Error using merge

[SuPrSh]

Hello, I am getting constant error while using merge command in ragtag

Mon Sep 27 20:53:00 2021 --- INFO: Building the scaffold graph from the AGP files
Traceback (most recent call last):
  File "/root/miniconda3/envs/myenv/bin/ragtag_merge.py", line 430, in <module>
    main()
  File "/root/miniconda3/envs/myenv/bin/ragtag_merge.py", line 362, in main
    agp_multi_sg.add_agps(agp_list, in_weights=weight_list, exclusion_set=comp_exclusion_set)
  File "/root/miniconda3/envs/myenv/lib/python3.6/site-packages/ragtag_utilities/ScaffoldGraph.py", line 606, in add_agps
    for ap in self._get_assembly_points(agp, weight):
  File "/root/miniconda3/envs/myenv/lib/python3.6/site-packages/ragtag_utilities/ScaffoldGraph.py", line 513, in _get_assembly_points
    raise RuntimeError("{} is in {} but not {}.".format(agp_line.comp, agp, self.components_fasta_fname))
RuntimeError: k141_114310 is in /mnt/sdb/P6260/megahit/R1/ragtag_output/ragtag.scaffold.agp but not /mnt/sdb/P6260/ragtag/ggan/ragtag.ggan.scaffold.fasta.

[malonge]

Hi there,

This is showing that there is a component in your AGP file (k141_114310) that is not in the assembly. In other words, that AGP file defines a scaffolding solution for some other assembly, not ragtag.ggan.scaffold.fasta. In order for RagTag "merge" to work, all AGP files must contain the exact same set of components as the assembly. Read here for more details.

[dgs108]

I would like to revisit this comment. I have a similar situation in that when scaffolding, SALSA2 corrected 8 of my contigs and broke them into 2. Thus, a contig that appears as ctg927 in the .fasta file appears as ctg927_1 and ctg927_2 in the resulting AGP file.

In this situation, would you advise to polish the preliminary assembly before scaffolding?

Thanks!