Canu 1.8 nanopore assembly

[biowackysci]

The CANU 1.8 command that I use is

#!/bin/bash
#PBS -V
#PBS -N Assembly_SE3
#PBS -q batch
#PBS -l nodes=1:ppn=16
#PBS -l walltime=1000:00:00
#PBS -l mem=100g
#PBS -M saila.vishwanathan@ecodev.vic.gov.au 
#PBS -m abe

#cp /group/pasture/Saila/MinION/Impact04_run2/20180426_0452_impact04_SV_26april2018/fastq/pass/fastq/ $TMPDIR/
cd $TMPDIR/
cp /group/pasture/Saila/MinION/all_Minion_fastq/prometh_min_all.fastq $TMPDIR/

#cd $PBS_O_WORKDIR

module load Java
module load canu

canu -p canu -d /group/pasture/Saila/Canu_hybrid genomeSize=2.8g -fast maxThreads=16 useGrid=false stopOnLowCoverage=10 corOutCoverage=1000 minOverlapLength=1000 -nanopore-raw /group/pasture/Saila/MinION/all_Minion_fastq/prometh_min_all.fastq

cp -r $TMPDIR/Prom_min_CANU_assembly /group/pasture/Saila/Canu_hybrid/

The CANU report is as follows

-- Canu 1.8
--
-- CITATIONS
-- CONFIGURE CANU
--
-- Detected Java(TM) Runtime Environment '1.8.0_172' (from '/usr/local/EasyBuild/software/Java/1.8.0_172/bin/java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 48 CPUs and 754 gigabytes of memory.
-- Limited to 16 CPUs from maxThreads option.
-- Detected Slurm with 'sinfo' binary in /usr/local/slurm/current/bin/sinfo.
-- Grid engine disabled per useGrid=false option.
--
--                            (tag)Concurrency
--                     (tag)Threads          |
--            (tag)Memory         |          |
--        (tag)         |         |          |     total usage     algorithm
--        -------  ------  --------   --------  -----------------  -----------------------------
-- Local: meryl     64 GB    8 CPUs x   2 jobs   128 GB   16 CPUs  (k-mer counting)
-- Local: hap       16 GB   16 CPUs x   1 job     16 GB   16 CPUs  (read-to-haplotype assignment)
-- Local: cormhap   48 GB   16 CPUs x   1 job     48 GB   16 CPUs  (overlap detection with mhap)
-- Local: obtmhap   48 GB   16 CPUs x   1 job     48 GB   16 CPUs  (overlap detection with mhap)
-- Local: utgmhap   48 GB   16 CPUs x   1 job     48 GB   16 CPUs  (overlap detection with mhap)
-- Local: ovb        4 GB    1 CPU  x  16 jobs    64 GB   16 CPUs  (overlap store bucketizer)
-- Local: ovs       32 GB    1 CPU  x  16 jobs   512 GB   16 CPUs  (overlap store sorting)
-- Local: red       16 GB    8 CPUs x   2 jobs    32 GB   16 CPUs  (read error detection)
-- Local: oea        8 GB    1 CPU  x  16 jobs   128 GB   16 CPUs  (overlap error adjustment)
-- Local: bat      512 GB   16 CPUs x   1 job    512 GB   16 CPUs  (contig construction with bogart)
-- Local: gfa       32 GB   16 CPUs x   1 job     32 GB   16 CPUs  (GFA alignment and processing)
--
-- In 'canu.seqStore', found Nanopore reads:
--   Raw:        88662
--   Corrected:  88639
--   Trimmed:    88469
--
-- Generating assembly 'canu' in '/group/pasture/Saila/Canu_hybrid'
--
-- Parameters:
--
--  genomeSize        2800000000
--
--  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%)
----------------------------------------
-- Starting command on Mon Jan  7 09:26:23 2019 with 38066.617 GB free disk space

    cd .
    /usr/local/EasyBuild/software/canu/1.8-intel-2018a/bin/sqStoreDumpFASTQ \
      -trimmed \
      -S ./canu.seqStore \
      -o ./canu.trimmedReads.gz \
      -fasta \
      -nolibname \
    > ./canu.trimmedReads.fasta.err 2>&1

