camsa2fasta error - scaffold extremity adjacent to more than one other scaffold

[ElifKoeksoy]

Hi aganezov,

Thanks for providing CAMSA! I could successfully merge scaffolds in several assemblies already. I have however encountered the following error for three different assemblies when using the command

~/camsa-env$ camsa_points2fasta.py --points M34_camsa_points --fasta M34.fna -o M34_merged.fasta

that I could not resolve myself:

2019-01-09 12:51:12,120 - CAMSA.utils.camsa_points2fasta - INFO - Starting the converting process 2019-01-09 12:51:12,120 - CAMSA.utils.camsa_points2fasta - INFO - Reading assembly points 2019-01-09 12:51:12,122 - CAMSA.utils.camsa_points2fasta - INFO - A total of 36 assembly points was obtained 2019-01-09 12:51:12,123 - CAMSA.utils.camsa_points2fasta - ERROR - Supplied assembly contained a conflict. 2019-01-09 12:51:12,123 - CAMSA.utils.camsa_points2fasta - ERROR - Scaffold Scaffold_27 by its extremity Scaffold_27t is reported as adjacent to more than one other scaffold's extremity.

How can I solve this? Looking forward to your response!

Best, -Elif

[aganezov]

Hi Elif, and thank you for interest in CAMSA!

The reason CAMSA complains here is because in the --points file the assembly points constitute an assembly that has a branching (at the Scaffold_27t extremity apparently). Only totally linear (i.e., non-branching assemblies can be translated into fasta). CAMSA shall not produce branching assemblies, so that is weird.

I wonder two things:

• does the M34_camsa_points file contain a collection of assembly points (i.e., assembly) that was produced by run_camsa.py tool?
• if so, can you share the M34_camsa_points file with me, so I check where the issue is, and how has it happened?