AGP file ENA submission error

Question

[rob234king]

I am trying to submit a chromsome level genome using AGP file which passes validation externally but when use the ENA webin jar it complains. I think I am missing something obvious? The 6th column is just made up names by a script is that wrong?

ERROR: The component does not exist: "contig1_0". [ line: 1]
ERROR: The component does not exist: "contig1_1". [ line: 3]
ERROR: The component does not exist: "contig1_2". [ line: 5]

chr1    1   2635192 1   W   contig1_0   1   2635192 +
chr1    2635193 2635692 2   N   500 scaffold    yes paired-ends
chr1    2635693 3190876 3   W   contig1_1   1   555184  +
chr1    3190877 3190901 4   N   25  scaffold    yes paired-ends
chr1    3190902 4309107 5   W   contig1_2   1   1118206 +
chr1    4309108 4309132 6   N   25  scaffold    yes paired-ends
chr1    4309133 4568877 7   W   contig1_3   1   259745  +

Answer 1

[lagartija]

It is a nightmare to submit to the EBI if that is what you are doing... You need to submit the contigs fasta and not the scaffolds. Is that what you are doing ? They also say they prefere you to submit contigs that already have an accesion number... It makes no sence

Answer 2

[Juke34]

There is a description how to well perform an AGP file here: https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/

The message says that contig1_0 is not a contig name existing in the associate fasta file. Check your fasta file and modify the AGP accordingly