-- Finished on Mon Jan  7 09:26:55 2019 (32 seconds) with 38066.019 GB free disk space
----------------------------------------
--
-- Trimmed reads saved in 'canu.trimmedReads.fasta.gz'.
-- Finished stage 'cor-dumpTrimmedReads', reset canuIteration.
--
--
-- BEGIN ASSEMBLY
--
----------------------------------------
-- Starting command on Mon Jan  7 09:26:55 2019 with 38066.019 GB free disk space

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

-- Finished on Mon Jan  7 09:26:55 2019 (lickety-split) with 38066.019 GB free disk space
----------------------------------------
--  segments   memory batches
--  -------- -------- -------
--        01  4.00 GB       1
--        02  2.00 GB       1
--        04  1.25 GB       1
--        06  0.88 GB       1
--        08  0.62 GB       1
--        12  0.44 GB       1
--        16  0.31 GB       1
--
--  For 88469 reads with 1913482715 bases, limit to 19 batches.
--  Will count kmers using 01 jobs, each using 6 GB and 8 threads.
--
-- Finished stage 'merylConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Mon Jan  7 09:26:55 2019 with 38066.019 GB free disk space (1 processes; 2 concurrently)

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

-- Finished on Mon Jan  7 09:30:38 2019 (223 seconds) with 38063.625 GB free disk space
----------------------------------------
-- Found 1 Kmer counting (meryl) outputs.
-- Finished stage 'utg-merylCountCheck', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Mon Jan  7 09:30:38 2019 with 38063.625 GB free disk space (1 processes; 2 concurrently)

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

-- Finished on Mon Jan  7 09:31:21 2019 (43 seconds) with 38064.042 GB free disk space
----------------------------------------
--
-- WARNING: gnuplot failed.
--
----------------------------------------
--
--  16-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1         0                                                                        0.0000 0.0000
--       2-     2 309788021 ********************************************************************** 0.6852 0.3340
--       3-     4  86153111 *******************                                                    0.7356 0.3709
--       5-     7  30651196 ******                                                                 0.8957 0.5319
--       8-    11  13173842 **                                                                     0.9579 0.6319
--      12-    16   5063734 *                                                                      0.9765 0.6786
--      17-    22   2378065                                                                        0.9850 0.7093
--      23-    29   1358011                                                                        0.9897 0.7323
--      30-    37    856312                                                                        0.9925 0.7503
--      38-    46    573021                                                                        0.9943 0.7650
--      47-    56    402699                                                                        0.9955 0.7775
--      57-    67    295398                                                                        0.9963 0.7883
--      68-    79    223043                                                                        0.9969 0.7980
--      80-    92    174960                                                                        0.9974 0.8066
--      93-   106    139973                                                                        0.9978 0.8146
--     107-   121    116002                                                                        0.9981 0.8220
--     122-   137     97646                                                                        0.9984 0.8291
--     138-   154     87689                                                                        0.9986 0.8358
--     155-   172     80386                                                                        0.9988 0.8427
--     173-   191     68688                                                                        0.9989 0.8498
--     192-   211     52894                                                                        0.9991 0.8565
--     212-   232     39915                                                                        0.9992 0.8621
--     233-   254     34070                                                                        0.9993 0.8668
--     255-   277     29844                                                                        0.9994 0.8713
--     278-   301     27042                                                                        0.9994 0.8756
--     302-   326     24030                                                                        0.9995 0.8798
--     327-   352     20169                                                                        0.9995 0.8838
--     353-   379     16998                                                                        0.9996 0.8875
--     380-   407     14558                                                                        0.9996 0.8908
--     408-   436     13069                                                                        0.9997 0.8939
--     437-   466     11456                                                                        0.9997 0.8968
--     467-   497     10282                                                                        0.9997 0.8996
--     498-   529      9198                                                                        0.9997 0.9023
--     530-   562      7945                                                                        0.9998 0.9048
--     563-   596      7109                                                                        0.9998 0.9072
--     597-   631      6357                                                                        0.9998 0.9094
--     632-   667      5827                                                                        0.9998 0.9115
--     668-   704      5311                                                                        0.9998 0.9135
--     705-   742      4771                                                                        0.9998 0.9155
--     743-   781      4272                                                                        0.9998 0.9173
--     782-   821      3922                                                                        0.9998 0.9191
--
--           0 (max occurrences)
--  1854775150 (total mers, non-unique)
--   452095997 (distinct mers, non-unique)
--           0 (unique mers)
-- Finished stage 'meryl-process', reset canuIteration.
--
-- OVERLAPPER (mhap) (assembly)
--
-- Set utgMhapSensitivity=high based on read coverage of 0.
--
-- PARAMETERS: hashes=128, minMatches=5, threshold=0.93
--
-- Given 43.2 GB, can fit 129600 reads per block.
-- For 2 blocks, set stride to 2 blocks.
-- Logging partitioning to 'unitigging/1-overlapper/partitioning.log'.
-- Configured 1 mhap precompute jobs.
-- Configured 1 mhap overlap jobs.
-- Finished stage 'utg-mhapConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'utgmhap' concurrent execution on Mon Jan  7 09:31:21 2019 with 38064.042 GB free disk space (1 processes; 1 concurrently)

