Make.sra with demultiplex paired end fastq files

[vca007]

Hi, I am trying to prepare a submission to SRA with the command make.sra. My raw files are already demultiplexed paired end fastq files. Within the fastq file, reads contain the targetted sequence in addition to the primer, but not the barcodes. For the make.sra command, I prepared therefore a 3 column file with the first column the name of the sample, R1.fastq files as second column and R2.fastq files as third column. An example of this file is:
Bact_1063_19cm Bact_1063_19cm_R1.fastq Bact_1063_19cm_R2.fastq
Bact_1063_1cm Bact_1063_1cm_R1.fastq Bact_1063_1cm_R2.fastq

For my oligos file, I prepared the following file:
primer CCTACGGGNGGCWGCAG
reverse GACTACHVGGGTATCTAATCC

After the command, i get this error message:
[ERROR]: You cannot have an oligosfile and 3 column file option at the same time. Aborting.

I am not sure here what I am getting wrong and would appreciate some help. Thanks!

[westcott]

Thanks for bringing this issue to our attention. The make.sra command cannot currently handle parsed samples with an oligos file. I will modify mothur to make it more flexible in our next release. In the meantime, I would like to help you prepare your submission. Could you send your file, project, mimarks, oligos and log files to mothur.bugs@gmail.com so I can create submission file for you?