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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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mostly harmless error occurred and Canu stopped #1365

Closed ashaneev closed 5 years ago

ashaneev commented 5 years ago

Hii.. Error occurs during the assembly process

 veena@veena-Lenovo-H30-50:~/Documents/TZ/canu$ canu -correct  -p xab -d xab  genomeSize=150k  -pacbio-raw  /home/veena/Documents/TZ/Mit/ProovreadOut/xab.fq 
 -- Canu snapshot v1.8 +160 changes (r9370 496f1e4fa60d36bd30222abcfe4fa50e4b35e39c)
 --
 -- 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_171' (from '/usr/lib/jvm/java-8-oracle/bin/java') with -d64 support.
 --
 -- WARNING:
 -- WARNING:  Failed to run gnuplot using command 'gnuplot'.
 -- WARNING:  Plots will be disabled.
 -- WARNING:
 --
 -- Detected 4 CPUs and 16 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   1 job     12 GB    4 CPUs  (k-mer counting)
 -- Local: hap        8 GB    4 CPUs x   1 job      8 GB    4 CPUs  (read-to-haplotype assignment)
 -- Local: cormhap    6 GB    4 CPUs x   1 job      6 GB    4 CPUs  (overlap detection with mhap)
 -- Local: obtovl     4 GB    4 CPUs x   1 job      4 GB    4 CPUs  (overlap detection)
 -- Local: utgovl     4 GB    4 CPUs x   1 job      4 GB    4 CPUs  (overlap detection)
 -- Local: cor      --- GB    4 CPUs x --- jobs   --- GB  --- CPUs  (read correction)
 -- Local: ovb        4 GB    1 CPU  x   4 jobs    16 GB    4 CPUs  (overlap store bucketizer)
 -- Local: ovs        8 GB    1 CPU  x   2 jobs    16 GB    2 CPUs  (overlap store sorting)
 -- Local: red        8 GB    4 CPUs x   1 job      8 GB    4 CPUs  (read error detection)
 -- Local: oea        4 GB    1 CPU  x   4 jobs    16 GB    4 CPUs  (overlap error adjustment)
 -- Local: bat       16 GB    4 CPUs x   1 job     16 GB    4 CPUs  (contig construction with bogart)
 -- Local: cns      --- GB    4 CPUs x --- jobs   --- GB  --- CPUs  (consensus)
 -- Local: gfa        8 GB    4 CPUs x   1 job      8 GB    4 CPUs  (GFA alignment and processing)
 --
 -- Found PacBio uncorrected reads in the input files.
 --
 -- Generating assembly 'xab' in '/home/veena/Documents/TZ/canu/xab'
 --
 -- Parameters:
 --
 --  genomeSize        150000
 --
 --  Overlap Generation Limits:
 --    corOvlErrorRate 0.2400 ( 24.00%)
 --    obtOvlErrorRate 0.0450 (  4.50%)
 --    utgOvlErrorRate 0.0450 (  4.50%)
 --
 --  Overlap Processing Limits:
 --    corErrorRate    0.3000 ( 30.00%)
 --    obtErrorRate    0.0450 (  4.50%)
 --    utgErrorRate    0.0450 (  4.50%)
 --    cnsErrorRate    0.0750 (  7.50%)
 --
 --
 -- BEGIN CORRECTION
 --
 ----------------------------------------
 -- Starting command on Fri May 17 17:31:35 2019 with 217.044 GB free disk space

     cd .
     /home/veena/Documents/TZ/canu/Linux-amd64/bin/sqStoreCreate \
       -o ./xab.seqStore.BUILDING \
       -minlength 1000 \
       ./xab.seqStore.ssi \
     > ./xab.seqStore.BUILDING.err 2>&1

