Coverage too low to be useful

[Iseez]

Hello, I'm using canu 1.8 to correct my Ustilago maydis reads, I'm using oxford nanopore reads. The correction failed and the error message says the following:

-- ERROR:  Read coverage (0) is too low to be useful.
-- ERROR:
-- ERROR:  This could be caused by an incorrect genomeSize or poor quality reads that could not
-- ERROR:  be sufficiently corrected.
-- ERROR:
-- ERROR:  You can force Canu to continue by decreasing parameter stopOnLowCoverage=10,
-- ERROR:  however, the quality of corrected reads and/or contiguity of contigs will be poor.
--

The full report generated when running canu like this

canu -correct -p Umaydis -d corrected_Umaydis_ndf genomeSize=19m -nanopore-raw ./porechop/no_adapters_Umaydis.fastq.gz useGrid=false

says the following:

-- Canu 1.8
--
-- 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
-- 
-- Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM.
-- De novo assembly of haplotype-resolved genomes with trio binning.
-- Nat Biotechnol. 2018
-- https//doi.org/10.1038/nbt.4277
-- 
-- 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
-- 
-- 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_322' (from 'java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 32 CPUs and 118 gigabytes of memory.
-- Detected Sun Grid Engine in '/cm/shared/apps/sge/2011.11p1/'.
-- Grid engine disabled per useGrid=false option.
--
--                            (tag)Concurrency
--                     (tag)Threads          |
--            (tag)Memory         |          |
--        (tag)         |         |          |     total usage     algorithm
--        -------  ------  --------   --------  -----------------  -----------------------------
-- Local: meryl     12 GB    4 CPUs x   8 jobs    96 GB   32 CPUs  (k-mer counting)
-- Local: hap        8 GB    4 CPUs x   8 jobs    64 GB   32 CPUs  (read-to-haplotype assignment)
-- Local: cormhap    6 GB   16 CPUs x   2 jobs    12 GB   32 CPUs  (overlap detection with mhap)
-- Local: obtovl     4 GB    8 CPUs x   4 jobs    16 GB   32 CPUs  (overlap detection)
-- Local: utgovl     4 GB    8 CPUs x   4 jobs    16 GB   32 CPUs  (overlap detection)
-- Local: ovb        4 GB    1 CPU  x  29 jobs   116 GB   29 CPUs  (overlap store bucketizer)
-- Local: ovs        8 GB    1 CPU  x  14 jobs   112 GB   14 CPUs  (overlap store sorting)
-- Local: red        8 GB    4 CPUs x   8 jobs    64 GB   32 CPUs  (read error detection)
-- Local: oea        4 GB    1 CPU  x  29 jobs   116 GB   29 CPUs  (overlap error adjustment)
-- Local: bat       16 GB    4 CPUs x   1 job     16 GB    4 CPUs  (contig construction with bogart)
-- Local: gfa        8 GB    4 CPUs x   1 job      8 GB    4 CPUs  (GFA alignment and processing)
--
-- Found Nanopore uncorrected reads in the input files.
--
-- Generating assembly 'Umaydis' in '/mnt/Timina/lmorales/Public/OxfordNanopore/Umaydis/corrected_Umaydis_ndf'
--
-- Parameters:
--
--  genomeSize        19000000
--
--  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%)
--
--
-- BEGIN CORRECTION
--
----------------------------------------
-- Starting command on Fri Jun 24 19:50:29 2022 with 673.588 GB free disk space

    cd .
    /cm/shared/apps/canu/1.8/Linux-amd64/bin/sqStoreCreate \
      -o ./Umaydis.seqStore.BUILDING \
      -minlength 1000 \
      ./Umaydis.seqStore.ssi \
    > ./Umaydis.seqStore.BUILDING.err 2>&1

