I have been using the Fetch taxonomic representation tool from Galaxy online to retrieve taxonomy from NCBI.
I m using tab delimited lists with name - gi number format.
I have noticed that the output randomly skips some lines and doesnt return taxonomy for some of the gi numbers. I have double checked and the data is present on NCBI with the full taxonomy. Also, I ve noticed that in many cases it doesnot return taxonomy for the "larger" most recent gi numbers I have as input.
Any ideas on why this is happening and how to fix it? The output is really good overall but the fact that some entries are missing randomly, means I have to check line by line to find what's missing. :(