search

marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
658 stars 179 forks source link

Issue with canu for metagenomics #1289

Closed Raymi1 closed 5 years ago

Raymi1 commented 5 years ago

Hello,

I tried to run canu in order to assemble bacterial metagenome with the following options (as suggest here : https://canu.readthedocs.io/en/latest/faq.html) :

canu -p prefix -d canu/ genomeSize=5m corOutCoverage=10000 corMhapSensitivity=high corMinCoverage=0 redMemory=32 oeaMemory=32 batMemory=200 gridEngineThreadsOption='--cpus-per-task THREADS' maxMemory=230G maxThreads=8 -nanopore-raw file.fastq

However the job fails with the following error message :

Using slow alignment for consensus (iteration '2'). Configured 9 contig and 6 unitig consensus jobs.

Consensus jobs failed, tried 2 times, giving up. job ctgcns/001.cns FAILED. job ctgcns/0002.cns FAILED. job ctgcns/0003.cns FAILED. job ctgcns/0004.cns FAILED. job ctgcns/0005.cns FAILED. job ctgcns/0008.cns FAILED. job ctgcns/0009.cns FAILED. job utgcns/0001.cns FAILED. job utgcns/0002.cns FAILED. job utgcns/0003.cns FAILED. job utgcns/0004.cns FAILED. job utgcns/0005.cns FAILED. job utgcns/0006.cns FAILED.

ABORT: ABORT: Canu snapshot v1.8 +151 changes (r9361 db9bfcc26004b26f21686f0c324ab69d37c5a885) ABORT: Don't panic, but a mostly harmless error occurred and Canu stopped. ABORT: Try restarting. If that doesn't work, ask for help.

I use Ubuntu 14.04.5 LTS with 64G RAM. I checked in the system log file and the issue doesn't seem to occur because of a lack of memory. I also tried to rerun the program but it still didn't work.

Thank you for any advice about how to run Canu for metagenomic assembly.

skoren commented 5 years ago

This is most likely the same as #1288, you're running in the middle of some consensus code changes. Try switching to the 1.8 release rather than a direct checkout of the latest code and see if consensus runs.

Raymi1 commented 5 years ago

I already have the 1.8 version. When I do canu --version, I get : Canu snapshot v1.8 +151 changes

skoren commented 5 years ago

You do not have version 1.8, it is reporting 1.8 + 151 changes, that means it is 151 commits ahead of the release. The latest code is also ahead of this point. So you're at a checkout somewhere from early march. The commit to fix this bug came a few days after it was introduced.

Download the 1.8 version from the release page or update to the latest code by doing a git pull and re-compile and it should be fixed.

skoren commented 5 years ago

Confirmed, this bug is fixed in tip so either update to latest from repo or use the release source.

Raymi1 commented 5 years ago

Thanks very much. It seems to work now.