I’m new using this program, I’m trying to use a big fasta files (3778 sequences) with different samples (19). I created a simple ID header like:
Each “E1,2,3,n…” corresponde to different sample. So when I import the data, there isn’t problem, but when I try to use vsearch command, I got an error “list index out of range”, but when I try to run just with a few samples (for example 4 from 19) it run perfectly so I don’t now where is the error or should I create another kind of FASTA ID header? And how it should be?
I’ll expect you can help me.
Welcome to the QIIME2 community!
In order to help you I think I need some more information. Can you upload the file you are using for the vsearch command and also the vsearch command you are using? Also anything else that might be helpful.
Hopefully that will give me a better idea of why this error is occuring!
nirs0.txt (3.0 MB)nirs0.qza (385.4 KB)
thank you so much for responding
the command is:
qiime vsearch dereplicate-sequences
Thank you for replying with additional information.
I was looking through your .txt file and I noticed that some of your headers have a tab at the end of it. Maybe that is the problem. I am not 100 percent sure that is the issue but I am sure that it is a header issue.
For reference, this user had the same exact same issue and fixed it by changing their headers.I hope that these suggestions help or at least point you in the right direction. I would try removing the trailing tab at your header, and then look into that user’s solution.
If none of that works please reach out again and we will do some more trouble shooting!
Sorry for my late response! I think I was off the mark on this issue. I believe that it does not have to do with the header but the sequences. In your .txt file, there is a 4 in your sequence.
I think this is the issue. I am honestly surprised that you were able to import though. I would go though and make sure there isn't any other numbers or invalid characters. Let me know if fixing this issue fixes it. If not, I'll be here for more debugging!