Benjamin Buchfink
Benjamin Buchfink
Should be safe to rebuild yes, as long as the sequences are in the same order it should not affect results in any way. This is what I have ready:...
v4 should be ok, never heard of earlier versions still being used.
Can you also provide your taxid map so I can try to reproduce this? The second error can be fixed by doing as the message says. The information is not...
got this from chatgpt: https://gist.github.com/bbuchfink/66df4adf1e3642d3412a51396aaa0d71
I tried to reproduce it on a small db with the same commands and it worked. Can you tell me if the error occurs for a small example, e.g. self-alignment...
> However, when we run the same workflow on a much larger database (~3 billion proteins), the runtime increases dramatically. In the log we sometimes see very long alignment phases,...
I will try to fix the errors. Yes, you can just split the query file and get the same results. You can also manually split the database file and merge...
@linweiliarchaea It should be possible to fix this adding `--connected-component-depth 0` to the greedy-vertex-cover call.
One reason could be the query-indexed mode that is automatically used for small query files, but does not have equivalent sensitivity to the default mode. You can explicitly control this...
The superkingdom rank has been replaced, so I don't intend to fix the skingdoms field by mapping it to something else. I will include new output fields for the other...