"[ERROR]: * is not in your file, please correct." when the seqname can be found from the files and summary.seqs works okay


I’m using the 1.39.5 version. I have a 2 part question:

  1. Why does rename.seqs give me an error message (topic) telling that a seq name can’t be found in my files, even when the same name occurs in both fasta and count_table that I’m trying to rename the sequences in. Summary.seqs works okay with the same fasta & count_table. I tried sorting the files but it didn’t help matching the names.

The reason why I’m renaming the sequences is because I had this same problem with merging count_tables:

  1. I used get.groups and remove.groups in order to extract the samples I needed to subsample into their own file. I used get.groups and renamed the output files. Then I used the same command, but replaced “get” with “remove” for the same groups in order to get the remaining samples in another file. The commands picked a different amount of sequences from the fasta file. After remove.groups the was a mismatch with fasta vs. count_table. Is there something funny that has happened somewhere along the way or do these commands do something differently when picking the groups?

Thanks for your time and help!


Could you post your logfile with the commands you ran up to this point? Also, I would recommend upgrading to our current version, https://github.com/mothur/mothur/releases/tag/v1.42.0.