Annoying and painful, but I haven't been able to figure out a better way, and doing it by hand (in SeqIn or whatever) would be far, far worse :) They will point out additional problems, and then the process starts from the top. Then submit to NCBI and wait for their feedback. You then put the coordinates of those segments in the adaptors.ini (which NNNs them out in the sequences), and then you re-submit.īoth these clarifications should demonstrate that this is a bit of an iterative process: run the pipeline, check the output of tbl2asn, correct the input, re-run, until there are no more tbl2asn errors. Consult the comments at the top of the products.ini, and the reports from tbl2asn, for this.Īs I mentioned before, the adaptors.ini is populated based on feedback from NCBI, i.e., you upload your data and they will run a pipeline and tell you which segments they consider contaminated. Centrosomal protein of 112 kDa=Centrosomal protein) or it can be a bit more involved. This can be as simple as removing the weight (e.g. For each of those problematic names, you must create a mapping to a valid name. Reply to this email directly, view it on GitHubįor the protein names, I ran the wgs2ncbi pipeline till the end (initially with nothing in the products.ini), and then checked the output of tbl2asn, which emits warnings about problematic protein names. You are receiving this because you authored the thread. It doesn't matter that much what you use because these are Name that is used as a prefix for these identifiers.
Temporary authority that generates identifiers. During the submission process, you, the submitter, become a Pipeline they use for identifying adaptors (and other contaminants) this isģ. The coordinates, and I put them in the INI file. I populated the contents of adaptors.ini based on feedback by NCBI.Īccording to them, some scaffolds contained adaptor sequences. each lineĬorrecting names are given at the top of the example fileĢ. Mappings from generated names to names accepted by NCBI, i.e.
The general idea is that the products.ini file contains, as needed,
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