sorry if this is not the most proper section, but I need support on a step. I am using Greengenes database downloaded by your website, and using it to run mothur pipeline by following MiSeq SOP.
I am using Mothur v.1.48 in a singularity container, and working on samples that were seqeunced in MiSeq to amplify the V3-V4 region. For this reason, I try to use pcr.seqs to customize mi database, as following:
mothur > pcr.seqs(fasta=Databases/gg_13_8_otus/mothur/gg_13_8_99.refalign/gg_13_8_99.fasta, start=6388, end=13861, keepdots=F, outputdir=Analysis/pipeline_comparison/Mothur_x_gg_13_8/gg_13_8)
Command works properly, and gives me output:
It took 7 secs to screen 203452 sequences.
Output File Names:
I then proceed with rename.file, with this command:
mothur > rename.file(fasta=Analysis/pipeline_comparison/Mothur_x_gg_13_8/gg_13_8/gg_13_8_99.pcr.fasta, new=Analysis/pipeline_comparison/Mothur_x_gg_13_8/gg_13_8.v3v4.fasta, outputdir=Analysis/pipeline_comparison/Mothur_x_gg_13_8)
Setting output directory to: Analysis/pipeline_comparison/Mothur_x_gg_13_8/
And I receive this error message:
[ERROR]: Analysis/pipeline_comparison/Mothur_x_gg_13_8/gg_13_8/gg_13_8_99.pcr.fasta is blank, aborting.
Is there anything that can be done?
Thanks in advance