I am battling the submission of scaffolded assembly to EBI, somehow I can not get AGP gap file right.
The only option seems to be using the Webin-CLI submission interface. For the scaffolded assembly submission, one needs the manifest file, the sequence (fasta or flat file), and AGP file, which denotes how contigs are glued together into scaffolds. I got already that the sequence file should contain only contigs, and EBI will glue them together using the AGP file.
ena-webin-cli -context genome -userName XXX -password XXX -manifest manifest_file -outputDir asm01_submission -inputDir ena_submission_input -ascp -validate
I got tons of errors with type
ERROR: Scaffold "NODE_667656" has only "1" component, minimum two components expected. ERROR: Scaffold "NODE_353389" has only "1" component, minimum two components expected. ...
supposedly for each contig that actually was not scaffolded. I am quite confused about this, as the example file contains tons of scaffold with one component only (for example the first one
What am I missing?
Sample of my AGP file (incl 1 scaffold and 3 contigs):
Path_2003 1 1672 1 W NODE_32694_length_1672_cov_36.024451 1 1672 + Path_2003 1673 1772 2 U 100 scaffold yes align_trnscpt Path_2003 1773 2521 3 W NODE_61726_length_749_cov_25.233631 1 749 + Path_2003 2522 2621 4 U 100 scaffold yes align_trnscpt Path_2003 2622 5705 5 W NODE_20424_length_3084_cov_26.290988 1 3084 + NODE_667656 1 86 1 W NODE_667656_length_86_cov_136.111111 1 86 + NODE_353389 1 155 1 W NODE_353389_length_155_cov_25.230769 1 155 +