Colton Baumler

Step 5. Profit!!!

This also allows for multiple `radius` values to be included in the config file and ran in a single workflow.

Thanks @taylorreiter. > you could try increasing the disc space or the time of the job. 360 min (6 hours) seems far too short to me, but I could be...

Maybe! I'll try removing that and get back to you. Edit minutes later: I did remove all protected commands. No Luck. I did find this though - https://github.com/spacegraphcats/spacegraphcats/issues/445

After reviewing #445 , I wrote this bash script into my shell section: ``` if [ -f "" ]; then rm fi ``` Outside of some of my own bugs,...

That all makes perfect sense! (now that you have explained it) I have tested some changes, I have been able to get the workflow running with by `protecting(...)` the db...

I changed tactics and tried a python conditional at the beginning of the snakefile. This seems to work! ``` if os.path.exists(f'{cdbg_dir}/bcalm.unitigs.db'): shell(f"chmod u+w {cdbg_dir}/bcalm.unitigs.db") ``` I tested this three ways...

Why did I move away from that? Most likely unsupervised curiosity. I was attempting to make the original script work with some additional code instead of deleting `chmod`. I'll update...

Just ran into this error myself on another workflow. Any further documentation on this issue?

Update: My OSError was due to faulty paired-end sequence metadata. Since interleaved-reads.py was piping into trim-low-abund.py the interleaved-reads.py error was masked. [See here](https://github.com/dib-lab/2022-dominating-set-differential-abundance-example/blob/8e844add4c3b30c53dd7739dd34b7d1904674716/00_select_query_species_for_dda.snakefile#L96)