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.