 -- Finished on Fri May 17 17:31:36 2019 (one second) with 217.033 GB free disk space
 ----------------------------------------
 --
 -- WARNING:  Potential problems with your input reads were detected.
 -- WARNING:
 -- WARNING:  Please review the logging in files:
 -- WARNING:    /home/veena/Documents/TZ/canu/xab/xab.seqStore.BUILDING.err
 -- WARNING:    /home/veena/Documents/TZ/canu/xab/xab.seqStore.BUILDING/errorLog
 -- 
 -- Proceeding with assembly because stopOnReadQuality=false.
 --
 -- WARNING: gnuplot failed.
 --
 ----------------------------------------
 --
 -- In sequence store './xab.seqStore':
 --   Found 12093 reads.
 --   Found 33705215 bases (224.7 times coverage).
 --
 --   Read length histogram (one '*' equals 90.67 reads):
 --     1000   1999   6347 **********************************************************************
 --     2000   2999   2689 *****************************
 --     3000   3999   1238 *************
 --     4000   4999    592 ******
 --     5000   5999    266 **
 --     6000   6999    213 **
 --     7000   7999    133 *
 --     8000   8999    120 *
 --     9000   9999     80 
 --    10000  10999     76 
 --    11000  11999     60 
 --    12000  12999     64 
 --    13000  13999     60 
 --    14000  14999     38 
 --    15000  15999     26 
 --    16000  16999     29 
 --    17000  17999     11 
 --    18000  18999     11 
 --    19000  19999      7 
 --    20000  20999      8 
 --    21000  21999      4 
 --    22000  22999      5 
 --    23000  23999      1 
 --    24000  24999      3 
 --    25000  25999      6 
 --    26000  26999      3 
 --    27000  27999      1 
 --    28000  28999      1 
 --    29000  29999      0 
 --    30000  30999      1 
 ----------------------------------------
 -- Starting command on Fri May 17 17:31:36 2019 with 217.033 GB free disk space

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

 -- Finished on Fri May 17 17:31:36 2019 (lickety-split) with 217.033 GB free disk space
 ----------------------------------------
 --  segments   memory batches
 --  -------- -------- -------
 --        01  0.12 GB       1
 --
 --  For 12093 reads with 33705215 bases, limit to 1 batch.
 --  Will count kmers using 01 jobs, each using 2 GB and 4 threads.
 --
 -- Finished stage 'merylConfigure', reset canuIteration.
 --
 -- Running jobs.  First attempt out of 2.
 ----------------------------------------
 -- Starting 'meryl' concurrent execution on Fri May 17 17:31:36 2019 with 217.033 GB free disk space (1 processes; 1 concurrently)

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

 -- Finished on Fri May 17 17:31:38 2019 (2 seconds) with 217.023 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 May 17 17:31:38 2019 with 217.023 GB free disk space (1 processes; 1 concurrently)

