Open ElifKoeksoy opened 5 years ago
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:
M34_camsa_points
file contain a collection of assembly points (i.e., assembly) that was produced by run_camsa.py
tool? M34_camsa_points
file with me, so I check where the issue is, and how has it happened?
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