Brian Walenz

git 1.8, as I recall, doesn't support submodules correctly. Canu uses this support to download three additional bits of source code from other projects. All the required source code is...

I was afraid of that. Two options: 1) upgrade git 2) in src/Makefile, comment out the first five lines, or just the `$(error git ... version .. too old ...)`...

Nice! I think this is expected. The kmer database is split into 64 pieces, which can be loaded in parallel, one per thread. There are two databases to load -...

Environment variable OMP_NUM_THREADS= will limit CPU usage to cores. There is no equivalent setting for memory usage, but you can (ab)use variables used by grid schedulers to achieve the same...

There's really no good solution here. Overlap store building was designed to run on multiple nodes with a high bandwidth storage system. Running on just one node limits bandwidth to...

The original incorrect placement was ``` asm.010.mergeOrphans.thr000.num000.log: First read 4490490 - placed 8 times asm.010.mergeOrphans.thr000.num000.log: read 4490490 at 14192489-14203923 asm.010.mergeOrphans.thr027.num000.log:tig 11458 read 4490490 -> tig 11435 ( 51664 reads) at...

Is this a restart from some other system? Canu correctly detects that Java doesn't want -d64: ``` -- Detected Java(TM) Runtime Environment '11.0.16' (from 'java') without -d64 support. ``` but...

You are aware that v1.7 is 4.5 years old, right? Assuming the store is valid (errors would be in earlier logs which are probably lost) you can simply rename it...

Hi. From the logging: - you've set genomeSize=1g - there are 54.8 million reads in the input - Canu claims there are only 1g * 0.05 = 50m bases in...

Nothing I can add without seeing a histogram of the read lengths and the error file, or the reads themselves.