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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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Read correction jobs failed #687

Closed krithikaarumugam closed 6 years ago

krithikaarumugam commented 7 years ago

Hi,

I've been trying use can-1.6 on metagenomic nanopore reads corrected using nanocorr. I seem to get the following error (log file pasted below). Am not sure if am missing the obvious.

Below is the command I used on Linux.

/export2/home/krithika/tools/assemblers/canu-1.6_optimus/Linux-amd64/bin/canu -d reads_2017_02_11_lrnanocorr_5m -p genome genomeSize=5m -nanopore-raw ../../nanocorr/reads-2017_02_11-nanocorr.fa gnuplot=/export2/home/krithika/tools/gnuplot-5.2.0/bin/gnuplot useGrid=false gnuplotTested=true

The following is the log file,

-- 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 '1.8.0_144' (from 'java').
-- Detected 88 CPUs and 504 gigabytes of memory.
-- Detected Sun Grid Engine in '/cm/shared/apps/sge/current/default'.
-- Grid engine disabled per useGrid=false option.
--
--                            (tag)Concurrency
--                     (tag)Threads          |
--            (tag)Memory         |          |
--        (tag)         |         |          |  algorithm
--        -------  ------  --------   --------  -----------------------------
-- Local: meryl      8 GB    4 CPUs x  22 jobs  (k-mer counting)
-- Local: cormhap    6 GB   11 CPUs x   8 jobs  (overlap detection with mhap)
-- Local: obtovl     8 GB    8 CPUs x  11 jobs  (overlap detection)
-- Local: utgovl     8 GB    8 CPUs x  11 jobs  (overlap detection)
-- Local: cor       11 GB    2 CPUs x  44 jobs  (read correction)
-- Local: ovb        4 GB    1 CPU  x  88 jobs  (overlap store bucketizer)
-- Local: ovs        8 GB    1 CPU  x  88 jobs  (overlap store sorting)
-- Local: red        2 GB    4 CPUs x  22 jobs  (read error detection)
-- Local: oea        1 GB    1 CPU  x  88 jobs  (overlap error adjustment)
-- Local: bat       16 GB    4 CPUs x  22 jobs  (contig construction)
-- Local: cns       22 GB    4 CPUs x  22 jobs  (consensus)
-- Local: gfa        8 GB    4 CPUs x  22 jobs  (GFA alignment and processing)
--
-- Found Nanopore uncorrected reads in the input files.
--
-- Generating assembly 'genome' in '/export2/home/krithika/nanopore/reads_2017-02-11/albacore_2.0.2/albacore_basecalled_wofilter/assembly/canu/reads_2017_02_11_lrnanocorr_5m'
--
-- Parameters:
--
--  genomeSize        5000000
--
--  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 Mon Oct 30 01:33:48 2017 with 4272.418 GB free disk space

    cd correction
    /export2/home/krithika/tools/assemblers/canu-1.6_optimus/Linux-amd64/bin/gatekeeperCreate \
      -minlength 1000 \
      -o ./genome.gkpStore.BUILDING \
      ./genome.gkpStore.gkp \
    > ./genome.gkpStore.BUILDING.err 2>&1

-- Finished on Mon Oct 30 01:33:52 2017 (4 seconds) with 4272.299 GB free disk space
----------------------------------------
--
-- WARNING: gnuplot failed; no plots will appear in HTML output.
--
----------------------------------------
--
-- In gatekeeper store 'correction/genome.gkpStore':
--   Found 85399 reads.
--   Found 420041103 bases (84 times coverage).
--
--   Read length histogram (one '*' equals 201.18 reads):
--        0    999      0 
--     1000   1999  14083 **********************************************************************
--     2000   2999  11706 **********************************************************
--     3000   3999  11747 **********************************************************
--     4000   4999  11443 ********************************************************
--     5000   5999  10036 *************************************************
--     6000   6999   7995 ***************************************
--     7000   7999   6099 ******************************
--     8000   8999   4381 *********************
--     9000   9999   3016 **************
--    10000  10999   1885 *********
--    11000  11999   1127 *****
--    12000  12999    706 ***
--    13000  13999    426 **
--    14000  14999    276 *
--    15000  15999    136 
--    16000  16999    106 
--    17000  17999     77 
--    18000  18999     52 
--    19000  19999     25 
--    20000  20999     27 
--    21000  21999     10 
--    22000  22999      7 
--    23000  23999     15 
--    24000  24999      7 
--    25000  25999      1 
--    26000  26999      3 
--    27000  27999      2 
--    28000  28999      1 
--    29000  29999      3 
--    30000  30999      1 
-- Finished stage 'cor-gatekeeper', reset canuIteration.
-- Finished stage 'merylConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Mon Oct 30 01:33:52 2017 with 4272.297 GB free disk space (1 processes; 22 concurrently)

