missing output files


I am currently attempting to use the merge.files command to merge 2 fasta files together and 2 qual files together. All files are in the same folder, and directory is set. I run the command and the output file is generated. However, the files do not appear in the specified folder, nor can I find them anywhere else. Any help would be greatly appreciated.

mothur > merge.files(input=pacbio_roots.6X.ccs.fasta-pacbio_roots.6X.ccs.rc.fasta, output=pacbio_roots.6X.combined.fasta)

Output File Names:

mothur > merge.files(input=pacbio_roots.6X.ccs.qual-pacbio_roots.6X.ccs.rc.qual, output=pacbio_roots.6X.combined.qual)

Output File Names:

Thanks for reading and for any feedback,

-Buck C.

Can you try running summary.seqs on the pacbio_roots.6X.combined.fasta file to see where mothur finds it?