-- Finished on Fri Jun 24 19:50:41 2022 (12 seconds) with 673.419 GB free disk space
----------------------------------------
--
-- WARNING:  Potential problems with your input reads were detected.
-- WARNING:
-- WARNING:  Please review the logging in files:
-- WARNING:    /mnt/Timina/lmorales/Public/OxfordNanopore/Umaydis/corrected_Umaydis_ndf/Umaydis.seqStore.BUILDING.err
-- WARNING:    /mnt/Timina/lmorales/Public/OxfordNanopore/Umaydis/corrected_Umaydis_ndf/Umaydis.seqStore.BUILDING/errorLog
-- 
-- Proceeding with assembly because stopOnReadQuality=false.
--
-- WARNING: gnuplot failed.
--
----------------------------------------
--
-- In sequence store './Umaydis.seqStore':
--   Found 83272 reads.
--   Found 454641649 bases (23.92 times coverage).
--
--   Read length histogram (one '*' equals 316.87 reads):
--     1000   1999  22181 **********************************************************************
--     2000   2999   9104 ****************************
--     3000   3999   6244 *******************
--     4000   4999   5752 ******************
--     5000   5999   6117 *******************
--     6000   6999   6749 *********************
--     7000   7999   6411 ********************
--     8000   8999   5471 *****************
--     9000   9999   4496 **************
--    10000  10999   3436 **********
--    11000  11999   2240 *******
--    12000  12999   1520 ****
--    13000  13999   1020 ***
--    14000  14999    701 **
--    15000  15999    480 *
--    16000  16999    343 *
--    17000  17999    235 
--    18000  18999    170 
--    19000  19999    140 
--    20000  20999    102 
--    21000  21999     76 
--    22000  22999     66 
--    23000  23999     36 
--    24000  24999     37 
--    25000  25999     24 
--    26000  26999     26 
--    27000  27999     21 
--    28000  28999     11 
--    29000  29999     13 
--    30000  30999     11 
--    31000  31999     11 
--    32000  32999      5 
--    33000  33999      4 
--    34000  34999      3 
--    35000  35999      2 
--    36000  36999      2 
--    37000  37999      1 
--    38000  38999      0 
--    39000  39999      3 
--    40000  40999      1 
--    41000  41999      1 
--    42000  42999      0 
--    43000  43999      1 
--    44000  44999      0 
--    45000  45999      0 
--    46000  46999      1 
--    47000  47999      0 
--    48000  48999      1 
--    49000  49999      0 
--    50000  50999      1 
--    51000  51999      2 
----------------------------------------
-- Starting command on Fri Jun 24 19:50:42 2022 with 673.418 GB free disk space

    cd correction/0-mercounts
    ./meryl-configure.sh \
    > ./meryl-configure.err 2>&1

-- Finished on Fri Jun 24 19:50:43 2022 (one second) with 673.418 GB free disk space
----------------------------------------
--  segments   memory batches
--  -------- -------- -------
--        01  1.19 GB       1
--        02  0.62 GB       1
--        04  0.31 GB       1
--
--  For 83272 reads with 454641649 bases, limit to 4 batches.
--  Will count kmers using 01 jobs, each using 3 GB and 4 threads.
--
-- Finished stage 'merylConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Fri Jun 24 19:50:43 2022 with 673.418 GB free disk space (1 processes; 8 concurrently)

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

-- Finished on Fri Jun 24 19:51:35 2022 (52 seconds) with 671.956 GB free disk space
----------------------------------------
-- Found 1 Kmer counting (meryl) outputs.
-- Finished stage 'cor-merylCountCheck', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Fri Jun 24 19:51:35 2022 with 671.956 GB free disk space (1 processes; 8 concurrently)

