Hello! I would like to use the PiCrust2 tool with a mapping file of KEGG pathways to their corresponding KOs. I have attached the file.
In an attempt to use it, I received an error of ‘Fatal error: Exit code 1 ()’ and that all my input sequences aligned poorly to reference sequences.
Additionally, I ran it without the mapping file and the program executed well, so I know with confidence that it is not my sequences. How do I get picrust to run mapping for the specific pathways in my file?
If you want to share your history with the run, we can provide some feedback here. How to share your work is in the banner at this forum, or see here How to get faster help with your question. You can generate, copy then post back the share link here along with your comments. You can unshare after we are done.
Sometimes errors are due to small technical issues, so that’s what I would be checking for first, but you could also do that. Cleaning up the format of the files is the first step – specifically, using the most “strict” version is where to fall back to after an error. Then items like read quality assurance is recommended. Then exploring parameters and such, and maybe sub-sampling the data. Some of this depends on the server where you are working, but the history share link will inform us about that part and we can give advice if another server is a better choice for a particular tool.
Thanks! I’ll watch for your reply, and let us know if you are able to solve this on your own, too!
That is just the command line, which doesn’t tell us anything about the data, how it was prepared, the format, and all of those related details.
What stuck out to me at first was inconsistent capitalization in your first file. Remember: tools are literal. Maybe make sure that the format in all files is the same, so that common values can be “matched up” correctly. The tool panel has many utilities that can help to standardize format, and we have some tutorials here with some examples: GTN Materials Search
