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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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Canu help with restarting failed run due to ovsMemory set too low. #668

Closed nextgenusfs closed 6 years ago

nextgenusfs commented 7 years ago

I've been trying to run Canu on ~ 30X nanopore 1D reads for a ~ 30Mb genome for the past month, I've encountered several problems. The reads are on the shorter end, i.e. lots of the data is < 1 kb. So I've tried to run this decreasing readLength to 500. I then ran out of disk space on a previous run, the overlaps from cormhap are taking up nearly 2 TB. At any rate, I first was using canu v1.6, but since I was having some problems, I upgraded to the tip release at the time:

canu -nanopore-raw SWJ5594.barcode04.fastq.gz -d canu_SWJ5594 -p SWJ5594 \
     genomeSize=30500000  minReadLength=500  minOverlapLength=500 maxThreads=18
-- Canu snapshot v1.6 +61 changes (r8473 86f53cff1401ce4229d2a579ed093afe68751e0a)
....
-- CONFIGURE CANU
--
-- Detected Java(TM) Runtime Environment '1.8.0_111' (from 'java').
-- Detected gnuplot version '5.0 patchlevel 6' (from 'gnuplot') and image format 'png'.
-- Detected 24 CPUs and 64 gigabytes of memory.
-- Limited to 18 CPUs from maxThreads option.
-- No grid engine detected, grid disabled.
--
--                            (tag)Concurrency
--                     (tag)Threads          |
--            (tag)Memory         |          |
--        (tag)         |         |          |  algorithm
--        -------  ------  --------   --------  -----------------------------
-- Local: meryl      8 GB    3 CPUs x   6 jobs  (k-mer counting)
-- Local: cormhap    6 GB    9 CPUs x   2 jobs  (overlap detection with mhap)
-- Local: obtovl     8 GB    6 CPUs x   3 jobs  (overlap detection)
-- Local: utgovl     8 GB    6 CPUs x   3 jobs  (overlap detection)
-- Local: ovb        3 GB    1 CPU  x  18 jobs  (overlap store bucketizer)
-- Local: ovs        8 GB    1 CPU  x  18 jobs  (overlap store sorting)
-- Local: red        2 GB    3 CPUs x   6 jobs  (read error detection)
-- Local: oea        1 GB    1 CPU  x  18 jobs  (overlap error adjustment)
-- Local: bat       10 GB    3 CPUs x   6 jobs  (contig construction)
-- Local: cns       10 GB    3 CPUs x   6 jobs  (consensus)
-- Local: gfa        8 GB    3 CPUs x   6 jobs  (GFA alignment and processing)
--
-- Found Nanopore uncorrected reads in the input files.
--
-- Generating assembly 'SWJ5594' in '/Volumes/LinuxHD/nanopore/SWJ_Anid/canu_SWJ5594'
--
-- Parameters:
--
--  genomeSize        30500000
--
--  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 Sep 28 12:23:57 2017 with 2025.31 GB free disk space

    cd correction
    /usr/local/canu/Darwin-amd64/bin/gatekeeperCreate \
      -minlength 500 \
      -o ./SWJ5594.gkpStore.BUILDING \
      ./SWJ5594.gkpStore.gkp \
    > ./SWJ5594.gkpStore.BUILDING.err 2>&1