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

-- Finished on Mon Jan  7 09:43:49 2019 (748 seconds) with 38060.871 GB free disk space
----------------------------------------
-- All 1 mhap precompute jobs finished successfully.
-- Finished stage 'utg-mhapPrecomputeCheck', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'utgmhap' concurrent execution on Mon Jan  7 09:43:49 2019 with 38062.652 GB free disk space (1 processes; 1 concurrently)

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

-- Finished on Mon Jan  7 10:11:46 2019 (1677 seconds) with 38062.578 GB free disk space
----------------------------------------
-- Found 1 mhap overlap output files.
-- Finished stage 'utg-mhapCheck', reset canuIteration.
----------------------------------------
-- Starting command on Mon Jan  7 10:11:46 2019 with 38062.578 GB free disk space

    cd unitigging
    /usr/local/EasyBuild/software/canu/1.8-intel-2018a/bin/ovStoreConfig \
     -S ../canu.seqStore \
     -M 16-32 \
     -L ./1-overlapper/ovljob.files \
     -create ./canu.ovlStore.config \
     > ./canu.ovlStore.config.txt \
    2> ./canu.ovlStore.config.err

-- Finished on Mon Jan  7 10:11:46 2019 (furiously fast) with 38062.578 GB free disk space
----------------------------------------
--
-- Creating overlap store unitigging/canu.ovlStore using:
--      1 bucket
--      2 slices
--        using at most 1 GB memory each
-- Finished stage 'utg-overlapStoreConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'ovB' concurrent execution on Mon Jan  7 10:11:46 2019 with 38062.578 GB free disk space (1 processes; 16 concurrently)

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

-- Finished on Mon Jan  7 10:11:47 2019 (one second) with 38062.578 GB free disk space
----------------------------------------
-- Overlap store bucketizer finished.
-- Finished stage 'utg-overlapStoreBucketizerCheck', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'ovS' concurrent execution on Mon Jan  7 10:11:47 2019 with 38062.578 GB free disk space (2 processes; 16 concurrently)

    cd unitigging/canu.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 Mon Jan  7 10:11:47 2019 (in the blink of an eye) with 38062.578 GB free disk space
----------------------------------------
-- Overlap store sorter finished.
-- Finished stage 'utg-overlapStoreSorterCheck', reset canuIteration.
----------------------------------------
-- Starting command on Mon Jan  7 10:11:47 2019 with 38062.578 GB free disk space

    cd unitigging
    /usr/local/EasyBuild/software/canu/1.8-intel-2018a/bin/ovStoreIndexer \
      -O  ./canu.ovlStore.BUILDING \
      -S ../canu.seqStore \
      -C  ./canu.ovlStore.config \
      -delete \
    > ./canu.ovlStore.BUILDING.index.err 2>&1

-- Finished on Mon Jan  7 10:11:47 2019 (furiously fast) with 38062.578 GB free disk space
----------------------------------------
-- Checking store.
----------------------------------------
-- Starting command on Mon Jan  7 10:11:47 2019 with 38062.578 GB free disk space

    cd unitigging
    /usr/local/EasyBuild/software/canu/1.8-intel-2018a/bin/ovStoreDump \
     -S ../canu.seqStore \
     -O  ./canu.ovlStore \
     -counts \
     > ./canu.ovlStore/counts.dat 2> ./canu.ovlStore/counts.err

