My error command (mothur): screen.seqs(fasta=stability.trim.contigs.unique.align, count=stabilit.trim.contigs.count_table, start=1968, end=11550). Helpppp
This is my summary.seqs()
Hello!
Maybe try with the summary file? I also advice using current instead of the full file path to make sure there are no mistakes in the file name. If problems persists, I also suggest to restart from the beginning. Sometime when Mothur encounter a mistake, some files become weird. It is better to run all commands from a clean state.
Best of success.
hey,
i still keep getting error when I filter.seqs(fasta=stability.trim.contigs.unique.good.align, vertical=, trump=.)
It took 3 secs to filter 39328 sequences.
Length of filtered alignment: 0
Number of columns removed: 13424
Length of the original alignment: 13424
Number of sequences used to construct filter: 39328
Output File Names:
stability.filter
stability.trim.contigs.unique.good.filter.fasta
Are you doing vertical= or vertical=T? Can you rerun the screen.seqs and filter.seqs commands in succession?
Finally, what version of mothur are you using? I recall we had an off by one error that caused some problems for people. You might double check that you have the latest version of mothur and try again.
Pat
Its working now, i am not sure why 
.Thank you for the help.
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