I am having a problem working with fastx_collapser in Galaxy.
When attempting to use the Collapse sequences tool, I get the following error message: "fastx_collapser: Invalid input: This looks like a multi-line FASTA file. Line 899 contains a nucleotides string instead of a '>' prefix. FASTX-Toolkit can't handle multi-line FASTA files. Please use the FASTA-Formatter tool to convert this file"
To remedy this problem, I use the FASTA Width formatter (Galaxy Version 1.0.0) to ensure that every odd line is a sequence identifier, and every even line is a nucleotides line. However, I still get the same error message as above.
I've exported the problem fasta file and attempted to view line 899, yet it looks normal to me (it is the sequence identifier, as expected).
I am out of ideas as to what this error message could mean otherwise. Any suggestions would be greatly appreciated.