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Question: Rename sequence error
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gravatar for kyle.hubbard
3.4 years ago by
kyle.hubbard • 0
United States
kyle.hubbard • 0 wrote:

Hello,

So I'm trying to create a metagenomic workflow, but I can't seem to get the formatting correct. I uploaded a FASTA file, then used the FASTA Manipulation/FASTA width formatter (set to 0) to get the nucleotide strings for each identifier/prefix on a single line.  I then attempted to use the NGS QC and Manipulation/Rename Sequences tool, but I get an error stating:

fastx_renamer: Invalid input: This looks like a multi-line FASTA file.
Line 7 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 into a single

If I used the FASTA width formatter and set to 0 so that the prefixes and strings are alternating every line, what's the issue?

Thanks!
galaxy • 1.0k views
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modified 3.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by kyle.hubbard • 0
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gravatar for Jennifer Hillman Jackson
3.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There may have been a format issue with the orignal upload file. Examine the line the error reports. Be aware that other lines could have a problem, as just the first occurrence of a problem is usually reported by tools.

Note: if you used certain text editors with this dataset, some can add in hidden characters. Avoid that type of manipulation or use a plain text editor instead. The dreaded "^M" (a type of "soft return") from Microsoft tools is a common issue encountered in input datasets for bioinformatics pipelines (more in this wiki: https://en.wikipedia.org/wiki/Newline#Common_problems)

Then, once you have fasta format, use unwrapped sequences with these manipulation tools as you were doing. Then wrap the final dataset before using with tools downstream to avoid other issues (some tools do not care about wrapping, in particular NGS mappers, but many others do).

More about format troubleshooting is here: CustomGenomes#Troubleshooting

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 3.4 years ago • written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k
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