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

-- Finished on Mon Oct 30 01:34:31 2017 (39 seconds) with 4271.73 GB free disk space
----------------------------------------
-- Meryl finished successfully.
-- Finished stage 'merylCheck', reset canuIteration.
--
-- WARNING: gnuplot failed; no plots will appear in HTML output.
--
----------------------------------------
--
-- WARNING: gnuplot failed; no plots will appear in HTML output.
--
----------------------------------------
--
--  16-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1  32622416 *******************************************************************--> 0.4587 0.0779
--       2-     2  11329121 ********************************************************************** 0.6180 0.1320
--       3-     4  11239643 *********************************************************************  0.7144 0.1811
--       5-     7   5779885 ***********************************                                    0.8144 0.2556
--       8-    11   3244252 ********************                                                   0.8714 0.3215
--      12-    16   1938640 ***********                                                            0.9107 0.3905
--      17-    22    738166 ****                                                                   0.9329 0.4454
--      23-    29    396467 **                                                                     0.9415 0.4747
--      30-    37    447783 **                                                                     0.9469 0.4992
--      38-    46    679434 ****                                                                   0.9533 0.5372
--      47-    56   1206829 *******                                                                0.9634 0.6116
--      57-    67   1061671 ******                                                                 0.9807 0.7664
--      68-    79    322175 *                                                                      0.9947 0.9136
--      80-    92     44382                                                                        0.9985 0.9613
--      93-   106     16248                                                                        0.9991 0.9691
--     107-   121     17601                                                                        0.9993 0.9729
--     122-   137     10131                                                                        0.9995 0.9777
--     138-   154      4795                                                                        0.9997 0.9805
--     155-   172      3391                                                                        0.9997 0.9822
--     173-   191      2737                                                                        0.9998 0.9835
--     192-   211      1339                                                                        0.9998 0.9846
--     212-   232      2316                                                                        0.9998 0.9853
--     233-   254       585                                                                        0.9999 0.9865
--     255-   277      1022                                                                        0.9999 0.9869
--     278-   301       451                                                                        0.9999 0.9875
--     302-   326       530                                                                        0.9999 0.9878
--     327-   352       349                                                                        0.9999 0.9882
--     353-   379      1036                                                                        0.9999 0.9885
--     380-   407       178                                                                        0.9999 0.9894
--     408-   436       855                                                                        0.9999 0.9895
--     437-   466       724                                                                        0.9999 0.9904
--     467-   497       523                                                                        0.9999 0.9912
--     498-   529       323                                                                        0.9999 0.9918
--     530-   562       571                                                                        0.9999 0.9922
--     563-   596       228                                                                        1.0000 0.9929
--     597-   631       162                                                                        1.0000 0.9932
--     632-   667       228                                                                        1.0000 0.9935
--     668-   704       102                                                                        1.0000 0.9938
--     705-   742       164                                                                        1.0000 0.9940
--     743-   781       121                                                                        1.0000 0.9943
--     782-   821        35                                                                        1.0000 0.9945
--
--       36592 (max occurrences)
--   386133208 (total mers, non-unique)
--    38497338 (distinct mers, non-unique)
--    32622416 (unique mers)
-- For mhap overlapping, set repeat k-mer threshold to 4187.
--
-- Found 418755624 16-mers; 71119754 distinct and 32622416 unique.  Largest count 36592.
-- Finished stage 'cor-meryl', reset canuIteration.
--
-- OVERLAPPER (mhap) (correction)
--
-- Set corMhapSensitivity=low based on read coverage of 84.
--
-- PARAMETERS: hashes=256, minMatches=3, threshold=0.85
--
-- Given 6 GB, can fit 18000 reads per block.
-- For 6 blocks, set stride to 2 blocks.
-- Logging partitioning to 'correction/1-overlapper/partitioning.log'.
-- Configured 5 mhap precompute jobs.
-- Configured 7 mhap overlap jobs.
-- Finished stage 'cor-mhapConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Mon Oct 30 01:34:33 2017 with 4272.026 GB free disk space (5 processes; 8 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