-- Finished on Thu Sep 28 12:24:19 2017 (22 seconds) with 2024.621 GB free disk space
----------------------------------------
--
-- In gatekeeper store 'correction/SWJ5594.gkpStore':
--   Found 916983 reads.
--   Found 1124659781 bases (36.87 times coverage).
--
--   Read length histogram (one '*' equals 7390.31 reads):
--        0    999 517322 **********************************************************************
--     1000   1999 293312 ***************************************
--     2000   2999  70983 *********
--     3000   3999  19935 **
--     4000   4999   6397 
--     5000   5999   2613 
--     6000   6999   1410 
--     7000   7999    965 
--     8000   8999    705 
--     9000   9999    601 
--    10000  10999    477 
--    11000  11999    403 
--    12000  12999    304 
--    13000  13999    253 
--    14000  14999    196 
--    15000  15999    139 
--    16000  16999    111 
--    17000  17999     75 
--    18000  18999     78 
--    19000  19999     54 
--    20000  20999     40 
--    21000  21999     44 
--    22000  22999     33 
--    23000  23999     48 
--    24000  24999     35 
--    25000  25999     33 
--    26000  26999     38 
--    27000  27999     15 
--    28000  28999     21 
--    29000  29999     25 
--    30000  30999     19 
--    31000  31999     23 
--    32000  32999     11 
--    33000  33999     18 
--    34000  34999     19 
--    35000  35999     17 
--    36000  36999      8 
--    37000  37999     17 
--    38000  38999     20 
--    39000  39999      8 
--    40000  40999     15 
--    41000  41999     12 
--    42000  42999     10 
--    43000  43999      8 
--    44000  44999      7 
--    45000  45999      5 
--    46000  46999      9 
--    47000  47999     10 
--    48000  48999      6 
--    49000  49999      5 
--    50000  50999      5 
--    51000  51999      5 
--    52000  52999      6 
--    53000  53999      8 
--    54000  54999      6 
--    55000  55999      4 
--    56000  56999      6 
--    57000  57999      2 
--    58000  58999      3 
--    59000  59999      5 
--    60000  60999      2 
--    61000  61999      2 
--    62000  62999      2 
--    63000  63999      0 
--    64000  64999      2 
--    65000  65999      1 
--    66000  66999      2 
--    67000  67999      2 
--    68000  68999      1 
--    69000  69999      1 
--    70000  70999      2 
--    71000  71999      1 
--    72000  72999      0 
--    73000  73999      0 
--    74000  74999      0 
--    75000  75999      0 
--    76000  76999      0 
--    77000  77999      0 
--    78000  78999      1 
--    79000  79999      0 
--    80000  80999      0 
--    81000  81999      1 
--    82000  82999      0 
--    83000  83999      0 
--    84000  84999      1 
-- Finished stage 'cor-gatekeeper', reset canuIteration.
-- Finished stage 'merylConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Thu Sep 28 12:24:39 2017 with 2024.624 GB free disk space (1 processes; 6 concurrently)