-- Finished on Mon Jan  7 10:11:47 2019 (like a bat out of hell) with 38062.578 GB free disk space
----------------------------------------
--
-- Overlap store 'unitigging/canu.ovlStore' successfully constructed.
-- Found 621480 overlaps for 88244 reads; 418 reads have no overlaps.
--
--
-- Purged 1.423 GB in 3 overlap output files.
----------------------------------------
-- Starting command on Mon Jan  7 10:11:47 2019 with 38063.378 GB free disk space

    cd unitigging
    /usr/local/EasyBuild/software/canu/1.8-intel-2018a/bin/ovStoreStats \
     -C 0 \
     -S ../canu.seqStore \
     -O  ./canu.ovlStore \
     -o  ./canu.ovlStore \
     > ./canu.ovlStore.summary.err 2>&1

-- Finished on Mon Jan  7 10:11:54 2019 (7 seconds) with 38063.976 GB free disk space
----------------------------------------
--
-- Overlap store 'unitigging/canu.ovlStore' contains:
--
--   category            reads     %          read length        feature size or coverage  analysis
--   ----------------  -------  -------  ----------------------  ------------------------  --------------------
--   middle-missing          6    0.01    14417.67 +- 3181.08       1575.67 +- 1207.88    (bad trimming)
--   middle-hump          3048    3.45    38256.40 +- 32117.50       200.63 +- 1299.84    (bad trimming)
--   no-5-prime            427    0.48    29099.72 +- 22735.32       255.84 +- 1341.99    (bad trimming)
--   no-3-prime            425    0.48    26466.44 +- 21469.24       247.16 +- 1151.41    (bad trimming)
--   
--   low-coverage            0    0.00        0.00 +- 0.00             0.00 +- 0.00       (easy to assemble, potential for lower quality consensus)
--   unique                  0    0.00        0.00 +- 0.00             0.00 +- 0.00       (easy to assemble, perfect, yay)
--   repeat-cont         84236   95.22    21013.73 +- 26640.03         4.33 +- 23.27      (potential for consensus errors, no impact on assembly)
--   repeat-dove           102    0.12    26249.58 +- 26621.19        45.92 +- 65.20      (hard to assemble, likely won't assemble correctly or even at all)
--   
--   span-repeat             0    0.00        0.00 +- 0.00             0.00 +- 0.00       (read spans a large repeat, usually easy to assemble)
--   uniq-repeat-cont        0    0.00        0.00 +- 0.00                                (should be uniquely placed, low potential for consensus errors, no impact on assembly)
--   uniq-repeat-dove        0    0.00        0.00 +- 0.00                                (will end contigs, potential to misassemble)
--   uniq-anchor             0    0.00        0.00 +- 0.00             0.00 +- 0.00       (repeat read, with unique section, probable bad read)
-- Finished stage 'utg-createOverlapStore', reset canuIteration.
--
-- Loading read lengths.
-- Loading number of overlaps per read.
--
-- Configure RED for 16gb memory.
--                   Batches of at most (unlimited) reads.
--                                      500000000 bases.
--                   Expecting evidence of at most 536870912 bases per iteration.
--
--           Total                                               Reads                 Olaps Evidence
--    Job   Memory      Read Range         Reads        Bases   Memory        Olaps   Memory   Memory  (Memory in MB)
--   ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------
--      1  8796.67         1-25349         25274    500010740  5722.96       149325     1.71  1024.00
--      2  8796.71     25350-47784         22384    500000459  5722.76       170955     1.96  1024.00
--      3  8796.79     47785-71570         23739    500017814  5723.00       156832     1.79  1024.00
--      4  7805.79     71571-88662         17072    413453702  4732.14       144368     1.65  1024.00
--   ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------
--                                                 1913482715                621480
-- Finished stage 'readErrorDetectionConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'red' concurrent execution on Mon Jan  7 10:11:54 2019 with 38063.976 GB free disk space (4 processes; 2 concurrently)

