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.

I have same issue with --n-hap 3. Only get two haploid genomes.

Unfortunately we will not have HiC for this data. Also HiC will not scaffold if homologous chromosomes have been concatenated as in our case. I need to manually break those...