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!
I validated my FASTQ file with fqtools:
fqtools validate all.subreads.fastq