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I have installed canu using conda in an environment containing Python 3 on a Mac OS X. I checked that canu is properly installed by pulling out the help and it works. I launched a canu assembly job by typing:

canu -p genome -d output genomeSize=105m -pacbio-raw all.subreads.fastq

My data comes from a PacBio Sequel machine. At first sight, the fastq file seems to be well formatted. I get the following error when I run canu:

merylStreamReader()-- ERROR: ./celegans.ms16.mcidx is not a merylStream index file!
merylStreamReader()-- ERROR: ./celegans.ms16.mcdat is not a merylStream data file!

Canu release v1.5 failed with:
  didn't find any mers?

My fastq file is not compressed. It contains subreads. Can anyone help me with this error, please?

Update: I uninstalled canu with conda and installed it with brew and re-ran the code and got a similar error:

CRASH: Canu 1.7
CRASH: Please panic, this is abnormal.
ABORT:
CRASH:   didn't find any mers?.
CRASH:
CRASH: Failed at /usr/local/Cellar/canu/1.7/Darwin-amd64/bin/../lib/site_perl/canu/Meryl.pm line 770.
CRASH:  canu::Meryl::merylProcess("celegans", "cor") called at /usr/local/bin/canu line 623
CRASH: 
CRASH: Last 50 lines of the relevant log file (correction/0-mercounts/celegans.ms16.histogram.info)

The file correction/0-mercounts/celegans.ms16.histogram.info contains:

merylStreamReader()-- ERROR: ./celegans.ms16.mcidx is not a merylStream index file!
merylStreamReader()-- ERROR: ./celegans.ms16.mcdat is not a merylStream data file!

Update:

I validated my FASTQ file with fqtools:

fqtools validate all.subreads.fastq OK

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    $\begingroup$ It seems like the file is not in the right format. Are you sure it is on the right format? What is your command to run canu? $\endgroup$ – llrs Mar 10 '18 at 9:01
  • $\begingroup$ I just checked the top of the fastq file with less and it has got the @, followed by lines of sequence, followed by a +, followed by quality values, and it repeats. There might be a problem somewhere further below, maybe? I will try to find a FASTQ format validator. Regarding the command I used to run canu, it's in the question. I just highlighted it as code now. $\endgroup$ – charlesdarwin Mar 10 '18 at 13:36
  • $\begingroup$ I updated my question with the FASTQ file validation using fqtools. $\endgroup$ – charlesdarwin Mar 10 '18 at 14:47
  • $\begingroup$ And what is the format of "./celegans.ms16.mcidx"? $\endgroup$ – llrs Mar 10 '18 at 15:02
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    $\begingroup$ No idea, but they seem relevant to what you are doing. Check how it should look like and how are they generated $\endgroup$ – llrs Mar 10 '18 at 16:53

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