-- Finished on Mon Oct 30 01:36:29 2017 (116 seconds) with 4269.422 GB free disk space
----------------------------------------
-- All 5 mhap precompute jobs finished successfully.
-- Finished stage 'cor-mhapPrecomputeCheck', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Mon Oct 30 01:36:30 2017 with 4269.381 GB free disk space (7 processes; 8 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

-- Finished on Mon Oct 30 01:36:59 2017 (29 seconds) with 4268.503 GB free disk space
----------------------------------------
-- Found 7 mhap overlap output files.
-- Finished stage 'cor-mhapCheck', reset canuIteration.
----------------------------------------
-- Starting command on Mon Oct 30 01:36:59 2017 with 4268.496 GB free disk space

    cd correction
    /export2/home/krithika/tools/assemblers/canu-1.6_optimus/Linux-amd64/bin/ovStoreBuild \
     -O ./genome.ovlStore.BUILDING \
     -G ./genome.gkpStore \
     -M 2-8 \
     -L ./1-overlapper/ovljob.files \
     > ./genome.ovlStore.err 2>&1

-- Finished on Mon Oct 30 01:37:04 2017 (5 seconds) with 4268.408 GB free disk space
----------------------------------------
-- Checking store.
----------------------------------------
-- Starting command on Mon Oct 30 01:37:04 2017 with 4268.408 GB free disk space

    cd correction
    /export2/home/krithika/tools/assemblers/canu-1.6_optimus/Linux-amd64/bin/ovStoreDump \
     -G ./genome.gkpStore \
     -O ./genome.ovlStore \
     -d -counts \
     > ./genome.ovlStore/counts.dat 2> ./genome.ovlStore/counts.err

