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 +
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rob234king
2 answers
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
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
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