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

-- Finished on Mon Jan  7 10:13:25 2019 (91 seconds) with 38063.972 GB free disk space
----------------------------------------
-- Found 4 read error detection output files.
-- Finished stage 'readErrorDetectionCheck', reset canuIteration.
--
-- Loading read lengths.
-- Loading number of overlaps per read.
--
-- Configure OEA for 8gb memory.
--                   Batches of at most (unlimited) reads.
--                                      300000000 bases.
--
--           Total                                               Reads                 Olaps  Adjusts
--    Job   Memory      Read Range         Reads        Bases   Memory        Olaps   Memory   Memory  (Memory in MB)
--   ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------
--      1  2670.76         1-14864         14815    300016859   294.57        86681     2.65   325.54
--      2  2671.28     14865-29820         14925    300014352   294.57       103543     3.16   325.54
--      3  2671.16     29821-42103         12267    300012714   294.49       102591     3.13   325.54
--      4  2670.82     42104-55956         13811    300008384   294.53        89892     2.74   325.54
--      5  2671.05     55957-71571         15580    300052793   294.63        94406     2.88   325.54
--      6  2671.49     71572-84389         12801    300040696   294.53       111790     3.41   325.54
--      7  2490.76     84390-88662          4270    113336917   116.22        32577     0.99   325.54
--   ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------
--                                                 1913482715                621480
-- Finished stage 'overlapErrorAdjustmentConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'oea' concurrent execution on Mon Jan  7 10:13:26 2019 with 38063.972 GB free disk space (7 processes; 16 concurrently)

    cd unitigging/3-overlapErrorAdjustment
    ./oea.sh 1 > ./oea.000001.out 2>&1
    ./oea.sh 2 > ./oea.000002.out 2>&1
    ./oea.sh 3 > ./oea.000003.out 2>&1
    ./oea.sh 4 > ./oea.000004.out 2>&1
    ./oea.sh 5 > ./oea.000005.out 2>&1
    ./oea.sh 6 > ./oea.000006.out 2>&1
    ./oea.sh 7 > ./oea.000007.out 2>&1

-- Finished on Mon Jan  7 10:15:38 2019 (132 seconds) with 38063.972 GB free disk space
----------------------------------------
-- Found 7 overlap error adjustment output files.
-- Finished stage 'overlapErrorAdjustmentCheck', reset canuIteration.
----------------------------------------
-- Starting command on Mon Jan  7 10:15:38 2019 with 38063.972 GB free disk space

    cd unitigging/3-overlapErrorAdjustment
    /usr/local/EasyBuild/software/canu/1.8-intel-2018a/bin/loadErates \
      -S ../../canu.seqStore \
      -O ../canu.ovlStore \
      -L ./oea.files \
    > ./oea.apply.err 2>&1

-- Finished on Mon Jan  7 10:15:38 2019 (in the blink of an eye) with 38063.972 GB free disk space
----------------------------------------
-- No report available.
-- Finished stage 'updateOverlapStore', reset canuIteration.
-- Finished stage 'unitig', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'bat' concurrent execution on Mon Jan  7 10:15:38 2019 with 38063.972 GB free disk space (1 processes; 1 concurrently)

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

-- Finished on Mon Jan  7 10:15:48 2019 (10 seconds) with 38063.855 GB free disk space
----------------------------------------
--
-- Bogart failed, retry
--
--
-- Running jobs.  Second attempt out of 2.
----------------------------------------
-- Starting 'bat' concurrent execution on Mon Jan  7 10:15:48 2019 with 38063.855 GB free disk space (1 processes; 1 concurrently)

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

-- Finished on Mon Jan  7 10:15:58 2019 (10 seconds) with 38063.75 GB free disk space
----------------------------------------
--
-- Bogart failed, tried 2 times, giving up.
--

