failed correction

[aldertzomer]

Canu 1.7.1

Correction fails when trying to assemble an E. coli genome with 2 ~10 kb plasmids that have a high copy number (70-100 or so) . I have 1500 megabase of sequence in my Sequel fasta file, which should be 300 fold coverage, but many of the reads are probably plasmid reads. Commands I used:

/usr/local/canu-1.7.1/Linux-amd64/bin/canu -d BVCB000015H -p BVCB000015H genomeSize=4.7m -pacbio-raw BVCB000015H_33514_subreads.fasta.gz

This failed. Manual suggests setting a high number for corOutCoverage in the case of uneven coverage distribution:

/usr/local/canu-1.7.1/Linux-amd64/bin/canu -d BVCB000015H2 -p BVCB000015H2 genomeSize=4.7m -pacbio-raw BVCB000015H_33514_subreads.fasta.gz corOutCoverage=999

also fails (same step). Something with falconsense (see below).

the failure Canu reports is:

-- Finished on Wed Sep  5 13:42:38 2018 (4693 seconds) with 10149.058 GB free disk space
----------------------------------------
--
-- Read correction jobs failed, retry.
--   job 2-correction/results/0002.cns FAILED.
--   job 2-correction/results/0056.cns FAILED.
--   job 2-correction/results/0059.cns FAILED.
--
--
-- Running jobs.  Second attempt out of 2.
----------------------------------------
-- Starting 'cor' concurrent execution on Wed Sep  5 13:42:39 2018 with 10149.058 GB free disk space (3 processes; 4 concurrently)

    cd correction/2-correction
    ./correctReads.sh 2 > ./correctReads.000002.out 2>&1
    ./correctReads.sh 56 > ./correctReads.000056.out 2>&1
    ./correctReads.sh 59 > ./correctReads.000059.out 2>&1

-- Finished on Wed Sep  5 13:51:11 2018 (512 seconds) with 10148.894 GB free disk space
----------------------------------------
--
-- Read correction jobs failed, tried 2 times, giving up.
--   job 2-correction/results/0002.cns FAILED.
--   job 2-correction/results/0056.cns FAILED.
--   job 2-correction/results/0059.cns FAILED.
--

ABORT:
ABORT: Canu 1.7.1
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:

exploring 0002.cns further:
$ tail -n 35 0002.err

ALIGN to 329-6553 length 6553
read18693 #16 location 0 to template 315-3783 length 3468 diff 0.207901
read18693 #16 location 1 to template 315-3784 length 3469 diff 0.207841
read18693 #16 location 2 to template 315-3785 length 3470 diff 0.207781
mapped 18693     0- 3398 to template    315-  3784 trimmed by      0-     1 TGATGGATAT TTATG-ATAT
ALIGN to 624-4142 length 6553
read366875 #20 location 0 to template 299-3194 length 2895 diff 0.204490
falconsense: overlapInCore/libedlib/edlib.C:347: 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.

Failed with 'Aborted'; backtrace (libbacktrace):
read134431 #17 location 0 to template 512-6202 length 5690 diff 0.235677
mapped 134431     0- 5884 to template    512-  6203 trimmed by      0-     0 GTT-TTGGCA TTTGTTGGCA
ALIGN to 936-2815 length 6553
read94346 #19 location 0 to template 537-5828 length 5291 diff 0.194292
mapped 94346     0- 5336 to template    866-  6158 trimmed by      0-     0 GTGGGT-TCA -TGGGTATCA
ALIGN to 621-6553 length 6553
read159249 #18 location 0 to template 598-6479 length 5881 diff 0.210848
read197332 #21 location 0 to template 143-1638 length 1495 diff 0.209365
mapped 197332     0- 1492 to template   1079-  2575 trimmed by      0-     0 AGCACAGAAC AGCACAGAAC
mapped 159249     0- 5995 to template    671-  6553 trimmed by      0-     6 TAACATTAAC T----T---C
ALIGN to 754-6553 length 6553
ALIGN to 1042-4847 length 6553
AS_UTL/AS_UTL_stackTrace.C::97 in _Z17AS_UTL_catchCrashiP7siginfoPv()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
overlapInCore/libedlib/edlib.C::347 in _Z23edlibAlignmentToStringsPKhiiiiiPKcS2_PcS3_()
correction/falconConsensus-alignTag.C::252 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
Aborted (core dumped)

[skoren]

Do you have non-ACGT bases in your reads? This would be the same as issue #881, #1026. The fix for this is only in the tip so you'd have to either remove non-ACGT bases from your input or compile the code from source.

[aldertzomer]

cat BVCB000015H_33514_subreads.fasta |grep -v ">" |tr -d [ATCGatcg] |tr -d "\n"
results in empty output, so no nonACGT bases. Thats not it unfortunately. I'm assembling now with a subset of the data.

[aldertzomer]

I may have found the issue.. For some reason this was in my fasta file from my sequence provider

[M::bam2fq_mainloop] processed 406256 reads

which does not really belong in a fasta file.