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

-- Finished on Thu Sep 28 12:36:08 2017 (689 seconds) with 2022.513 GB free disk space
----------------------------------------
-- Meryl finished successfully.
-- Finished stage 'merylCheck', reset canuIteration.
--
--  16-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1 377015170 *******************************************************************--> 0.7146 0.3394
--       2-     2  83893886 ********************************************************************** 0.8736 0.4904
--       3-     4  32039089 **************************                                             0.9177 0.5533
--       5-     7  11561972 *********                                                              0.9432 0.6061
--       8-    11  11847249 *********                                                              0.9622 0.6688
--      12-    16   8079422 ******                                                                 0.9831 0.7716
--      17-    22   2205619 *                                                                      0.9953 0.8560
--      23-    29    410451                                                                        0.9983 0.8843
--      30-    37    158871                                                                        0.9990 0.8922
--      38-    46     91435                                                                        0.9992 0.8966
--      47-    56     62592                                                                        0.9994 0.8999
--      57-    67     44863                                                                        0.9995 0.9027
--      68-    79     34127                                                                        0.9996 0.9051
--      80-    92     25445                                                                        0.9997 0.9073
--      93-   106     19553                                                                        0.9997 0.9093
--     107-   121     15111                                                                        0.9997 0.9110
--     122-   137     11516                                                                        0.9998 0.9125
--     138-   154      9080                                                                        0.9998 0.9139
--     155-   172      7614                                                                        0.9998 0.9150
--     173-   191      6363                                                                        0.9998 0.9161
--     192-   211      5448                                                                        0.9998 0.9172
--     212-   232      4616                                                                        0.9998 0.9182
--     233-   254      4167                                                                        0.9999 0.9191
--     255-   277      3714                                                                        0.9999 0.9200
--     278-   301      3380                                                                        0.9999 0.9209
--     302-   326      2878                                                                        0.9999 0.9217
--     327-   352      2626                                                                        0.9999 0.9226
--     353-   379      2718                                                                        0.9999 0.9234
--     380-   407      2627                                                                        0.9999 0.9242
--     408-   436      2660                                                                        0.9999 0.9252
--     437-   466      2836                                                                        0.9999 0.9262
--     467-   497      3047                                                                        0.9999 0.9273
--     498-   529      3092                                                                        0.9999 0.9287
--     530-   562      3300                                                                        0.9999 0.9301
--     563-   596      3454                                                                        0.9999 0.9317
--     597-   631      3564                                                                        0.9999 0.9335
--     632-   667      3471                                                                        0.9999 0.9355
--     668-   704      3196                                                                        0.9999 0.9375
--     705-   742      2949                                                                        1.0000 0.9395
--     743-   781      2688                                                                        1.0000 0.9414
--     782-   821      2323                                                                        1.0000 0.9433
--
--      603046 (max occurrences)
--   733889866 (total mers, non-unique)
--   150609211 (distinct mers, non-unique)
--   377015170 (unique mers)
-- For mhap overlapping, set repeat k-mer threshold to 11109.
--
-- Found 1110905036 16-mers; 527624381 distinct and 377015170 unique.  Largest count 603046.
-- Finished stage 'cor-meryl', reset canuIteration.
--
-- OVERLAPPER (mhap) (correction)
--
-- Set corMhapSensitivity=normal based on read coverage of 36.
--
-- PARAMETERS: hashes=512, minMatches=3, threshold=0.83
--
-- Given 6 GB, can fit 18000 reads per block.
-- For 52 blocks, set stride to 13 blocks.
-- Logging partitioning to 'correction/1-overlapper/partitioning.log'.
-- Configured 51 mhap precompute jobs.
-- Configured 123 mhap overlap jobs.
-- Finished stage 'cor-mhapConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Thu Sep 28 12:36:33 2017 with 2024.606 GB free disk space (51 processes; 2 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
    ./precompute.sh 13 > ./precompute.000013.out 2>&1
    ./precompute.sh 14 > ./precompute.000014.out 2>&1
    ./precompute.sh 15 > ./precompute.000015.out 2>&1
    ./precompute.sh 16 > ./precompute.000016.out 2>&1
    ./precompute.sh 17 > ./precompute.000017.out 2>&1
    ./precompute.sh 18 > ./precompute.000018.out 2>&1
    ./precompute.sh 19 > ./precompute.000019.out 2>&1
    ./precompute.sh 20 > ./precompute.000020.out 2>&1
    ./precompute.sh 21 > ./precompute.000021.out 2>&1
    ./precompute.sh 22 > ./precompute.000022.out 2>&1
    ./precompute.sh 23 > ./precompute.000023.out 2>&1
    ./precompute.sh 24 > ./precompute.000024.out 2>&1
    ./precompute.sh 25 > ./precompute.000025.out 2>&1
    ./precompute.sh 26 > ./precompute.000026.out 2>&1
    ./precompute.sh 27 > ./precompute.000027.out 2>&1
    ./precompute.sh 28 > ./precompute.000028.out 2>&1
    ./precompute.sh 29 > ./precompute.000029.out 2>&1
    ./precompute.sh 30 > ./precompute.000030.out 2>&1
    ./precompute.sh 31 > ./precompute.000031.out 2>&1
    ./precompute.sh 32 > ./precompute.000032.out 2>&1
    ./precompute.sh 33 > ./precompute.000033.out 2>&1
    ./precompute.sh 34 > ./precompute.000034.out 2>&1
    ./precompute.sh 35 > ./precompute.000035.out 2>&1
    ./precompute.sh 36 > ./precompute.000036.out 2>&1
    ./precompute.sh 37 > ./precompute.000037.out 2>&1
    ./precompute.sh 38 > ./precompute.000038.out 2>&1
    ./precompute.sh 39 > ./precompute.000039.out 2>&1
    ./precompute.sh 40 > ./precompute.000040.out 2>&1
    ./precompute.sh 41 > ./precompute.000041.out 2>&1
    ./precompute.sh 42 > ./precompute.000042.out 2>&1
    ./precompute.sh 43 > ./precompute.000043.out 2>&1
    ./precompute.sh 44 > ./precompute.000044.out 2>&1
    ./precompute.sh 45 > ./precompute.000045.out 2>&1
    ./precompute.sh 46 > ./precompute.000046.out 2>&1
    ./precompute.sh 47 > ./precompute.000047.out 2>&1
    ./precompute.sh 48 > ./precompute.000048.out 2>&1
    ./precompute.sh 49 > ./precompute.000049.out 2>&1
    ./precompute.sh 50 > ./precompute.000050.out 2>&1
    ./precompute.sh 51 > ./precompute.000051.out 2>&1

