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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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error in "correct" link #2256

Closed Xoey0314 closed 1 year ago

Xoey0314 commented 1 year ago

Hello,

I met some problems when I assembled the genome.

command, version and error information as follow:

command: canu -correct -p ath -d pb_ath minThreads=10 useGrid=true genomeSize=1000m -pacbio-raw /md/cc/S_raw/01.S/subreads_L500.fa.gz

version: Canu v0.0 (+0 commits) r0 unknown-hash-tag-no-repository-available.

error:


canu failed with 'can't open correction output '/md/cc/zz/02.g/01.canu/02.s/canu_correct/pb_ath/correction/2-correction/correction_outputs/0062.fasta' for reading: No such file or directory

I've assembled two genomes from the same species at the same time, which in theory should be of the same magnitude. But because of the error in “correct” link, I get corrective ath. correctedReads. fasta. gz is only 625018317, but not the data size gained by the genome data of error correction for 9824670725.

Looking forward to your reply.

Best wishes, Xin

skoren commented 1 year ago

The error implies there were some files that are missing/removed during the run. However, your version and this error message implies your canu installation is very old, likely v1.6 or similar as that message no longer exists in later versions. I would suggest downloading the latest release from the releases page and re-running your assembly from scratch it instead to see if it still has an error. Make sure you use unique -d and -p values for each of your runs as well.

Xoey0314 commented 1 year ago

Ok, thanks for your response. I will try it by canu V2.2.

skoren commented 1 year ago

If you encounter errors with 2.2, please open a new issue, thanks.