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

-- Finished on Fri Jun 24 19:52:16 2022 (41 seconds) with 672.955 GB free disk space
----------------------------------------
--
-- WARNING: gnuplot failed.
--
----------------------------------------
--
--  16-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1         0                                                                        0.0000 0.0000
--       2-     2  52250845 ********************************************************************** 0.6549 0.4892
--       3-     4  21792376 *****************************                                          0.8532 0.7114
--       5-     7   4607242 ******                                                                 0.9609 0.8847
--       8-    11    881778 *                                                                      0.9907 0.9584
--      12-    16    185564                                                                        0.9977 0.9843
--      17-    22     45007                                                                        0.9993 0.9931
--      23-    29     13099                                                                        0.9998 0.9964
--      30-    37      4623                                                                        0.9999 0.9978
--      38-    46      1964                                                                        0.9999 0.9984
--      47-    56       967                                                                        1.0000 0.9988
--      57-    67       559                                                                        1.0000 0.9990
--      68-    79       360                                                                        1.0000 0.9991
--      80-    92       243                                                                        1.0000 0.9993
--      93-   106       183                                                                        1.0000 0.9993
--     107-   121       115                                                                        1.0000 0.9994
--     122-   137        63                                                                        1.0000 0.9995
--     138-   154        68                                                                        1.0000 0.9995
--     155-   172        29                                                                        1.0000 0.9996
--     173-   191        26                                                                        1.0000 0.9996
--     192-   211        29                                                                        1.0000 0.9996
--     212-   232        19                                                                        1.0000 0.9996
--     233-   254        11                                                                        1.0000 0.9997
--     255-   277         8                                                                        1.0000 0.9997
--     278-   301         1                                                                        1.0000 0.9997
--     302-   326         5                                                                        1.0000 0.9997
--     327-   352         2                                                                        1.0000 0.9997
--     353-   379         5                                                                        1.0000 0.9997
--     380-   407         7                                                                        1.0000 0.9997
--     408-   436         5                                                                        1.0000 0.9997
--     437-   466         3                                                                        1.0000 0.9997
--     467-   497         2                                                                        1.0000 0.9997
--     498-   529         0                                                                        0.0000 0.0000
--     530-   562         5                                                                        1.0000 0.9997
--     563-   596         4                                                                        1.0000 0.9998
--     597-   631         3                                                                        1.0000 0.9998
--     632-   667         3                                                                        1.0000 0.9998
--     668-   704         3                                                                        1.0000 0.9998
--
--           0 (max occurrences)
--   213606141 (total mers, non-unique)
--    79785241 (distinct mers, non-unique)
--           0 (unique mers)
-- Finished stage 'meryl-process', reset canuIteration.
--
-- OVERLAPPER (mhap) (correction)
--
--
-- PARAMETERS: hashes=512, minMatches=3, threshold=0.83
--
-- Given 5.4 GB, can fit 16200 reads per block.
-- For 7 blocks, set stride to 2 blocks.
-- Logging partitioning to 'correction/1-overlapper/partitioning.log'.
-- Configured 6 mhap precompute jobs.
-- Configured 10 mhap overlap jobs.
-- Finished stage 'cor-mhapConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Fri Jun 24 19:52:17 2022 with 672.955 GB free disk space (6 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

-- Finished on Fri Jun 24 20:04:20 2022 (723 seconds) with 676.586 GB free disk space
----------------------------------------
-- All 6 mhap precompute jobs finished successfully.
-- Finished stage 'cor-mhapPrecomputeCheck', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Fri Jun 24 20:04:20 2022 with 676.586 GB free disk space (10 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

-- Finished on Fri Jun 24 20:05:27 2022 (67 seconds) with 676.512 GB free disk space
----------------------------------------
-- Found 10 mhap overlap output files.
-- Finished stage 'cor-mhapCheck', reset canuIteration.
----------------------------------------
-- Starting command on Fri Jun 24 20:05:27 2022 with 676.512 GB free disk space

    cd correction
    /cm/shared/apps/canu/1.8/Linux-amd64/bin/ovStoreConfig \
     -S ../Umaydis.seqStore \
     -M 4-8 \
     -L ./1-overlapper/ovljob.files \
     -create ./Umaydis.ovlStore.config \
     > ./Umaydis.ovlStore.config.txt \
    2> ./Umaydis.ovlStore.config.err

-- Finished on Fri Jun 24 20:05:27 2022 (lickety-split) with 676.512 GB free disk space
----------------------------------------
--
-- Creating overlap store correction/Umaydis.ovlStore using:
--      3 buckets
--      3 slices
--        using at most 1 GB memory each
-- Finished stage 'cor-overlapStoreConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'ovB' concurrent execution on Fri Jun 24 20:05:27 2022 with 676.512 GB free disk space (3 processes; 29 concurrently)

    cd correction/Umaydis.ovlStore.BUILDING
    ./scripts/1-bucketize.sh 1 > ./logs/1-bucketize.000001.out 2>&1
    ./scripts/1-bucketize.sh 2 > ./logs/1-bucketize.000002.out 2>&1
    ./scripts/1-bucketize.sh 3 > ./logs/1-bucketize.000003.out 2>&1

