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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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Installing 1.8 but showing 1.6 #1155

Closed piiboo closed 6 years ago

piiboo commented 6 years ago

Hello, I managed to install Canu by following the instructions in release. I downloaded the binary 'canu-1.8.Linux-amd64.tar.xz', then installed with command 'tar -xJf canu-1.8.*.tar.xz'. In terminal it showed success. However when I check the version using canu -version, it shows canu 1.6. And it does not run correctly. 

-- Canu 1.6
--
-- 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 '10.0.2' (from 'java').
-- Detected gnuplot version '5.2 patchlevel 2' (from 'gnuplot') and image format 'png'.
-- Detected 40 CPUs and 126 gigabytes of memory.
-- No grid engine detected, grid disabled.
--
--                            (tag)Concurrency
--                     (tag)Threads          |
--            (tag)Memory         |          |
--        (tag)         |         |          |  algorithm
--        -------  ------  --------   --------  -----------------------------
-- Local: meryl      8 GB    4 CPUs x  10 jobs  (k-mer counting)
-- Local: cormhap    6 GB   10 CPUs x   4 jobs  (overlap detection with mhap)
-- Local: obtovl     8 GB    8 CPUs x   5 jobs  (overlap detection)
-- Local: utgovl     8 GB    8 CPUs x   5 jobs  (overlap detection)
-- Local: cor        6 GB    2 CPUs x  20 jobs  (read correction)
-- Local: ovb        3 GB    1 CPU  x  40 jobs  (overlap store bucketizer)
-- Local: ovs        8 GB    1 CPU  x  40 jobs  (overlap store sorting)
-- Local: red        2 GB    4 CPUs x  10 jobs  (read error detection)
-- Local: oea        1 GB    1 CPU  x  40 jobs  (overlap error adjustment)
-- Local: bat       12 GB    4 CPUs x  10 jobs  (contig construction)
-- Local: cns       12 GB    4 CPUs x  10 jobs  (consensus)
-- Local: gfa        8 GB    4 CPUs x  10 jobs  (GFA alignment and processing)
--
-- Found Nanopore uncorrected reads in the input files.
--
-- Generating assembly 'lambdaDevono' in '/home/geneious/lambdarun'
--
-- Parameters:
--
--  genomeSize        48500
--
--  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 Tue Nov 13 21:05:24 2018 with 62.856 GB free disk space

    cd correction
    /usr/lib/canu/gatekeeperCreate \
      -minlength 1000 \
      -o ./lambdaDevono.gkpStore.BUILDING \
      ./lambdaDevono.gkpStore.gkp \
    > ./lambdaDevono.gkpStore.BUILDING.err 2>&1

-- Finished on Tue Nov 13 21:05:47 2018 (23 seconds) with 62.561 GB free disk space
----------------------------------------
--
-- In gatekeeper store 'correction/lambdaDevono.gkpStore':
--   Found 141265 reads.
--   Found 1053670231 bases (21725.15 times coverage).
--
--   Read length histogram (one '*' equals 270.92 reads):
--        0    999      0 
--     1000   1999  18965 **********************************************************************
--     2000   2999  17182 ***************************************************************
--     3000   3999  15155 *******************************************************
--     4000   4999  13015 ************************************************
--     5000   5999  11302 *****************************************
--     6000   6999   9630 ***********************************
--     7000   7999   8212 ******************************
--     8000   8999   7076 **************************
--     9000   9999   5875 *********************
--    10000  10999   5155 *******************
--    11000  11999   4371 ****************
--    12000  12999   3728 *************
--    13000  13999   3204 ***********
--    14000  14999   2772 **********
--    15000  15999   2317 ********
--    16000  16999   2018 *******
--    17000  17999   1690 ******
--    18000  18999   1484 *****
--    19000  19999   1123 ****
--    20000  20999   1026 ***
--    21000  21999    803 **
--    22000  22999    679 **
--    23000  23999    575 **
--    24000  24999    492 *
--    25000  25999    351 *
--    26000  26999    314 *
--    27000  27999    323 *
--    28000  28999    328 *
--    29000  29999    289 *
--    30000  30999    235 
--    31000  31999    214 
--    32000  32999    193 
--    33000  33999    174 
--    34000  34999    150 
--    35000  35999    144 
--    36000  36999    110 
--    37000  37999     99 
--    38000  38999     91 
--    39000  39999     71 
--    40000  40999     77 
--    41000  41999     36 
--    42000  42999     57 
--    43000  43999     38 
--    44000  44999     38 
--    45000  45999     36 
--    46000  46999     22 
--    47000  47999     23 
--    48000  48999      3 
-- Finished stage 'cor-gatekeeper', reset canuIteration.
-- Finished stage 'merylConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Tue Nov 13 21:05:48 2018 with 62.557 GB free disk space (1 processes; 10 concurrently)