-- Finished on Thu Sep 28 13:33:13 2017 (3400 seconds) with 2006.908 GB free disk space
----------------------------------------
-- All 51 mhap precompute jobs finished successfully.
-- Finished stage 'cor-mhapPrecomputeCheck', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Thu Sep 28 13:33:18 2017 with 2006.908 GB free disk space (123 processes; 2 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
    ./mhap.sh 38 > ./mhap.000038.out 2>&1
    ./mhap.sh 39 > ./mhap.000039.out 2>&1
    ./mhap.sh 40 > ./mhap.000040.out 2>&1
    ./mhap.sh 41 > ./mhap.000041.out 2>&1
    ./mhap.sh 42 > ./mhap.000042.out 2>&1
    ./mhap.sh 43 > ./mhap.000043.out 2>&1
    ./mhap.sh 44 > ./mhap.000044.out 2>&1
    ./mhap.sh 45 > ./mhap.000045.out 2>&1
    ./mhap.sh 46 > ./mhap.000046.out 2>&1
    ./mhap.sh 47 > ./mhap.000047.out 2>&1
    ./mhap.sh 48 > ./mhap.000048.out 2>&1
    ./mhap.sh 49 > ./mhap.000049.out 2>&1
    ./mhap.sh 50 > ./mhap.000050.out 2>&1
    ./mhap.sh 51 > ./mhap.000051.out 2>&1
    ./mhap.sh 52 > ./mhap.000052.out 2>&1
    ./mhap.sh 53 > ./mhap.000053.out 2>&1
    ./mhap.sh 54 > ./mhap.000054.out 2>&1
    ./mhap.sh 55 > ./mhap.000055.out 2>&1
    ./mhap.sh 56 > ./mhap.000056.out 2>&1
    ./mhap.sh 57 > ./mhap.000057.out 2>&1
    ./mhap.sh 58 > ./mhap.000058.out 2>&1
    ./mhap.sh 59 > ./mhap.000059.out 2>&1
    ./mhap.sh 60 > ./mhap.000060.out 2>&1
    ./mhap.sh 61 > ./mhap.000061.out 2>&1
    ./mhap.sh 62 > ./mhap.000062.out 2>&1
    ./mhap.sh 63 > ./mhap.000063.out 2>&1
    ./mhap.sh 64 > ./mhap.000064.out 2>&1
    ./mhap.sh 65 > ./mhap.000065.out 2>&1
    ./mhap.sh 66 > ./mhap.000066.out 2>&1
    ./mhap.sh 67 > ./mhap.000067.out 2>&1
    ./mhap.sh 68 > ./mhap.000068.out 2>&1
    ./mhap.sh 69 > ./mhap.000069.out 2>&1
    ./mhap.sh 70 > ./mhap.000070.out 2>&1
    ./mhap.sh 71 > ./mhap.000071.out 2>&1
    ./mhap.sh 72 > ./mhap.000072.out 2>&1
    ./mhap.sh 73 > ./mhap.000073.out 2>&1
    ./mhap.sh 74 > ./mhap.000074.out 2>&1
    ./mhap.sh 75 > ./mhap.000075.out 2>&1
    ./mhap.sh 76 > ./mhap.000076.out 2>&1
    ./mhap.sh 77 > ./mhap.000077.out 2>&1
    ./mhap.sh 78 > ./mhap.000078.out 2>&1
    ./mhap.sh 79 > ./mhap.000079.out 2>&1
    ./mhap.sh 80 > ./mhap.000080.out 2>&1
    ./mhap.sh 81 > ./mhap.000081.out 2>&1
    ./mhap.sh 82 > ./mhap.000082.out 2>&1
    ./mhap.sh 83 > ./mhap.000083.out 2>&1
    ./mhap.sh 84 > ./mhap.000084.out 2>&1
    ./mhap.sh 85 > ./mhap.000085.out 2>&1
    ./mhap.sh 86 > ./mhap.000086.out 2>&1
    ./mhap.sh 87 > ./mhap.000087.out 2>&1
    ./mhap.sh 88 > ./mhap.000088.out 2>&1
    ./mhap.sh 89 > ./mhap.000089.out 2>&1
    ./mhap.sh 90 > ./mhap.000090.out 2>&1
    ./mhap.sh 91 > ./mhap.000091.out 2>&1
    ./mhap.sh 92 > ./mhap.000092.out 2>&1
    ./mhap.sh 93 > ./mhap.000093.out 2>&1
    ./mhap.sh 94 > ./mhap.000094.out 2>&1
    ./mhap.sh 95 > ./mhap.000095.out 2>&1
    ./mhap.sh 96 > ./mhap.000096.out 2>&1
    ./mhap.sh 97 > ./mhap.000097.out 2>&1
    ./mhap.sh 98 > ./mhap.000098.out 2>&1
    ./mhap.sh 99 > ./mhap.000099.out 2>&1
    ./mhap.sh 100 > ./mhap.000100.out 2>&1
    ./mhap.sh 101 > ./mhap.000101.out 2>&1
    ./mhap.sh 102 > ./mhap.000102.out 2>&1
    ./mhap.sh 103 > ./mhap.000103.out 2>&1
    ./mhap.sh 104 > ./mhap.000104.out 2>&1
    ./mhap.sh 105 > ./mhap.000105.out 2>&1
    ./mhap.sh 106 > ./mhap.000106.out 2>&1
    ./mhap.sh 107 > ./mhap.000107.out 2>&1
    ./mhap.sh 108 > ./mhap.000108.out 2>&1
    ./mhap.sh 109 > ./mhap.000109.out 2>&1
    ./mhap.sh 110 > ./mhap.000110.out 2>&1
    ./mhap.sh 111 > ./mhap.000111.out 2>&1
    ./mhap.sh 112 > ./mhap.000112.out 2>&1
    ./mhap.sh 113 > ./mhap.000113.out 2>&1
    ./mhap.sh 114 > ./mhap.000114.out 2>&1
    ./mhap.sh 115 > ./mhap.000115.out 2>&1
    ./mhap.sh 116 > ./mhap.000116.out 2>&1
    ./mhap.sh 117 > ./mhap.000117.out 2>&1
    ./mhap.sh 118 > ./mhap.000118.out 2>&1
    ./mhap.sh 119 > ./mhap.000119.out 2>&1
    ./mhap.sh 120 > ./mhap.000120.out 2>&1
    ./mhap.sh 121 > ./mhap.000121.out 2>&1
    ./mhap.sh 122 > ./mhap.000122.out 2>&1
    ./mhap.sh 123 > ./mhap.000123.out 2>&1

