RBGV Bioinformatics

ls -lah Arabidopsis_simulated.plastome/seed/embplant_pt.index ls: cannot access 'Arabidopsis_simulated.plastome/seed/embplant_pt.index': No such file or directory ls -lah Arabidopsis_simulated.plastome/seed/ total 15M drwxr-sr-x 2 ta0341 nm31 33K Feb 22 15:44 . drwxr-sr-x 3 ta0341 nm31...

I also checked that all the other python scripts were #!/usr/bin/env python3, as is required for my system.

I deleted the dependency version of spades and use my (working) system version. Get the same error - see attached log. Thanks [get_org.log.txt](https://github.com/Kinggerm/GetOrganelle/files/8121654/get_org.log.txt) .

ah yes, spades problem.. spades.py --test == Warning == No assembly mode was specified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option. Command line: /g/data/nm31/bin/SPAdes-3.15.2-Linux/bin/spades.py --test System...

Updated to spades 3.15.4, which works with python 3.10, and issue is now solved. Thanks.

Was this resolved? I am seeing the same problem on a large genome (5 Gbp) but have about 40X reads). Exactly the same strange histogram and hifiasm either times out...

Was this resolved? I am seeing the same problem on a large genome (5 Gbp) but have about 40X reads). Exactly the same strange histogram and hifiasm either times out...

I have now discovered something similar - one library that has a very large excess of 5S reads. It seems this problem often arises from mixtures or overrepresentation.