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

 -- Finished on Fri May 17 17:31:51 2019 (13 seconds) with 217.021 GB free disk space
 ----------------------------------------
 --
 -- WARNING: gnuplot failed.
 --
 ----------------------------------------
 --
 --  16-mers                                                                                           Fraction
 --    Occurrences   NumMers                                                                         Unique Total
 --       1-     1         0                                                                        0.0000 0.0000
 --       2-     2    248875 ********************************************************************** 0.2125 0.0151
 --       3-     4    238327 *******************************************************************    0.3374 0.0285
 --       5-     7    173854 ************************************************                       0.4719 0.0496
 --       8-    11    146475 *****************************************                              0.5960 0.0798
 --      12-    16    121262 **********************************                                     0.7179 0.1250
 --      17-    22     95652 **************************                                             0.8075 0.1719
 --      23-    29     56061 ***************                                                        0.8852 0.2281
 --      30-    37     17622 ****                                                                   0.9262 0.2664
 --      38-    46      6043 *                                                                      0.9383 0.2808
 --      47-    56      4596 *                                                                      0.9431 0.2881
 --      57-    67      2885                                                                        0.9470 0.2953
 --      68-    79      1989                                                                        0.9493 0.3005
 --      80-    92      1806                                                                        0.9510 0.3049
 --      93-   106      1490                                                                        0.9525 0.3097
 --     107-   121      1602                                                                        0.9538 0.3141
 --     122-   137      1226                                                                        0.9551 0.3197
 --     138-   154      1369                                                                        0.9561 0.3243
 --     155-   172      1489                                                                        0.9573 0.3305
 --     173-   191      2171                                                                        0.9586 0.3380
 --     192-   211      1999                                                                        0.9605 0.3502
 --     212-   232      3501                                                                        0.9622 0.3625
 --     233-   254      4037 *                                                                      0.9652 0.3867
 --     255-   277      5252 *                                                                      0.9687 0.4169
 --     278-   301      6618 *                                                                      0.9733 0.4607
 --     302-   326      6937 *                                                                      0.9789 0.5193
 --     327-   352      4926 *                                                                      0.9848 0.5847
 --     353-   379      3611 *                                                                      0.9889 0.6348
 --     380-   407      2579                                                                        0.9920 0.6748
 --     408-   436      1284                                                                        0.9941 0.7047
 --     437-   466       588                                                                        0.9952 0.7207
 --     467-   497       435                                                                        0.9957 0.7285
 --     498-   529       633                                                                        0.9961 0.7351
 --     530-   562       560                                                                        0.9966 0.7451
 --     563-   596       511                                                                        0.9971 0.7543
 --     597-   631       552                                                                        0.9975 0.7633
 --     632-   667       248                                                                        0.9980 0.7734
 --     668-   704       431                                                                        0.9982 0.7783
 --     705-   742       197                                                                        0.9986 0.7875
 --     743-   781         6                                                                        0.9987 0.7915
 --     782-   821         6                                                                        0.9987 0.7916
 --
 --           0 (max occurrences)
 --    32894512 (total mers, non-unique)
 --     1171195 (distinct mers, non-unique)
 --           0 (unique mers)
 -- Finished stage 'meryl-process', reset canuIteration.
 --
 -- OVERLAPPER (mhap) (correction)
 --
 -- Set corMhapSensitivity=low based on read coverage of 224.
 --
 -- PARAMETERS: hashes=256, minMatches=3, threshold=0.8
 --
 -- Given 5.4 GB, can fit 16200 reads per block.
 -- For 2 blocks, set stride to 2 blocks.
 -- Logging partitioning to 'correction/1-overlapper/partitioning.log'.
 -- Configured 1 mhap precompute jobs.
 -- Configured 1 mhap overlap jobs.
 -- Finished stage 'cor-mhapConfigure', reset canuIteration.
 --
 -- Running jobs.  First attempt out of 2.
 ----------------------------------------
 -- Starting 'cormhap' concurrent execution on Fri May 17 17:31:51 2019 with 217.021 GB free disk space (1 processes; 1 concurrently)

     cd correction/1-overlapper
     ./precompute.sh 1 > ./precompute.000001.out 2>&1

 -- Finished on Fri May 17 17:33:22 2019 (91 seconds) with 217.352 GB free disk space
 ----------------------------------------
 -- All 1 mhap precompute jobs finished successfully.
 -- Finished stage 'cor-mhapPrecomputeCheck', reset canuIteration.
 --
 -- Running jobs.  First attempt out of 2.
 ----------------------------------------
 -- Starting 'cormhap' concurrent execution on Fri May 17 17:33:22 2019 with 217.352 GB free disk space (1 processes; 1 concurrently)

     cd correction/1-overlapper
     ./mhap.sh 1 > ./mhap.000001.out 2>&1

 -- Finished on Fri May 17 17:36:13 2019 (171 seconds) with 217.304 GB free disk space
 ----------------------------------------
 -- Found 1 mhap overlap output files.
 -- Finished stage 'cor-mhapCheck', reset canuIteration.
 ----------------------------------------
 -- Starting command on Fri May 17 17:36:13 2019 with 217.304 GB free disk space

     cd correction
     /home/veena/Documents/TZ/canu/Linux-amd64/bin/ovStoreConfig \
      -S ../xab.seqStore \
      -M 4-8 \
      -L ./1-overlapper/ovljob.files \
      -create ./xab.ovlStore.config \
      > ./xab.ovlStore.config.txt \
     2> ./xab.ovlStore.config.err

 -- Finished on Fri May 17 17:36:13 2019 (fast as lightning) with 217.304 GB free disk space
 ----------------------------------------
 --
 -- Creating overlap store correction/xab.ovlStore using:
 --      1 bucket
 --      2 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 May 17 17:36:13 2019 with 217.304 GB free disk space (1 processes; 4 concurrently)

     cd correction/xab.ovlStore.BUILDING
     ./scripts/1-bucketize.sh 1 > ./logs/1-bucketize.000001.out 2>&1

