splitReads \
      -G  ../X.gkpStore \
      -O  ../X.ovlStore \
      -Ci ./X.1.trimReads.clear \
      -Co ./X.2.splitReads.clear \
      -e  0.144 \
      -minlength 1000 \
      -o  ./X.2.splitReads \
    >     ./X.2.splitReads.err 2>&1

-- Finished on Mon Apr 16 10:17:45 2018 (112 seconds) with 296.452 GB free disk space
----------------------------------------
--  PARAMETERS:
--  ----------
--     1000    (reads trimmed below this many bases are deleted)
--   0.1440    (use overlaps at or below this fraction error)
--  INPUT READS:
--  -----------
--  367734 reads   3818102449 bases (reads processed)
--  173974 reads    741670455 bases (reads not processed, previously deleted)
--       0 reads            0 bases (reads not processed, in a library where trimming isn't allowed)
--  
--  PROCESSED:
--  --------
--       0 reads            0 bases (no overlaps)
--    8559 reads     65241370 bases (no coverage after adjusting for trimming done already)
--       0 reads            0 bases (processed for chimera)
--       0 reads            0 bases (processed for spur)
--  359175 reads   3752861079 bases (processed for subreads)
--  
--  READS WITH SIGNALS:
--  ------------------
--       0 reads            0 signals (number of 5' spur signal)
--       0 reads            0 signals (number of 3' spur signal)
--       0 reads            0 signals (number of chimera signal)
--    1162 reads         1188 signals (number of subread signal)
--  
--  SIGNALS:
--  -------
--       0 reads            0 bases (size of 5' spur signal)
--       0 reads            0 bases (size of 3' spur signal)
--       0 reads            0 bases (size of chimera signal)
--    1188 reads       525123 bases (size of subread signal)
--  
--  TRIMMING:
--  --------
--     557 reads      1222432 bases (trimmed from the 5' end of the read)
--     613 reads      1417511 bases (trimmed from the 3' end of the read)
----------------------------------------
-- Starting command on Mon Apr 16 10:17:45 2018 with 296.452 GB free disk space

    cd trimming/3-overlapbasedtrimming
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/loadTrimmedReads \
      -G ../X.gkpStore \
      -c ./X.2.splitReads.clear \
    > ./X.loadtrimmedReads.err 2>&1

-- Finished on Mon Apr 16 10:17:45 2018 (lickety-split) with 296.452 GB free disk space
----------------------------------------
--
-- In gatekeeper store './X.gkpStore':
--   Found 367639 reads.
--   Found 1639346059 bases (1.63 times coverage).
--
--   Read length histogram (one '*' equals 1606.47 reads):
--        0    999      0 
--     1000   1999 112453 **********************************************************************
--     2000   2999  70814 ********************************************
--     3000   3999  48740 ******************************
--     4000   4999  32532 ********************
--     5000   5999  22956 **************
--     6000   6999  16387 **********
--     7000   7999  12466 *******
--     8000   8999   9487 *****
--     9000   9999   7578 ****
--    10000  10999   6371 ***
--    11000  11999   5073 ***
--    12000  12999   4110 **
--    13000  13999   3318 **
--    14000  14999   2857 *
--    15000  15999   2257 *
--    16000  16999   1852 *
--    17000  17999   1575 
--    18000  18999   1220 
--    19000  19999   1014 
--    20000  20999    870 
--    21000  21999    691 
--    22000  22999    563 
--    23000  23999    431 
--    24000  24999    373 
--    25000  25999    329 
--    26000  26999    243 
--    27000  27999    205 
--    28000  28999    188 
--    29000  29999    123 
--    30000  30999    112 
--    31000  31999     90 
--    32000  32999     75 
--    33000  33999     54 
--    34000  34999     37 
--    35000  35999     35 
--    36000  36999     27 
--    37000  37999     28 
--    38000  38999     29 
--    39000  39999     14 
--    40000  40999      9 
--    41000  41999     11 
--    42000  42999     11 
--    43000  43999      4 
--    44000  44999      6 
--    45000  45999      3 
--    46000  46999      7 
--    47000  47999      2 
--    48000  48999      2 
--    49000  49999      2 
--    50000  50999      1 
--    51000  51999      1 
--    52000  52999      0 
--    53000  53999      0 
--    54000  54999      0 
--    55000  55999      0 
--    56000  56999      2 
--    57000  57999      0 
--    58000  58999      0 
--    59000  59999      1 
--
-- Overlaps used for trimming saved.
----------------------------------------
-- Starting command on Mon Apr 16 10:17:49 2018 with 296.45 GB free disk space