-- Finished on Tue Oct 10 13:33:26 2017 (1036808 seconds) with 514.568 GB free disk space
----------------------------------------
-- Found 123 mhap overlap output files.
-- Finished stage 'cor-mhapCheck', reset canuIteration.
----------------------------------------
-- Starting command on Tue Oct 10 13:33:26 2017 with 514.568 GB free disk space

    cd correction
    /usr/local/canu/Darwin-amd64/bin/ovStoreBuild \
     -O ./SWJ5594.ovlStore.BUILDING \
     -G ./SWJ5594.gkpStore \
     -M 2-8 \
     -L ./1-overlapper/ovljob.files \
     > ./SWJ5594.ovlStore.err 2>&1

-- Finished on Tue Oct 10 13:33:31 2017 (5 seconds) with 514.568 GB free disk space
----------------------------------------
ERROR:
ERROR:  Failed with exit code 1.  (rc=256)
ERROR:

ABORT:
ABORT: Canu snapshot v1.6 +61 changes (r8473 86f53cff1401ce4229d2a579ed093afe68751e0a)
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:   failed to create the overlap store.
ABORT:
ABORT: Disk space available:  514.568 GB
ABORT:
ABORT: Last 50 lines of the relevant log file (correction/SWJ5594.ovlStore.err):
ABORT:
ABORT:

After 14 days, the cormhap step finished, but then it immediately errors out on the next step, which after I looked at the correction log file says that there was not enough memory allocated to the ovs step. 