-- Finished on Mon Oct 30 01:37:04 2017 (lickety-split) with 4268.407 GB free disk space
----------------------------------------
--
-- Overlap store 'correction/genome.ovlStore' successfully constructed.
-- Found 8491832 overlaps for 82876 reads; 2523 reads have no overlaps.
--
FILE correction/1-overlapper/results/000001.ovb
FILE correction/1-overlapper/results/000002.ovb
FILE correction/1-overlapper/results/000003.ovb
FILE correction/1-overlapper/results/000004.ovb
FILE correction/1-overlapper/results/000005.ovb
FILE correction/1-overlapper/results/000006.ovb
FILE correction/1-overlapper/results/000007.ovb
FILE correction/1-overlapper/results/000001.counts
FILE correction/1-overlapper/results/000002.counts
FILE correction/1-overlapper/results/000003.counts
FILE correction/1-overlapper/results/000004.counts
FILE correction/1-overlapper/results/000005.counts
FILE correction/1-overlapper/results/000006.counts
FILE correction/1-overlapper/results/000007.counts
DIRECTORY correction/1-overlapper/queries
DIRECTORY correction/1-overlapper/queries/000001
FILE correction/1-overlapper/queries/000001/000002.dat
FILE correction/1-overlapper/queries/000001/000003.dat
DIRECTORY correction/1-overlapper/queries/000002
FILE correction/1-overlapper/queries/000002/000004.dat
FILE correction/1-overlapper/queries/000002/000005.dat
DIRECTORY correction/1-overlapper/queries/000003
FILE correction/1-overlapper/queries/000003/000003.dat
FILE correction/1-overlapper/queries/000003/000004.dat
DIRECTORY correction/1-overlapper/queries/000004
FILE correction/1-overlapper/queries/000004/000005.dat
DIRECTORY correction/1-overlapper/queries/000005
FILE correction/1-overlapper/queries/000005/000004.dat
FILE correction/1-overlapper/queries/000005/000005.dat
DIRECTORY correction/1-overlapper/queries/000006
FILE correction/1-overlapper/queries/000006/000005.dat
DIRECTORY correction/1-overlapper/queries/000007
FILE correction/1-overlapper/blocks/000001.dat
FILE correction/1-overlapper/blocks/000002.dat
FILE correction/1-overlapper/blocks/000003.dat
FILE correction/1-overlapper/blocks/000004.dat
FILE correction/1-overlapper/blocks/000005.dat
REMOVE TREE correction/1-overlapper/queries/000003
REMOVE TREE correction/1-overlapper/queries
REMOVE TREE correction/1-overlapper/queries/000002
REMOVE TREE correction/1-overlapper/queries/000001
REMOVE TREE correction/1-overlapper/queries/000005
REMOVE TREE correction/1-overlapper/queries/000006
REMOVE TREE correction/1-overlapper/queries/000004
REMOVE TREE correction/1-overlapper/queries/000007
--
-- Purged 4.243 GB in 29 overlap output files.
-- Overlap store 'correction/genome.ovlStore' statistics not available (skipped in correction and trimming stages).
--
-- Finished stage 'cor-createOverlapStore', reset canuIteration.
-- Set corMinCoverage=4 based on read coverage of 84.
-- Computing global filter scores 'correction/2-correction/genome.globalScores'.
----------------------------------------
-- Starting command on Mon Oct 30 01:37:05 2017 with 4269.925 GB free disk space

    cd correction/2-correction
    /export2/home/krithika/tools/assemblers/canu-1.6_optimus/Linux-amd64/bin/filterCorrectionOverlaps \
      -G ../genome.gkpStore \
      -O ../genome.ovlStore \
      -S ./genome.globalScores.WORKING \
      -c 40 \
      -l 0 \
    > ./genome.globalScores.err 2>&1

-- Finished on Mon Oct 30 01:37:05 2017 (lickety-split) with 4269.916 GB free disk space
----------------------------------------
--  PARAMETERS:
--  ----------
--  
--       40 (expected coverage)
--        0 (don't use overlaps shorter than this)
--    0.000 (don't use overlaps with erate less than this)
--    1.000 (don't use overlaps with erate more than this)
--  
--  OVERLAPS:
--  --------
--  
--  IGNORED:
--  
--             0 (< 0.0000 fraction error)
--             0 (> 0.4095 fraction error)
--             0 (< 0 bases long)
--             0 (> 2097151 bases long)
--  
--  FILTERED:
--  
--       6202940 (too many overlaps, discard these shortest ones)
--  
--  EVIDENCE:
--  
--       2288892 (longest overlaps)
--  
--  TOTAL:
--  
--       8491832 (all overlaps)
--  
--  READS:
--  -----
--  
--          2523 (no overlaps)
--         38901 (no overlaps filtered)
--         10147 (<  50% overlaps filtered)
--         37410 (<  80% overlaps filtered)
--         41969 (<  95% overlaps filtered)
--         43975 (< 100% overlaps filtered)
--  
-- Computing expected corrected read lengths 'correction/2-correction/genome.estimate.log'.
----------------------------------------
-- Starting command on Mon Oct 30 01:37:05 2017 with 4269.916 GB free disk space

    cd correction/2-correction
    /export2/home/krithika/tools/assemblers/canu-1.6_optimus/Linux-amd64/bin/generateCorrectionLayouts \
      -G ../genome.gkpStore \
      -O ../genome.ovlStore \
      -S ./genome.globalScores \
      -c 4 \
      -C 80 \
      -p ./genome.estimate.WORKING