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

-- Finished on Tue Nov 13 21:07:17 2018 (89 seconds) with 62.099 GB free disk space
----------------------------------------
-- Meryl finished successfully.
-- Finished stage 'merylCheck', reset canuIteration.
--
--  16-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1  77962580 *******************************************************************--> 0.6898 0.0741
--       2-     2  13915978 ********************************************************************** 0.8130 0.1006
--       3-     4   8689914 *******************************************                            0.8625 0.1166
--       5-     7   4412050 **********************                                                 0.9074 0.1377
--       8-    11   2429480 ************                                                           0.9360 0.1588
--      12-    16   1467642 *******                                                                0.9538 0.1783
--      17-    22    948809 ****                                                                   0.9651 0.1964
--      23-    29    653220 ***                                                                    0.9728 0.2130
--      30-    37    470207 **                                                                     0.9782 0.2285
--      38-    46    350924 *                                                                      0.9821 0.2430
--      47-    56    268934 *                                                                      0.9851 0.2567
--      57-    67    211673 *                                                                      0.9874 0.2696
--      68-    79    168982                                                                        0.9892 0.2818
--      80-    92    137902                                                                        0.9907 0.2935
--      93-   106    112994                                                                        0.9919 0.3046
--     107-   121     92549                                                                        0.9929 0.3151
--     122-   137     76900                                                                        0.9937 0.3251
--     138-   154     64532                                                                        0.9943 0.3345
--     155-   172     55861                                                                        0.9949 0.3433
--     173-   191     48301                                                                        0.9954 0.3520
--     192-   211     42765                                                                        0.9958 0.3603
--     212-   232     36360                                                                        0.9962 0.3684
--     233-   254     32568                                                                        0.9965 0.3761
--     255-   277     28628                                                                        0.9968 0.3836
--     278-   301     25305                                                                        0.9970 0.3908
--     302-   326     22661                                                                        0.9973 0.3977
--     327-   352     20425                                                                        0.9975 0.4044
--     353-   379     18355                                                                        0.9976 0.4110
--     380-   407     16045                                                                        0.9978 0.4174
--     408-   436     14556                                                                        0.9979 0.4234
--     437-   466     13189                                                                        0.9981 0.4292
--     467-   497     12227                                                                        0.9982 0.4348
--     498-   529     11102                                                                        0.9983 0.4404
--     530-   562     10130                                                                        0.9984 0.4458
--     563-   596      9328                                                                        0.9985 0.4511
--     597-   631      8373                                                                        0.9986 0.4562
--     632-   667      7893                                                                        0.9986 0.4611
--     668-   704      7132                                                                        0.9987 0.4660
--     705-   742      6518                                                                        0.9988 0.4706
--     743-   781      6132                                                                        0.9988 0.4751
--     782-   821      5615                                                                        0.9989 0.4795
--
--       58824 (max occurrences)
--   973588676 (total mers, non-unique)
--    35053579 (distinct mers, non-unique)
--    77962580 (unique mers)
-- For mhap overlapping, set repeat k-mer threshold to 10515.
--
-- Found 1051551256 16-mers; 113016159 distinct and 77962580 unique.  Largest count 58824.
-- Finished stage 'cor-meryl', reset canuIteration.
--
-- OVERLAPPER (mhap) (correction)
--
-- Set corMhapSensitivity=low based on read coverage of 21725.
--
-- PARAMETERS: hashes=256, minMatches=3, threshold=0.85
--
-- Given 6 GB, can fit 18000 reads per block.
-- For 9 blocks, set stride to 2 blocks.
-- Logging partitioning to 'correction/1-overlapper/partitioning.log'.
-- Configured 8 mhap precompute jobs.
-- Configured 17 mhap overlap jobs.
-- Finished stage 'cor-mhapConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Tue Nov 13 21:07:20 2018 with 62.556 GB free disk space (8 processes; 4 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

