trim.flows command does not accept oligos file

Commands in mothur
1

Hi,

I am stuck in the 454 SOP to analyse my 454 data. My previous post disappeared somehow from this forum but I really hope someone could see what I am doing wrong.

mothur > sffinfo(sff=HD13.sff, flow=T)

Extracting info from HD13.sff …
10000
18736
It took 17 secs to extract 18736.
Output File Names:
HD13.fasta
HD13.qual
HD13.flow


mothur > trim.flows(flow=HD13.flow, oligos= primerseq.oligos, order=B)

bash: syntax error near unexpected token `flow=HD13.flow,’

My oligos file looks like this:

  • forward ATTAGATACCCNGGTAG vF
    reverse ACGGGCGGTGWGTRC vR

No barcodes are needed since I have already demultiplexed data. The pool.trim.flow file has as its first line “450”. Let me know If you need more information.

Any help is welcome :slight_smile:
Jan

2

You have a space between the equals sign and the oligos file name. Remove that extra space and you should be good to go.

Pat