my first question is: Does the oligos file need to be a .oligos file or can it be .txt? The barcode file we were provided by the sequencer is not in a format that mothur can read, and it’s a text file, so I reformatted it, but it’s still a .txt file.
The other issue I’m having is with trimming sequences. I am attempting to trim the original fna file, and I keep getting an error message and booted off. It is:
mothur > trim.seqs(fasta=baileyb.fna, oligos=baileybmoth.txt, qfile=baileyb.qual, maxambig=0, maxhomop=8, flip=t, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, processors=1)
[ERROR]: St9bad_alloc has occurred in the QualityScores class function QualityScores. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.
Lastly, is there any way to create a group file without doing the sequence trimming? A collaborator did create a file in which the barcodes and linker primer sequences are trimmed but he didn’t provide me with a group file.
my first question is: Does the oligos file need to be a .oligos file or can it be .txt? The barcode file we were provided by the sequencer is not in a format that mothur can read, and it’s a text file, so I reformatted it, but it’s still a .txt file.
Everything in mothur (except for sff files) are text files, so as long as it’s in the right layout and saved as a text file you should be good.
The other issue I’m having is with trimming sequences. I am attempting to trim the original fna file, and I keep getting an error message and booted off. It is:
What version of mothur are you using? Based on your next issue, I suspect that the fasta file has been trimmed, but the quality file has not been and this is causing your problems. I’d strongly encourage you to get all of the raw data you can from your collaborator - try getting the sff file if at all possible.
Lastly, is there any way to create a group file without doing the sequence trimming? A collaborator did create a file in which the barcodes and linker primer sequences are trimmed but he didn’t provide me with a group file.
You can write a script to do it or you can use the make.group command