-- Finished on Tue Nov 13 21:07:22 2018 (2 seconds) with 61.545 GB free disk space
----------------------------------------
--
-- Mhap precompute jobs failed, retry.
--   job correction/1-overlapper/blocks/000001.dat FAILED.
--   job correction/1-overlapper/blocks/000002.dat FAILED.
--   job correction/1-overlapper/blocks/000003.dat FAILED.
--   job correction/1-overlapper/blocks/000004.dat FAILED.
--   job correction/1-overlapper/blocks/000005.dat FAILED.
--   job correction/1-overlapper/blocks/000006.dat FAILED.
--   job correction/1-overlapper/blocks/000007.dat FAILED.
--   job correction/1-overlapper/blocks/000008.dat FAILED.
--
--
-- Running jobs.  Second attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Tue Nov 13 21:07:22 2018 with 61.545 GB free disk space (8 processes; 4 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

-- Finished on Tue Nov 13 21:07:25 2018 (3 seconds) with 61.545 GB free disk space
----------------------------------------
--
-- Mhap precompute jobs failed, tried 2 times, giving up.
--   job correction/1-overlapper/blocks/000001.dat FAILED.
--   job correction/1-overlapper/blocks/000002.dat FAILED.
--   job correction/1-overlapper/blocks/000003.dat FAILED.
--   job correction/1-overlapper/blocks/000004.dat FAILED.
--   job correction/1-overlapper/blocks/000005.dat FAILED.
--   job correction/1-overlapper/blocks/000006.dat FAILED.
--   job correction/1-overlapper/blocks/000007.dat FAILED.
--   job correction/1-overlapper/blocks/000008.dat FAILED.
--

ABORT:
ABORT: Canu 1.6
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 am new to Linux, could anyone help me about this error? Thank you.

skoren commented 6 years ago

You probably already have a canu installation in your path while your new install is not in the path. Provide the full path to your downloaded Canu location (e.g. /full/path/to/where/you/extracted/canu-1.8/*/bin/canu).

piiboo commented 6 years ago

Thank you skoren, I managed to find the canu 1.6 and uninstalled it, then I install canu 1.8 at the location I know. Then I run it again but still without success, is it related to the java version mentioned in previous issues? Here is the log when I run canu agian:

canu-1.8//bin/canu -d lambdarun -p lambdaDevono genomeSize=48.5k -nanopore-raw .fastq.gz -- 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_192' (from 'java') with -d64 support. -- Detected gnuplot version '5.2 patchlevel 2 ' (from 'gnuplot') and image format 'png'. -- Detected 40 CPUs and 126 gigabytes of memory. -- No grid engine detected, grid disabled.

-- (tag)Concurrency -- (tag)Threads -- (tag)Memory -- (tag) total usage algorithm

-- Local: meryl 12 GB 4 CPUs x 10 jobs 120 GB 40 CPUs (k-mer counting) -- Local: hap 8 GB 4 CPUs x 10 jobs 80 GB 40 CPUs (read-to-haplotype assignment) -- Local: cormhap 6 GB 10 CPUs x 4 jobs 24 GB 40 CPUs (overlap detection with mhap) -- Local: obtovl 4 GB 8 CPUs x 5 jobs 20 GB 40 CPUs (overlap detection) -- Local: utgovl 4 GB 8 CPUs x 5 jobs 20 GB 40 CPUs (overlap detection) -- Local: ovb 4 GB 1 CPU x 31 jobs 124 GB 31 CPUs (overlap store bucketizer) -- Local: ovs 8 GB 1 CPU x 15 jobs 120 GB 15 CPUs (overlap store sorting) -- Local: red 8 GB 4 CPUs x 10 jobs 80 GB 40 CPUs (read error detection) -- Local: oea 4 GB 1 CPU x 31 jobs 124 GB 31 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 'lambdaDevono' in '/home/geneious/lambdarun'