 -- Finished on Fri May 17 17:36:14 2019 (one second) with 217.213 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 May 17 17:36:14 2019 with 217.213 GB free disk space (2 processes; 2 concurrently)

     cd correction/xab.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

 -- Finished on Fri May 17 17:36:16 2019 (2 seconds) with 217.094 GB free disk space
 ----------------------------------------
 -- Overlap store sorter finished.
 -- Finished stage 'cor-overlapStoreSorterCheck', reset canuIteration.
 ----------------------------------------
 -- Starting command on Fri May 17 17:36:16 2019 with 217.094 GB free disk space

     cd correction
     /home/veena/Documents/TZ/canu/Linux-amd64/bin/ovStoreIndexer \
       -O  ./xab.ovlStore.BUILDING \
       -S ../xab.seqStore \
       -C  ./xab.ovlStore.config \
       -delete \
     > ./xab.ovlStore.BUILDING.index.err 2>&1

 -- Finished on Fri May 17 17:36:16 2019 (furiously fast) with 217.187 GB free disk space
 ----------------------------------------
 -- Checking store.
 ----------------------------------------
 -- Starting command on Fri May 17 17:36:16 2019 with 217.187 GB free disk space

     cd correction
     /home/veena/Documents/TZ/canu/Linux-amd64/bin/ovStoreDump \
      -S ../xab.seqStore \
      -O  ./xab.ovlStore \
      -counts \
      > ./xab.ovlStore/counts.dat 2> ./xab.ovlStore/counts.err

 -- Finished on Fri May 17 17:36:16 2019 (lickety-split) with 217.186 GB free disk space
 ----------------------------------------
 --
 -- Overlap store 'correction/xab.ovlStore' successfully constructed.
 -- Found 6208626 overlaps for 12083 reads; 10 reads have no overlaps.
 --
 --
 -- Purged 0.25 GB in 3 overlap output files.
 -- Finished stage 'cor-createOverlapStore', reset canuIteration.
 -- Set corMinCoverage=4 based on read coverage of 224.
 -- Global filter scores will be estimated.
 -- Computing correction layouts.
 ----------------------------------------
 -- Starting command on Fri May 17 17:36:16 2019 with 217.438 GB free disk space

     cd correction
     /home/veena/Documents/TZ/canu/Linux-amd64/bin/generateCorrectionLayouts \
       -S ../xab.seqStore \
       -O  ./xab.ovlStore \
       -C  ./xab.corStore.WORKING \
       -eC 80 \
     > ./xab.corStore.err 2>&1

 -- Finished on Fri May 17 17:36:17 2019 (one second) with 217.422 GB free disk space
 ----------------------------------------
 -- Finished stage 'cor-buildCorrectionLayoutsConfigure', reset canuIteration.
 -- Computing correction layouts.
 ----------------------------------------
 -- Starting command on Fri May 17 17:36:17 2019 with 217.422 GB free disk space

     cd correction/2-correction
     /home/veena/Documents/TZ/canu/Linux-amd64/bin/filterCorrectionLayouts \
       -S  ../../xab.seqStore \
       -C     ../xab.corStore \
       -R      ./xab.readsToCorrect.WORKING \
       -cc 4 \
       -cl 1000 \
       -g  150000 \
       -c  40 \
     > ./xab.readsToCorrect.err 2>&1

 -- Finished on Fri May 17 17:36:17 2019 (furiously fast) with 217.421 GB free disk space
 ----------------------------------------
 --                             original      original
 --                            raw reads     raw reads
 --   category                w/overlaps  w/o/overlaps
 --   -------------------- ------------- -------------
 --   Number of Reads              10945          1148
 --   Number of Bases           32227345       1464576
 --   Coverage                   214.849         9.764
 --   Median                        2054          1149
 --   Mean                          2944          1275
 --   N50                           3491          1220
 --   Minimum                       1000             0
 --   Maximum                      30605         13364
 --   
 --                                        --------corrected---------  ----------rescued----------
 --                             evidence                     expected                     expected
 --   category                     reads            raw     corrected            raw     corrected
 --   -------------------- -------------  ------------- -------------  ------------- -------------
 --   Number of Reads               2185            458           458           6051          6051
 --   Number of Bases           13114649        6152923       6004265       14802236      13528070
 --   Coverage                    87.431         41.019        40.028         98.682        90.187
 --   Median                        4463          12590         12365           2155          1906
 --   Mean                          6002          13434         13109           2446          2235
 --   N50                           8992          13420         13084           2708          2506
 --   Minimum                       1000           8992          8984           1004          1001
 --   Maximum                      30605          30605         27239          11699          7770
 --   
 --                        --------uncorrected--------
 --                                           expected
 --   category                       raw     corrected
 --   -------------------- ------------- -------------
 --   Number of Reads               5584          5584
 --   Number of Bases           12736762       6399293
 --   Coverage                    84.912        42.662
 --   Median                        1520             0
 --   Mean                          2280          1146
 --   N50                           2628          5502
 --   Minimum                          0             0
 --   Maximum                      28566         28183
 --   
 --   Maximum Memory           801837638
 -- Finished stage 'cor-filterCorrectionLayouts', reset canuIteration.
 --
 --                            (tag)Concurrency
 --                     (tag)Threads          |
 --            (tag)Memory         |          |
 --        (tag)         |         |          |     total usage     algorithm
 --        -------  ------  --------   --------  -----------------  -----------------------------
 -- Local: cor        5 GB    4 CPUs x   1 job      5 GB    4 CPUs  (read correction)
 --
 -- Using overlaps no worse than 0.3 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 May 17 17:36:17 2019 with 217.421 GB free disk space (3 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

