search

ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
513 stars 94 forks source link

Is RAM an issue to build contig layout file after alignments are built? #140

Closed vinayciba closed 4 years ago

vinayciba commented 5 years ago

Hi, I am running wtdbg2 on sequel data to generate assembly of a highly repetitive genome which is 2.5 Gb length. The run stopped after building alignments file. Attached the logs, in brief. I have two queries. First, Is insufficient RAM, the issue? If yes, which parameter should i tweak for another run? Second, Can i restart the run in same folder to generate .ctg.lay.gz file, as alignment file is already there? If yes, how to do it? Thank you in advance. issue_wtdbg2.txt

ruanjue commented 5 years ago

Out of memory. Restart the job by appending --load-alignments and --load-clips. PS. you were using an old version of wtdbg2, upgrate to wtdbg-2.5 to get better results.

vinayciba commented 5 years ago

Hai, Thank you for sharing additional arguments. I have updated to wtdbg2.5. The run did actually start from the same folder with these arguments. But, the RAM issue persisted. I have only 512 GB of RAM. Is there any way I could limit RAM usage by wtdbg?

ruanjue commented 5 years ago

1, try decrease the seq coverage cutoff from -X70 to -X50 or smaller.
2, try use -x rs instead of -x sq, because kmer coverage is very high, you can use a larger kmer-size.