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:
ABORT: Disk space available:  38063.75 GB
ABORT:
ABORT: Last 50 lines of the relevant log file (unitigging/4-unitigger/unitigger.err):
ABORT:
ABORT:   optimizePositions()--     Checking convergence.
ABORT:   optimizePositions()--     converged:  86849 reads
ABORT:   optimizePositions()--     changed:     1814 reads
ABORT:   optimizePositions()--   Expanding short reads with 16 threads.
ABORT:   optimizePositions()--   Updating positions.
ABORT:   optimizePositions()--   Finished.
ABORT:   
ABORT:   ==> MERGE ORPHANS.
ABORT:   
ABORT:   computeErrorProfiles()-- Computing error profiles for 45817 tigs, with 16 threads.
ABORT:   computeErrorProfiles()-- Finished.
ABORT:   
ABORT:   findPotentialOrphans()-- working on 45817 tigs.
ABORT:   mergeOrphans()-- Found 198 potential orphans.
ABORT:   mergeOrphans()-- placed        0 unique orphan tigs
ABORT:   mergeOrphans()-- shattered     0 repeat orphan tigs
ABORT:   mergeOrphans()--
ABORT:   classifyAsUnassembled()--      1 tigs        7489 bases -- singleton
ABORT:   classifyAsUnassembled()--      0 tigs           0 bases -- too few reads        (< 2 reads)
ABORT:   classifyAsUnassembled()--      0 tigs           0 bases -- too short            (< 0 bp)
ABORT:   classifyAsUnassembled()--      0 tigs           0 bases -- single spanning read (> 1.000000 tig length)
ABORT:   classifyAsUnassembled()--   4095 tigs   141814833 bases -- low coverage         (> 0.500000 tig length at < 3 coverage)
ABORT:   classifyAsUnassembled()--     25 tigs      730216 bases -- acceptable contigs
ABORT:   
ABORT:   
ABORT:   ==> GENERATING ASSEMBLY GRAPH.
ABORT:   
ABORT:   computeErrorProfiles()-- Computing error profiles for 45817 tigs, with 16 threads.
ABORT:   computeErrorProfiles()-- Finished.
ABORT:   
ABORT:   AssemblyGraph()-- allocating vectors for placements, 4.059MB
ABORT:   AssemblyGraph()-- finding edges for 9548 reads (3348 contained), ignoring 79114 unplaced reads, with 16 threads.
ABORT:   AssemblyGraph()-- building reverse edges.
ABORT:   AssemblyGraph()-- build complete.
ABORT:   AssemblyGraph()-- generating './canu.initial.assembly.gfa'.
ABORT:   AssemblyGraph()-- Found 0 edges to unassembled contigs.
ABORT:   AssemblyGraph()--        0 bubble placements
ABORT:   AssemblyGraph()--        0 repeat placements
ABORT:   
ABORT:   AssemblyGraph()-- Intratig edges:            0 contained         0 5'         0 3' (in both contig and unitig)
ABORT:   AssemblyGraph()-- Contig only edges:       161 contained       419 5'       415 3'
ABORT:   AssemblyGraph()-- Unitig only edges:         0 contained         0 5'         0 3'
ABORT:   AssemblyGraph()-- Intercontig edges:       139 contained       248 5'       269 3' (in neither contig nor unitig)
ABORT:   
ABORT:   ==> BREAK REPEATS.
ABORT:   
ABORT:   computeErrorProfiles()-- Computing error profiles for 45817 tigs, with 16 threads.
ABORT:   computeErrorProfiles()-- Finished.
ABORT:   
ABORT:   Failed with 'ABORT:
cp: cannot stat ‘/tmp/Prom_min_CANU_assembly’: No such file or directory

I use it on a grid Can someone please help me with this issue? Thanks heaps in advance Saila

[brianwalenz]

There are a couple of weird things going on in this script that are possibly confusing the issue. You're cding into $TMPDIR, but then running canu in /group/pasture/Saila/Canu_hybrid (the -d option). This will probably work; it's easier to just run canu from /group/pasture/Saila, e.g., (canu -p canu -d Canu_hybrid ...). That, at least, explains the 'cp' error at the end.

The preferred way to run canu in grid mode it to run it directly on your head node, without submitting it in a script. Canu will do all job management for you. The way you're running it, canu is limited to 1 node.

But that's not the real problem. The meryl configure step is reporting that you have less than 1x coverage in corrected reads:

--  For 88469 reads with 1913482715 bases, limit to 19 batches.

Do you have any logs from the correction and trimming phases? How much coverage do you have?

[biowackysci]

Thanks for the reply. i have about 21 X coverage here. Apparently there are no trimming and correcting files generated. I am not sure what is going on here

[skoren]

There is far less than 21x from raw to correction. You can see the read counts start at only 88662 which would mean you need an average read length of 500k to get that coverage. Whatever input file you provided was only 1x which is why you got the error. The trimming did run as you can see in the logs.

[skoren]

Idle.