    cd .
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/gatekeeperDumpFASTQ \
      -trimmed \
      -G ./X.gkpStore \
      -o ./X.trimmedReads.gz \
      -fasta \
      -nolibname \
    > ./X.trimmedReads.fasta.err 2>&1

-- Finished on Mon Apr 16 10:18:12 2018 (23 seconds) with 295.927 GB free disk space
----------------------------------------
--
-- Trimmed reads saved in 'X.trimmedReads.fasta.gz'.
--
--
-- BEGIN ASSEMBLY
--
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Mon Apr 16 10:18:12 2018 with 295.927 GB free disk space (1 processes; 1 concurrently)

    cd unitigging/0-mercounts
    ./meryl.sh 1 > ./meryl.000001.out 2>&1

-- Finished on Mon Apr 16 10:21:51 2018 (219 seconds) with 291.889 GB free disk space
----------------------------------------
-- Meryl finished successfully.
--
--  22-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1 579416226 *******************************************************************--> 0.7664 0.3551
--       2-     2  81460796 ********************************************************************** 0.8741 0.4550
--       3-     4  57861153 *************************************************                      0.9258 0.5268
--       5-     7  19940760 *****************                                                      0.9641 0.6040
--       8-    11   7312439 ******                                                                 0.9805 0.6552
--      12-    16   3787728 ***                                                                    0.9880 0.6910
--      17-    22   2124025 *                                                                      0.9923 0.7202
--      23-    29   1203745 *                                                                      0.9948 0.7434
--      30-    37    726497                                                                        0.9962 0.7612
--      38-    46    470397                                                                        0.9971 0.7753
--      47-    56    321515                                                                        0.9977 0.7869
--      57-    67    238769                                                                        0.9981 0.7968
--      68-    79    184370                                                                        0.9984 0.8056
--      80-    92    145426                                                                        0.9987 0.8138
--      93-   106    119817                                                                        0.9989 0.8213
--     107-   121    101882                                                                        0.9990 0.8286
--     122-   137     85737                                                                        0.9992 0.8356
--     138-   154     74241                                                                        0.9993 0.8424
--     155-   172     63258                                                                        0.9994 0.8490
--     173-   191     51200                                                                        0.9994 0.8553
--     192-   211     42861                                                                        0.9995 0.8609
--     212-   232     37288                                                                        0.9996 0.8662
--     233-   254     32703                                                                        0.9996 0.8712
--     255-   277     28710                                                                        0.9997 0.8761
--     278-   301     24508                                                                        0.9997 0.8807
--     302-   326     20097                                                                        0.9997 0.8850
--     327-   352     17902                                                                        0.9998 0.8889
--     353-   379     16227                                                                        0.9998 0.8926
--     380-   407     14122                                                                        0.9998 0.8962
--     408-   436     12337                                                                        0.9998 0.8996
--     437-   466     10744                                                                        0.9998 0.9028
--     467-   497      9433                                                                        0.9998 0.9057
--     498-   529      8197                                                                        0.9999 0.9085
--     530-   562      7574                                                                        0.9999 0.9111
--     563-   596      6316                                                                        0.9999 0.9136
--     597-   631      5443                                                                        0.9999 0.9158
--     632-   667      4675                                                                        0.9999 0.9179
--     668-   704      4138                                                                        0.9999 0.9197
--     705-   742      3931                                                                        0.9999 0.9215
--     743-   781      3826                                                                        0.9999 0.9232
--     782-   821      3508                                                                        0.9999 0.9250
--
--       72567 (max occurrences)
--  1052209414 (total mers, non-unique)
--   176646505 (distinct mers, non-unique)
--   579416226 (unique mers)
----------------------------------------
-- Starting command on Mon Apr 16 10:21:51 2018 with 291.889 GB free disk space

