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

[Laney]

Hi,

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:

splitting merging II

Let me give you an example to explain what is going on. Fasta file: seq1 attgc… seq2 ggcta… Count file: Representative_Sequence total A B C seq1 3 1 2 0 seq2 10 1 4 5 … The split.groups command would result in 6 files. Fasta and count files for sample A, B would contain seq1 and seq2, where as the files for sample C would only contain seq2. NOTE: Split.groups does NOT change any sequence names. This is done so that you can easily relate the reads in the individual samples to the o…

2. 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!

L

[westcott]

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.