ERROR:  Cannot sort 227929.06 million overlaps using 8.00 GB memory; too few file handles available.
ERROR:    minMemory      2147483648
ERROR:    maxMemory      8589934592
ERROR:    olapsPerBucket 260046848
ERROR:    buckets        877
ERROR:    SC_CHILD_MAX   709
ERROR:    SC_OPEN_MAX    256
ERROR:  Increase memory size (in canu, ovsMemory; in ovStoreBuild, -M)

However, when I try to restart using more memory, then I get the following error:

$canu -nanopore-raw SWJ5594.barcode04.fastq.gz -d canu_SWJ5594 -p SWJ5594  \
   genomeSize=30500000  minReadLength=500  minOverlapLength=500 maxThreads=18 ovsMemory=48g
--
--                            (tag)Concurrency
--                     (tag)Threads          |
--            (tag)Memory         |          |
--        (tag)         |         |          |  algorithm
--        -------  ------  --------   --------  -----------------------------
-- Local: meryl      8 GB    3 CPUs x   6 jobs  (k-mer counting)
-- Local: cormhap    6 GB    9 CPUs x   2 jobs  (overlap detection with mhap)
-- Local: obtovl     8 GB    6 CPUs x   3 jobs  (overlap detection)
-- Local: utgovl     8 GB    6 CPUs x   3 jobs  (overlap detection)
-- Local: ovb        3 GB    1 CPU  x  18 jobs  (overlap store bucketizer)
-- Local: ovs       48 GB    1 CPU  x  18 jobs  (overlap store sorting)
-- Local: red        2 GB    3 CPUs x   6 jobs  (read error detection)
-- Local: oea        1 GB    1 CPU  x  18 jobs  (overlap error adjustment)
-- Local: bat       10 GB    3 CPUs x   6 jobs  (contig construction)
-- Local: cns       10 GB    3 CPUs x   6 jobs  (consensus)
-- Local: gfa        8 GB    3 CPUs x   6 jobs  (GFA alignment and processing)
--
-- Found unknown  reads in 'correction/SWJ5594.gkpStore'.

ABORT:
ABORT: Canu snapshot v1.6 +61 changes (r8473 86f53cff1401ce4229d2a579ed093afe68751e0a)
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:   ERROR: Failed to determine the sequencing technology of the reads.
ABORT:

I feel like perhaps there are some intermediate files that I can remove for this to restart? I don't want to compute the overlaps again if I can avoid it, considering the run time....

skoren commented 7 years ago

Unfortunately, you updated to tip in the middle of some large-scale changes. The bug you hit is probably fixed but wouldn't be backwards compatible so you have to restart from scratch using the latest in tip or the 1.6 release.

As for the assembly itself, I think you won't get a very good assembly. The main determinants of assembly quality are read length and coverage and you don't have too much coverage and the reads are all very short (avg 1200). Canu/MHAP weren't really optimized for finding overlaps for such short reads, you've got all the downsides of nanopore data (e.g. error rate) but none of the advantages (e.g. long reads). You could try using minimap as the overlapper as it may be better for finding these short overlaps (corOverlapper=minimap after installing minimap2 and symlinking/copying the executable to the canu bin folder) but as I said, I don't think you're going to get a very good assembly.

nextgenusfs commented 7 years ago

Thanks for the input. Yes I'm aware the data isn't the greatest, unfortunately getting high proportions of high MW DNA without also have short fragments from filamentous fungi is difficult. I'll give the minimap2 a whirl.

skoren commented 6 years ago

Inactive, and not much for us to address here. Canu isn't going to be optimized for <1kb reads.