-- Parameters:

-- genomeSize 48500

-- 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 Wed Nov 14 10:53:12 2018 with 61.963 GB free disk space

cd .
/home/geneious/canu-1.8/Linux-amd64/bin/sqStoreCreate \
  -o ./lambdaDevono.seqStore.BUILDING \
  -minlength 1000 \
  ./lambdaDevono.seqStore.ssi \
> ./lambdaDevono.seqStore.BUILDING.err 2>&1

-- Finished on Wed Nov 14 10:53:34 2018 (22 seconds) with 61.667 GB free disk space

-- -- In sequence store './lambdaDevono.seqStore': -- Found 141265 reads. -- Found 1053670231 bases (21725.15 times coverage).

-- Read length histogram (one '*' equals 270.92 reads): -- 1000 1999 18965 ** -- 2000 2999 17182 ***** -- 3000 3999 15155 * -- 4000 4999 13015 **** -- 5000 5999 11302 *** -- 6000 6999 9630 * -- 7000 7999 8212 ** -- 8000 8999 7076 ** -- 9000 9999 5875 ** -- 10000 10999 5155 -- 11000 11999 4371 **** -- 12000 12999 3728 ** -- 13000 13999 3204 -- 14000 14999 2772 ** -- 15000 15999 2317 **** -- 16000 16999 2018 * -- 17000 17999 1690 **** -- 18000 18999 1484 * -- 19000 19999 1123 * -- 20000 20999 1026 -- 21000 21999 803 -- 22000 22999 679 -- 23000 23999 575 * -- 24000 24999 492 -- 25000 25999 351 -- 26000 26999 314 -- 27000 27999 323 -- 28000 28999 328 -- 29000 29999 289 * -- 30000 30999 235 -- 31000 31999 214 -- 32000 32999 193 -- 33000 33999 174 -- 34000 34999 150 -- 35000 35999 144 -- 36000 36999 110 -- 37000 37999 99 -- 38000 38999 91 -- 39000 39999 71 -- 40000 40999 77 -- 41000 41999 36 -- 42000 42999 57 -- 43000 43999 38 -- 44000 44999 38 -- 45000 45999 36 -- 46000 46999 22 -- 47000 47999 23 -- 48000 48999 3

-- Starting command on Wed Nov 14 10:53:36 2018 with 61.666 GB free disk space

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

-- Finished on Wed Nov 14 10:53:36 2018 (lickety-split) with 61.666 GB free disk space

-- segments memory batches

-- 01 2.50 GB 1 -- 02 1.38 GB 1 -- 04 0.69 GB 1 -- 06 0.50 GB 1 -- 08 0.38 GB 1

-- For 141265 reads with 1053670231 bases, limit to 10 batches. -- Will count kmers using 01 jobs, each using 4 GB and 4 threads.

-- Finished stage 'merylConfigure', reset canuIteration.

-- Running jobs. First attempt out of 2.

-- Starting 'meryl' concurrent execution on Wed Nov 14 10:53:36 2018 with 61.666 GB free disk space (1 processes; 10 concurrently)

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

-- Finished on Wed Nov 14 10:54:55 2018 (79 seconds) with 61.154 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 Wed Nov 14 10:54:55 2018 with 61.154 GB free disk space (1 processes; 10 concurrently)

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

-- Finished on Wed Nov 14 10:55:14 2018 (19 seconds) with 61.5 GB free disk space