-- Finished on Mon Oct 30 01:37:06 2017 (1 second) with 4269.915 GB free disk space
----------------------------------------
-- Sorting reads by expected corrected length.
-- Sorting reads by uncorrected length.
-- Loading expected corrected read lengths.
-- Picking longest corrected reads.
-- Writing longest corrected reads to 'correction/2-correction/genome.readsToCorrect'.
-- Summarizing filter.
--
-- Reads to be corrected:
--   26103 reads longer than 6432 bp
--   205047454 bp
-- Expected corrected reads:
--   26103 reads
--   200004865 bp
--   5051 bp minimum length
--   7662 bp mean length
--   17708 bp n50 length
--
-- WARNING: gnuplot failed; no plots will appear in HTML output.
--
----------------------------------------
-- Using overlaps no worse than 0.5 fraction error for correcting reads (from corErrorRate parameter).
-- Finished stage 'cor-buildCorrectionLayouts', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cor' concurrent execution on Mon Oct 30 01:37:08 2017 with 4269.892 GB free disk space (18 processes; 44 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
    ./correctReads.sh 18 > ./correctReads.000018.out 2>&1

-- Finished on Mon Oct 30 01:41:49 2017 (281 seconds) with 4270.248 GB free disk space
----------------------------------------
--
-- Read correction jobs failed, retry.
--   job correction/2-correction/correction_outputs/0014.fasta FAILED.
--
--
-- Running jobs.  Second attempt out of 2.
----------------------------------------
-- Starting 'cor' concurrent execution on Mon Oct 30 01:41:49 2017 with 4270.248 GB free disk space (1 processes; 44 concurrently)

    cd correction/2-correction
    ./correctReads.sh 14 > ./correctReads.000014.out 2>&1

-- Finished on Mon Oct 30 01:44:17 2017 (148 seconds) with 4269.61 GB free disk space
----------------------------------------
--
-- Read correction jobs failed, tried 2 times, giving up.
--   job correction/2-correction/correction_outputs/0014.fasta 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:

Also when I try to use only the -trim and -assemble options for corrected nanopore reads, the job seems to complete but I get the same assembly statistics (N50, mean etc) when I vary the genome size. am I missing the obvious here ?

P.S. - the job did finish successfully if I use the same command on uncorrected nanopore reads (without using nanocorr).

Thanks In advance for any help.

skoren commented 7 years ago

I don't think it makes sense to specify -nanopore-raw for the corrected reads, -nanopore-corrected would run what you need (trim/assembly only). Given that it works on raw input reads and we've made some significant changes in this code post the 1.6 release, I'd rather hold off on troubleshooting the crash and recommend you stick with -nanopore-raw for uncorrected and -nanopore-corrected for nanocorr reads.

As for the second question, the genome size isn't really well defined for a metagenome but it is used by Canu to select the longest reads for correction. In your case, you'd be losing about 50% of your coverage. However, if the metagenome is not very complex it may be reconstructing the most abundant organism fine without the extra data. See the FAQ: http://canu.readthedocs.io/en/latest/faq.html#what-parameters-can-i-tweak for our current suggested parameters for metagenomes to get all the data corrected, regardless of genome size. The genome will then just be used for NG stats computations.

krithikaarumugam commented 7 years ago

Thanks for the quick reply. Was just trying to take advantage of the option -nanopore-raw incase any reads were missed during correction.

skoren commented 7 years ago

If the input is the data from nanocorr canu won't ever see the uncorrected reads and the consensus will be based completely on the nanocorr reads so I don't think any of them are going to be improved much and it won't find reads that weren't corrected since those wouldn't have been output by nanocorr. You can compare the uncorrected raw data assembled with -nanopore-raw (without nanocorr) to the -nanopore-corrected (with nanocorr) and see which gives a better assembly and use that one.

skoren commented 6 years ago

Inactive, reads corrected by other tools (nanocorr, lordec, etc) should typically be input as nanopore-corrected or pacbio-corrected not raw.