I tried to submit an agp file to ENA but it didn't work. I had 4 times this error message:
USER ERROR: "linkage_evidence" qualifier is allowed in "assembly_gap" feature only when "gap_type" qualifier value equals to "within scaffold" or "repeat within scaffold". [{FILE_NAME=xxx.agp.gz, STAGE=VALIDATE_SCAFFOLD_AGP}]
The thing is, they don't provide the line of the error and just suggested to check the file using the NCBI validator. Using the NCBI validator I have only Warnings and no error.
I have cases where my original contig is broken by gap (here ap_contig1) :
chr1 238500 1804287 3 W ap_contig2 1 1565788 +
chr1 1804288 1868745 4 W ap_contig1 2407 66864 +
chr1 1868746 1912216 5 N 43471 scaffold yes map
chr1 1912217 2102800 6 W ap_contig1 106535 297118 +
Could it be the problem ?
Any clue is very welcome, Thx
Thy the email helpdesk, my experience (with NCBI, never submitted to ENA) is they are really helpful with these kind of problems.