-- Finished on Fri Jun 24 20:05:28 2022 (one second) with 676.511 GB free disk space
----------------------------------------
-- Overlap store bucketizer finished.
-- Finished stage 'cor-overlapStoreBucketizerCheck', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'ovS' concurrent execution on Fri Jun 24 20:05:28 2022 with 676.511 GB free disk space (3 processes; 14 concurrently)

    cd correction/Umaydis.ovlStore.BUILDING
    ./scripts/2-sort.sh 1 > ./logs/2-sort.000001.out 2>&1
    ./scripts/2-sort.sh 2 > ./logs/2-sort.000002.out 2>&1
    ./scripts/2-sort.sh 3 > ./logs/2-sort.000003.out 2>&1

-- Finished on Fri Jun 24 20:05:28 2022 (like a bat out of hell) with 676.497 GB free disk space
----------------------------------------
-- Overlap store sorter finished.
-- Finished stage 'cor-overlapStoreSorterCheck', reset canuIteration.
----------------------------------------
-- Starting command on Fri Jun 24 20:05:28 2022 with 676.497 GB free disk space

    cd correction
    /cm/shared/apps/canu/1.8/Linux-amd64/bin/ovStoreIndexer \
      -O  ./Umaydis.ovlStore.BUILDING \
      -S ../Umaydis.seqStore \
      -C  ./Umaydis.ovlStore.config \
      -delete \
    > ./Umaydis.ovlStore.BUILDING.index.err 2>&1

-- Finished on Fri Jun 24 20:05:28 2022 (lickety-split) with 676.503 GB free disk space
----------------------------------------
-- Checking store.
----------------------------------------
-- Starting command on Fri Jun 24 20:05:28 2022 with 676.503 GB free disk space

    cd correction
    /cm/shared/apps/canu/1.8/Linux-amd64/bin/ovStoreDump \
     -S ../Umaydis.seqStore \
     -O  ./Umaydis.ovlStore \
     -counts \
     > ./Umaydis.ovlStore/counts.dat 2> ./Umaydis.ovlStore/counts.err

-- Finished on Fri Jun 24 20:05:28 2022 (fast as lightning) with 676.502 GB free disk space
----------------------------------------
--
-- Overlap store 'correction/Umaydis.ovlStore' successfully constructed.
-- Found 27006 overlaps for 16099 reads; 67173 reads have no overlaps.
--
--
-- Purged 6.667 GB in 41 overlap output files.
-- Finished stage 'cor-createOverlapStore', reset canuIteration.
-- Set corMinCoverage=4 based on read coverage of 23.
-- Global filter scores will be estimated.
-- Computing correction layouts.
----------------------------------------
-- Starting command on Fri Jun 24 20:05:29 2022 with 678.673 GB free disk space

    cd correction
    /cm/shared/apps/canu/1.8/Linux-amd64/bin/generateCorrectionLayouts \
      -S ../Umaydis.seqStore \
      -O  ./Umaydis.ovlStore \
      -C  ./Umaydis.corStore.WORKING \
      -eC 80 \
    > ./Umaydis.corStore.err 2>&1

-- Finished on Fri Jun 24 20:05:30 2022 (one second) with 678.666 GB free disk space
----------------------------------------
-- Finished stage 'cor-buildCorrectionLayoutsConfigure', reset canuIteration.
-- Computing correction layouts.
----------------------------------------
-- Starting command on Fri Jun 24 20:05:30 2022 with 678.666 GB free disk space

    cd correction/2-correction
    /cm/shared/apps/canu/1.8/Linux-amd64/bin/filterCorrectionLayouts \
      -S  ../../Umaydis.seqStore \
      -C     ../Umaydis.corStore \
      -R      ./Umaydis.readsToCorrect.WORKING \
      -cc 4 \
      -cl 1000 \
      -g  19000000 \
      -c  40 \
    > ./Umaydis.readsToCorrect.err 2>&1