-- -- 16-mers Fraction -- Occurrences NumMers Unique Total -- 1- 1 77962580 *****--> 0.6898 0.0741 -- 2- 2 13915978 ** 0.8130 0.1006 -- 3- 4 8689914 * 0.8625 0.1166 -- 5- 7 4412050 ** 0.9074 0.1377 -- 8- 11 2429480 **** 0.9360 0.1588 -- 12- 16 1467642 * 0.9538 0.1783 -- 17- 22 948809 0.9651 0.1964 -- 23- 29 653220 * 0.9728 0.2130 -- 30- 37 470207 * 0.9782 0.2285 -- 38- 46 350924 0.9821 0.2430 -- 47- 56 268934 0.9851 0.2567 -- 57- 67 211673 0.9874 0.2696 -- 68- 79 168982 0.9892 0.2818 -- 80- 92 137902 0.9907 0.2935 -- 93- 106 112994 0.9919 0.3046 -- 107- 121 92549 0.9929 0.3151 -- 122- 137 76900 0.9937 0.3251 -- 138- 154 64532 0.9943 0.3345 -- 155- 172 55861 0.9949 0.3433 -- 173- 191 48301 0.9954 0.3520 -- 192- 211 42765 0.9958 0.3603 -- 212- 232 36360 0.9962 0.3684 -- 233- 254 32568 0.9965 0.3761 -- 255- 277 28628 0.9968 0.3836 -- 278- 301 25305 0.9970 0.3908 -- 302- 326 22661 0.9973 0.3977 -- 327- 352 20425 0.9975 0.4044 -- 353- 379 18355 0.9976 0.4110 -- 380- 407 16045 0.9978 0.4174 -- 408- 436 14556 0.9979 0.4234 -- 437- 466 13189 0.9981 0.4292 -- 467- 497 12227 0.9982 0.4348 -- 498- 529 11102 0.9983 0.4404 -- 530- 562 10130 0.9984 0.4458 -- 563- 596 9328 0.9985 0.4511 -- 597- 631 8373 0.9986 0.4562 -- 632- 667 7893 0.9986 0.4611 -- 668- 704 7132 0.9987 0.4660 -- 705- 742 6518 0.9988 0.4706 -- 743- 781 6132 0.9988 0.4751 -- 782- 821 5615 0.9989 0.4795

-- 0 (max occurrences) -- 0 (total mers, non-unique) -- 0 (distinct mers, non-unique) -- 0 (unique mers) -- Finished stage 'meryl-process', reset canuIteration.

-- Running jobs. First attempt out of 2.

-- Starting 'cormhap' concurrent execution on Wed Nov 14 10:55:15 2018 with 61.5 GB free disk space (8 processes; 4 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

-- Finished on Wed Nov 14 10:55:15 2018 (furiously fast) with 61.5 GB free disk space

-- -- Mhap precompute jobs failed, retry. -- job correction/1-overlapper/blocks/000001.dat FAILED. -- job correction/1-overlapper/blocks/000002.dat FAILED. -- job correction/1-overlapper/blocks/000003.dat FAILED. -- job correction/1-overlapper/blocks/000004.dat FAILED. -- job correction/1-overlapper/blocks/000005.dat FAILED. -- job correction/1-overlapper/blocks/000006.dat FAILED. -- job correction/1-overlapper/blocks/000007.dat FAILED. -- job correction/1-overlapper/blocks/000008.dat FAILED.

-- -- Running jobs. Second attempt out of 2.

-- Starting 'cormhap' concurrent execution on Wed Nov 14 10:55:15 2018 with 61.5 GB free disk space (8 processes; 4 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

-- Finished on Wed Nov 14 10:55:15 2018 (in the blink of an eye) with 61.5 GB free disk space

-- -- Mhap precompute jobs failed, tried 2 times, giving up. -- job correction/1-overlapper/blocks/000001.dat FAILED. -- job correction/1-overlapper/blocks/000002.dat FAILED. -- job correction/1-overlapper/blocks/000003.dat FAILED. -- job correction/1-overlapper/blocks/000004.dat FAILED. -- job correction/1-overlapper/blocks/000005.dat FAILED. -- job correction/1-overlapper/blocks/000006.dat FAILED. -- job correction/1-overlapper/blocks/000007.dat FAILED. -- job correction/1-overlapper/blocks/000008.dat FAILED.

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:

piiboo commented 6 years ago

Sorry I didn't realize your suggestion. I provided full path to canu and now it works well. Thank you.