failed to read estimated mer threshold

[skbrimer]

Hello Canu Gurus, I am using Canu version 1.4 with the following command

 ~/software/canu/Linux-amd64/bin/canu -p fw205_1f31d2g3 -d fw205_1f31d2g3_minion genomeSize=165k minReadLength=100 minOverlapLength=50 -nanopore-raw fw205_1f31d2g3.fastq 

on a ubuntu laptop version 16.04 using Nanopore reads to construct a viral genome. This is the third sample in and the first 2 worked without issue. All samples are from the same sequencing run as well.

I am getting the following error.

-- Finished on Mon Jul 10 10:47:17 2017 (lickety-split) with 56.906 GB free disk space
----------------------------------------
-- Meryl finished successfully.
-- Finished stage 'merylCheck', reset canuIteration.
Use of uninitialized value $error[0] in join or string at /usr/share/perl/5.22/Carp.pm line 457.
================================================================================
Please panic.  Canu failed, and it shouldn't have.

Stack trace:

 at /home/sbrimer/software/canu/Linux-amd64/bin/lib/canu/Meryl.pm line 576.
    canu::Meryl::merylProcess("fw205_1f31d2g3", "obt") called at /home/sbrimer/software/canu/Linux-amd64/bin/canu line 568

Canu snapshot v1.4 +161 changes (r8156 6cb65e92d90587caa580df7b1c11c76071447844) failed with:
  failed to read estimated mer threshold from 'trimming/0-mercounts/fw205_1f31d2g3.ms22.estMerThresh.out'

Best I can tell it is not writing to the file it is looking, when I look in the directory it talks about in the trace this is what is there.

sbrimer@LEN943:~/Desktop$ ls -l fw205_1f31d2g3_minion/trimming/0-mercounts/
total 4120
-rw-rw-r-- 1 sbrimer sbrimer     557 Jul 10 10:47 fw205_1f31d2g3.ms22.estMerThresh.err
-rw-rw-r-- 1 sbrimer sbrimer       0 Jul 10 10:47 fw205_1f31d2g3.ms22.estMerThresh.out.WORKING
-rw-rw-r-- 1 sbrimer sbrimer    2696 Jul 10 10:47 fw205_1f31d2g3.ms22.histogram
-rw-rw-r-- 1 sbrimer sbrimer      99 Jul 10 10:47 fw205_1f31d2g3.ms22.histogram.info
-rw-rw-r-- 1 sbrimer sbrimer 3145264 Jul 10 10:47 fw205_1f31d2g3.ms22.mcdat
-rw-rw-r-- 1 sbrimer sbrimer 1048608 Jul 10 10:47 fw205_1f31d2g3.ms22.mcidx
-rw-rw-r-- 1 sbrimer sbrimer    2660 Jul 10 10:47 meryl.000001.out
-rwxrwxr-x 1 sbrimer sbrimer    1618 Jul 10 10:47 meryl.sh
-rw-rw-r-- 1 sbrimer sbrimer       0 Jul 10 10:47 meryl.success

Thank you in advance for any help or guidance on this issue.

Please let me know if you require more information and I will provide all that I can! Sean

[brianwalenz]

v1.4 is pretty old, you should update to at least v1.5, or the git tip.

What is in 'fw205_1f31d2g3.ms22.estMerThresh.err'? I'm going to guess this is the same as issue #486.

[skbrimer]

It is a segmentation fault error,

RAW MER COUNTS:
  distinct:       520969 (different kmer sequences)
  unique:         362191 (single-copy kmers)
  total:         1159540 (kmers in sequences)

Set maxCount to 20 (13 kmers), which will cover 99.75% of distinct mers and 95.01% of all mers.

Failed with 'Segmentation fault'; backtrace (libbacktrace):
AS_UTL/AS_UTL_stackTrace.C::102 in _Z17AS_UTL_catchCrashiP9siginfo_tPv()
(null)::0 in (null)()
meryl/estimate-mer-threshold.C::258 in main()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
Segmentation fault (core dumped)

but I don't understand why it happened. The files are no larger than the others that are working so I don't think it is resource issue. The genome and data sets are small. Also I agree with you that this is pretty much the same issue as #486 so I apologize for posting again. I will update to the current version and try again.

Thanks,

Sean

[skbrimer]

Updating to canu-1.5 did resolve the issue thank you :)