    cd unitigging/0-mercounts
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/meryl \
      -Dt \
      -n 1055 \
      -s ./X.ms22 \
    > ./X.ms22.frequentMers.fasta \
    2> ./X.ms22.frequentMers.fasta.err

-- Finished on Mon Apr 16 10:22:03 2018 (12 seconds) with 291.888 GB free disk space
----------------------------------------
-- Reset utgOvlMerThreshold from auto to 1055.
--
-- Found 1631625640 22-mers; 756062731 distinct and 579416226 unique.  Largest count 72567.
--
-- OVERLAPPER (normal) (assembly) erate=0.144
--
----------------------------------------
-- Starting command on Mon Apr 16 10:22:04 2018 with 295.925 GB free disk space

    cd unitigging/1-overlapper
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/overlapInCorePartition \
     -G  ../X.gkpStore \
     -hl 341248000 \
     -rl 15000000000 \
     -ol 500 \
     -o  ./X.partition \
    > ./X.partition.err 2>&1

-- Finished on Mon Apr 16 10:22:04 2018 (lickety-split) with 295.925 GB free disk space
----------------------------------------
--
-- Configured 5 overlapInCore jobs.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'utgovl' concurrent execution on Mon Apr 16 10:22:04 2018 with 295.925 GB free disk space (5 processes; 1 concurrently)

    cd unitigging/1-overlapper
    ./overlap.sh 1 > ./overlap.000001.out 2>&1
    ./overlap.sh 2 > ./overlap.000002.out 2>&1
    ./overlap.sh 3 > ./overlap.000003.out 2>&1
    ./overlap.sh 4 > ./overlap.000004.out 2>&1
    ./overlap.sh 5 > ./overlap.000005.out 2>&1

-- Finished on Wed Apr 18 07:20:24 2018 (161900 seconds) with 294.66 GB free disk space
----------------------------------------
-- Found 5 overlapInCore output files.
--
-- overlapInCore compute 'unitigging/1-overlapper':
--   kmer hits
--     with no overlap        789660588  57932117.6 +- 87655117.084
--     with an overlap         75693357  15138671.4 +- 8118637.791
--
--   overlaps                  75693357  15138671.4 +- 8118637.791
--     contained               35464854   7092970.8 +- 3824192.859
--     dovetail                40228503   8045700.6 +- 4295090.15
--
--   overlaps rejected
--     multiple per pair              0           0 +- 0
--     bad short window               0           0 +- 0
--     bad long window                0           0 +- 0
----------------------------------------
-- Starting command on Wed Apr 18 07:20:24 2018 with 294.66 GB free disk space

    cd unitigging
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/ovStoreBuild \
     -O ./X.ovlStore.BUILDING \
     -G ./X.gkpStore \
     -M 4-32 \
     -L ./1-overlapper/ovljob.files \
     > ./X.ovlStore.err 2>&1

-- Finished on Wed Apr 18 07:21:44 2018 (80 seconds) with 291.794 GB free disk space
----------------------------------------
-- Checking store.
----------------------------------------
-- Starting command on Wed Apr 18 07:21:44 2018 with 291.794 GB free disk space

    cd unitigging
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/ovStoreDump \
     -G ./X.gkpStore \
     -O ./X.ovlStore \
     -d -counts \
     > ./X.ovlStore/counts.dat 2> ./X.ovlStore/counts.err

