JL Weissman

Could be, it's very large - the gzipped file is 75GB. Is there a way to set a memory limit for spacegraphcats? I didn't see this as an option in...

Ah ok, thanks! I'll try that. Any guidance on how big those chunks can be and at what size you would start to see major performance problems? (e.g., if I...

Hi Titus - that makes sense - thanks for the warning! That file doesn't exist ``` $ ls -la my_test_k21_r1/ total 8 drwxrwxr-x 2 jake jake 4096 Sep 20 09:16...

``` $ ls -la my_test total 113713432 drwxrwxr-x 2 jake jake 53248 Sep 20 05:35 . drwxrwxr-x 22 jake jake 4096 Sep 22 00:35 .. -rw-rw-r-- 1 jake jake 52...

Thanks! Here's what it gives me: ``` (sgc2) jake@squid:/media/ink/spacegraphcats$ python -m spacegraphcats my_test search Found configfile at /media/ink/spacegraphcats/spacegraphcats/./conf/my_test.yaml -------- details! snakefile: /media/ink/spacegraphcats/spacegraphcats/./conf/Snakefile config: /media/ink/spacegraphcats/spacegraphcats/./conf/my_test.yaml targets: ['search'] -------- ...sgc is updating...

Awesome thanks! I'm really excited to use this tool - it's great that you all are so responsive!

I just tried it again - I cancelled the job when it hit 90% memory usage (out of 0.5TB - so a lot) to save my other processes. Maybe the...

According to `top` it was python

Sorry for the delay - missed this. It's ERR599057.

Hi - had an idea for a workaround that I wanted to run by you all. Would it be kosher to try and remove reads from particular organisms to reduce...