 -- Finished on Fri May 17 17:37:59 2019 (102 seconds) with 217.395 GB free disk space
 ----------------------------------------
 --
 -- Read correction jobs failed, retry.
 --   job 2-correction/results/0001.cns FAILED.
 --   job 2-correction/results/0002.cns FAILED.
 --   job 2-correction/results/0003.cns FAILED.
 --
 --
 -- Running jobs.  Second attempt out of 2.
 ----------------------------------------
 -- Starting 'cor' concurrent execution on Fri May 17 17:37:59 2019 with 217.395 GB free disk space (3 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

 -- Finished on Fri May 17 17:39:42 2019 (103 seconds) with 217.395 GB free disk space
 ----------------------------------------
 --
 -- Read correction jobs failed, tried 2 times, giving up.
 --   job 2-correction/results/0001.cns FAILED.
 --   job 2-correction/results/0002.cns FAILED.
 --   job 2-correction/results/0003.cns FAILED.
 --

 ABORT:
 ABORT: Canu snapshot v1.8 +160 changes (r9370 496f1e4fa60d36bd30222abcfe4fa50e4b35e39c)
 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:
skoren commented 5 years ago

Your correction jobs are all failing, there should be more information in the 2-correction/*.out files, post those.

ashaneev commented 5 years ago

There are 3 out files and has the following contents

 Found perl:
    /usr/bin/perl
    This is perl 5, version 18, subversion 2 (v5.18.2) built for x86_64-linux-gnu-thread-multi

 Found java:
    /usr/lib/jvm/java-8-oracle/bin/java
    java version "1.8.0_171"

 Found canu:
    /home/veena/Documents/TZ/canu/Linux-amd64/bin/canu
    Canu snapshot v1.8 +160 changes (r9370 496f1e4fa60d36bd30222abcfe4fa50e4b35e39c)

Running job 10 based on command line options.
skoren commented 5 years ago

That doesn't show any error message but it also says it is running job 10 but you only have 3 jobs. Post the contents of your 2-correction and your 2-correction/results folder. Also post your correctReads.sh script.

ashaneev commented 5 years ago

please find the attached 2-correction file.thank you.

2-correction.zip

skoren commented 5 years ago

Thanks, I see the error is due to failed alignments:

falconsense: utility/edlib.C:400: void edlibAlignmentToStrings(const unsigned char*, int, int, int, int, int, const char*, const char*, char*, char*): Assertion `strlen(qry_aln_str) == alignmentLength && strlen(tgt_aln_str) == alignmentLength' failed.

Do you reads have non-ACGT characters? Are you able to share the input reads?

Based on your command these reads seem to already corrected by Provread. In that case you shouldn't need to correct them again and supply them as pacbio-corrected. Have you tried running Canu with the raw reads off the sequencer to see if you have the same error?

brianwalenz commented 5 years ago

Did you ever get an assembly? Can you upload the failing assembly for debugging (or even the original reads)? I'd like to see what broke even if you got it to work. Directions are in the FAQ.

skoren commented 5 years ago

Will close as this seems the same as issue #1370, non-ACGT characters. If possible we'd still like these reads to reproduce locally so please upload them to the FTP if you can.