No reference genome in prefix.prep_MP, but multiple in prep_RM

[hevmarriott]

Hello,

When using TEFLoN preparation script teflon_prep_custom.py multiple times, there is no reference genome in the MP folder, but there are multiple reference genome versions in the RM file -.fa.align, fa.cat.gz, fa.masked, fa.tbl, fa.out.

Therefore, I was wondering if this was a problem with the tool itself, or whether one of these versions can actually be provided as a genome for the main TEFLoN script.

P.S. The hierarchy and bed files are there and looks complete

[jradrion]

Hi @hevmarriott. Sorry that you are experiencing these issues. Can you provide the standard output and error streams when you run teflon_prep_custom.py so I can try to figure out what might be going on.

[hevmarriott]

Hi,

There were no error streams, and the standard output is as follows:

• sample.prep_MP: no files
• sample.prep_RM: sample.bed, hg38.fa, hg38.fa.align, hg38.fa.cat.gz, hg38.fa.masked hg38.fa.tbl, hg38.fa.out
• sample.prep_TF: sample.hier

[jradrion]

Can you copy the exact command you used and whatever was printed to the console.

Are you trying to run this on your own data? Have you been able to successfully run Teflon on the test files provided in this repo?