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