-- Finished on Fri Jun 24 20:05:30 2022 (lickety-split) with 678.66 GB free disk space
----------------------------------------
--                             original      original
--                            raw reads     raw reads
--   category                w/overlaps  w/o/overlaps
--   -------------------- ------------- -------------
--   Number of Reads              16099         67173
--   Number of Bases           42317464             0
--   Coverage                     2.227         0.000
--   Median                        1792             0
--   Mean                          2628             0
--   N50                           3325             0
--   Minimum                       1000             0
--   Maximum                      26488             0
--   
--                                        --------corrected---------  ----------rescued----------
--                             evidence                     expected                     expected
--   category                     reads            raw     corrected            raw     corrected
--   -------------------- -------------  ------------- -------------  ------------- -------------
--   Number of Reads               1733            718           718              0             0
--   Number of Bases            5572778        2123213         59367              0             0
--   Coverage                     0.293          0.112         0.003          0.000         0.000
--   Median                        1902           1745            11              0             0
--   Mean                          3215           2957            82              0             0
--   N50                           5065           4252           353              0             0
--   Minimum                       1000           1000             1              0             0
--   Maximum                      26488          24032           906              0             0
--   
--                        --------uncorrected--------
--                                           expected
--   category                       raw     corrected
--   -------------------- ------------- -------------
--   Number of Reads              82554         82554
--   Number of Bases           40194251          1417
--   Coverage                     2.115         0.000
--   Median                           0             0
--   Mean                           486             0
--   N50                           3293             0
--   Minimum                          0             0
--   Maximum                      26488          1417
--   
--   Maximum Memory           762061730
-- Finished stage 'cor-filterCorrectionLayouts', reset canuIteration.
--
--                            (tag)Concurrency
--                     (tag)Threads          |
--            (tag)Memory         |          |
--        (tag)         |         |          |     total usage     algorithm
--        -------  ------  --------   --------  -----------------  -----------------------------
-- Local: cor        3 GB    4 CPUs x   8 jobs    24 GB   32 CPUs  (read correction)
--
-- Using overlaps no worse than 0.5 fraction error for correcting reads (from corErrorRate parameter).
-- Finished stage 'cor-generateCorrectedReadsConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cor' concurrent execution on Fri Jun 24 20:05:30 2022 with 678.66 GB free disk space (17 processes; 8 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

-- Finished on Fri Jun 24 20:05:35 2022 (5 seconds) with 678.653 GB free disk space
----------------------------------------
-- Found 17 read correction output files.
-- Finished stage 'cor-generateCorrectedReadsCheck', reset canuIteration.
-- Found 17 read correction output files.
-- Finished stage 'cor-generateCorrectedReadsCheck', reset canuIteration.
--
-- Loading corrected reads into corStore and seqStore.
----------------------------------------
-- Starting command on Fri Jun 24 20:05:35 2022 with 678.653 GB free disk space

    cd correction
    /cm/shared/apps/canu/1.8/Linux-amd64/bin/loadCorrectedReads \
      -S ../Umaydis.seqStore \
      -C ./Umaydis.corStore \
      -L ./2-correction/corjob.files \
    >  ./Umaydis.loadCorrectedReads.log \
    2> ./Umaydis.loadCorrectedReads.err

-- Finished on Fri Jun 24 20:05:35 2022 (furiously fast) with 678.65 GB free disk space
----------------------------------------
--
-- WARNING: gnuplot failed.
--
----------------------------------------
--
-- ERROR:  Read coverage (0) is too low to be useful.
-- ERROR:
-- ERROR:  This could be caused by an incorrect genomeSize or poor quality reads that could not
-- ERROR:  be sufficiently corrected.
-- ERROR:
-- ERROR:  You can force Canu to continue by decreasing parameter stopOnLowCoverage=10,
-- ERROR:  however, the quality of corrected reads and/or contiguity of contigs will be poor.
-- 

ABORT:
ABORT: Canu 1.8
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:

I tried the solution posted here adding corMhapSensitivity=normal but nothing changes.

I would really appreciate some help.

[skoren]

First, v1.8 is almost 4 yrs old so you should update to a recent release. Second, your coverage is quite low and the reads look to be pretty short (I'm guessing this is what the error in sqStore logs is, have you checked?) and low quality, almost none of them have overlaps. If you haven't already, I'd see if you can re-call the ONT data with the latest base caller as well.

You need to increase the sensitivity and reduce corMinCoverage (see FAQ about low coverage) so try adding corMhapSensitivity=high corMinCoverage=0. That said, it's not a very good dataset for assembly so I wouldn't expect it to assemble well.

[skoren]

Idle