-- Finished on Wed Apr 18 07:21:44 2018 (lickety-split) with 291.789 GB free disk space
----------------------------------------
--
-- Overlap store 'unitigging/X.ovlStore' successfully constructed.
-- Found 151386714 overlaps for 357130 reads; 184578 reads have no overlaps.
--
--
-- Purged 1.265 GB in 15 overlap output files.
----------------------------------------
-- Starting command on Wed Apr 18 07:21:44 2018 with 293.059 GB free disk space

    cd unitigging
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/ovStoreStats \
     -G ./X.gkpStore \
     -O ./X.ovlStore \
     -C 1 \
     -o ./X.ovlStore \
     > ./X.ovlStore.summary.err 2>&1

-- Finished on Wed Apr 18 07:22:06 2018 (22 seconds) with 293.05 GB free disk space
----------------------------------------

ERROR:
ERROR:  Failed with exit code 139.  (rc=35584)
ERROR:
--
-- WARNING: failed to generate statistics for the overlap store; no summary will appear in report.
--
----------------------------------------
--
-- Loading read lengths.
-- Loading number of overlaps per read.
--
-- Configure RED for 8gb memory.
--                   Batches of at most (unlimited) reads.
--                                      500000000 bases.
--                   Expecting evidence of at most 336753168 bases per iteration.
--
--           Total                                               Reads                 Olaps Evidence
--    Job   Memory      Read Range         Reads        Bases   Memory        Olaps   Memory   Memory  (Memory in MB)
--   ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------
--      1  8192.03         1-138688        96822    438117109  5016.90     42364558   484.82   642.31
--      2  8192.11    138689-270320        95245    439516189  5032.86     40976622   468.94   642.31
--      3  8192.01    270321-423126        98936    442165506  5063.30     38308301   438.40   642.31
--      4  6689.96    423127-541708        76636    319547255  3659.34     29737233   340.32   642.31
--   ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------
--                                                 1639346059             151386714
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'red' concurrent execution on Wed Apr 18 07:22:10 2018 with 293.05 GB free disk space (4 processes; 2 concurrently)

    cd unitigging/3-overlapErrorAdjustment
    ./red.sh 1 > ./red.000001.out 2>&1
    ./red.sh 2 > ./red.000002.out 2>&1
    ./red.sh 3 > ./red.000003.out 2>&1
    ./red.sh 4 > ./red.000004.out 2>&1

-- Finished on Wed Apr 18 09:13:57 2018 (6707 seconds) with 292.978 GB free disk space
----------------------------------------
-- Found 4 read error detection output files.
--
-- Loading read lengths.
-- Loading number of overlaps per read.
--
-- Configure OEA for 4gb memory.
--                   Batches of at most (unlimited) reads.
--                                      300000000 bases.
--
--           Total                                               Reads                 Olaps  Adjusts
--    Job   Memory      Read Range         Reads        Bases   Memory        Olaps   Memory   Memory  (Memory in MB)
--   ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------
--      1  3744.75         1-98278         67049    300005450   296.15     29051658   886.59   514.01
--      2  3731.63     98279-188103        65125    300001462   296.09     28623556   873.52   514.01
--      3  3705.53    188104-276885        64712    300003813   296.08     27768665   847.43   514.01
--      4  3643.20    276886-380247        66512    300002845   296.13     25724694   785.06   514.01
--      5  3696.35    380248-488962        70811    300002091   296.27     27461820   838.07   514.01
--      6  3093.20    488963-541708        33430    139330398   141.90     12756321   389.29   514.01
--   ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------
--                                                 1639346059             151386714
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'oea' concurrent execution on Wed Apr 18 09:14:01 2018 with 292.978 GB free disk space (6 processes; 6 concurrently)

    cd unitigging/3-overlapErrorAdjustment
    ./oea.sh 1 > ./oea.000001.out 2>&1
    ./oea.sh 2 > ./oea.000002.out 2>&1
    ./oea.sh 3 > ./oea.000003.out 2>&1
    ./oea.sh 4 > ./oea.000004.out 2>&1
    ./oea.sh 5 > ./oea.000005.out 2>&1
    ./oea.sh 6 > ./oea.000006.out 2>&1

