Using mothur v.1.42.1
I am using the Miseq SOP. I am able to make stability files using make.file. However, when I run make.contigs and then check the files with summary.seqs, I get the same error:
#[ERROR]: stability.trim.contigs.fasta is blank. Please correct. Error in reading your fastafile, at position -1. Blank name.
Here is the log from my last run:
mothur > make.contigs(file=stability.files, processors=20, oligos=OligoFluridoneRev3.txt) Using 20 processors. >>>>> Processing file pair Undetermined_S0_L001_I1_001.fastq - Undetermined_S0_L001_I2_001.fastq (files 1 of 2) <<<<< Making contigs... Done. It took 775 secs to assemble 10351587 reads. >>>>> Processing file pair Undetermined_S0_L001_R1_001.fastq - Undetermined_S0_L001_R2_001.fastq (files 2 of 2) <<<<< Making contigs... Done. It took 6324 secs to assemble 10351587 reads. It took 7104 secs to process 20703174 sequences. Output File Names: stability.trim.contigs.fasta stability.trim.contigs.qual stability.scrap.contigs.fasta stability.scrap.contigs.qual stability.contigs.report mothur > summary.seqs(fasta=stability.trim.contigs.fasta) Using 20 processors. [ERROR]: stability.trim.contigs.fasta is blank. Please correct. Error in reading your fastafile, at position -1. Blank name.
The first three lines of my oligo file looks like this:
Where each | is a tab. I have tried several iterations of the oligo file, using full oligos, or not using the reverse complement of the reverse barcode, or not including the oligo file at all. I get the same error for most runs.
My input files at the start are:
I appreciate your help.