Make.sra error with single-end fastq

Hi Patrick,
I am trying to generate an xml file for uploading single-end 16S sequences to NCBI SRA:
mothur > make.sra(project=exp35_project_file.txt, mimark=exp35_v2.txt, file=exp35_v5.file, platform=ILLUMINA, orientation=forward, libstrategy=AMPLICON, instrument=Illumina_MiSeq)

My file.file has 3 columns:
group fastq.file NONE (each column separated by a Tab)
Here is the first row of the file.file:
g1m1_130720_AACGCA AACGCA_S100_L001_R1_001.fastq NONE

I’m getting the following error:
Unable to open NONE. Trying MOTHUR_FILES directory C:\mothur_47\mothur\NONE.
Unable to open C:\mothur_47\mothur\NONE. Trying mothur’s executable directory C:\mothur_47\mothur\NONE.
Unable to open C:\mothur_47\mothur\NONE.

Apparently mothur is looking for a fastq file in column 3. If I make a 3rd column by repeating the 2nd column:
g1m1_130720_AACGCA AACGCA_S100_L001_R1_001.fastq AACGCA_S100_L001_R1_001.fastq
make.sra runs error free. Surely, entering the same R1 file twice is not the right way to do it.

Running v.1.47.0

many thanks,


Thanks for reporting this bug. It will be fixed in our next release coming soon. In the meantime your workaround will resolve the bug without causing issues.

The fix is included in this release, Release Version 1.48.0 · mothur/mothur · GitHub