-- Finished on Wed Apr 18 10:57:34 2018 (6213 seconds) with 292.696 GB free disk space
----------------------------------------
-- Found 6 overlap error adjustment output files.
----------------------------------------
-- Starting command on Wed Apr 18 10:57:34 2018 with 292.696 GB free disk space

    cd unitigging/3-overlapErrorAdjustment
    /home/hal9000/soft/canu-1.7/Linux-amd64/bin/ovStoreBuild \
      -G ../X.gkpStore \
      -O ../X.ovlStore \
      -evalues \
      -L ./oea.files \
    > ./oea.apply.err 2>&1

-- Finished on Wed Apr 18 10:57:35 2018 (1 second) with 292.414 GB free disk space
----------------------------------------
-- No report available.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'bat' concurrent execution on Wed Apr 18 10:57:35 2018 with 292.414 GB free disk space (1 processes; 1 concurrently)

    cd unitigging/4-unitigger
    ./unitigger.sh 1 > ./unitigger.000001.out 2>&1

-- Finished on Wed Apr 18 10:58:26 2018 (51 seconds) with 292.385 GB free disk space
----------------------------------------
--
-- Bogart failed, retry
--
--
-- Running jobs.  Second attempt out of 2.
----------------------------------------
-- Starting 'bat' concurrent execution on Wed Apr 18 10:58:26 2018 with 292.385 GB free disk space (1 processes; 1 concurrently)

    cd unitigging/4-unitigger
    ./unitigger.sh 1 > ./unitigger.000001.out 2>&1

-- Finished on Wed Apr 18 10:59:16 2018 (50 seconds) with 292.385 GB free disk space
----------------------------------------
--
-- Bogart failed, tried 2 times, giving up.
--

ABORT:
ABORT: Canu 1.7
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:

Can you help me? thank you Bessem

[brianwalenz]

See issue #873 for a probable fix. Though that refers to 1.6, the same applies to 1.7.

Note that after trimming you've only got 1.6x coverage. The only assembly you'll get is of repeats.

-- In gatekeeper store './X.gkpStore':
--   Found 367639 reads.
--   Found 1639346059 bases (1.63 times coverage).

[Bessem06]

Thank you for the prompt response,

I tried to use the fix as in #873 but after compiling canu and restarting the assembly, I had the same error message. Is there another way to solve the problem?

Thank you Bessem

[brianwalenz]

Another patch over at #873. For now, I'm keeping these two issues separate, since you're running different versions. But all I said there applies here.

[Bessem06]

I tried the new patch, but the compilation failed. I used "make -j 12" I am working under Ubuntu 16.04.4

[brianwalenz]

Remove the entire Linux-amd64/ directory and try again. If that fails, post the error generated by a normal make (no -j option).

[Bessem06]

I re-compiled again but with normal make and here is the error message I get:

bogart/AS_BAT_OverlapCache.C: In member function ‘void OverlapCache::computeOverlapLimit(ovStore*, uint64)’:
bogart/AS_BAT_OverlapCache.C:234:33: error: ‘class ovStore’ has no member named ‘numOverlapsPerFrag’
   uint32 *numPer    = ovlStore->numOverlapsPerFrag(frstRead, lastRead);
                                 ^
Makefile:659: recipe for target '/home/hal9000/soft/canu-1.7/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o' failed
make: *** [/home/hal9000/soft/canu-1.7/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o] Error 1

[brianwalenz]

Sorry, I only tested those patches against 1.6. Here's all the changed files, tested against 1.7.

fix3.tar.gz

[Bessem06]

Thank you, I was able to correctly compile canu 1.7 and finish the assembly