NanoPreProcess is successfully running but it's not giving me a clear output?
rober136 opened this issue · 1 comments
I've been messing around with the MoP pipeline to get it running on a SLURM cluster, and have just gotten it to work. Problem is, it's not giving me an output where I told it to. Here is the parameters I have set up in the nanopreprocess.nf file:
`kit : SQK-LSK112
flowcell : FLO-MIN107
fast5 : /home/rober136/scratch/WhyardData/NextFlow/MockData/*.fast5
reference : /home/rober136/scratch/WhyardData/NextFlow/genome.fna
annotation : /home/rober136/scratch/WhyardData/NextFlow/genome.gtf
ref_type : genome
seq_type : RNA
output : /home/rober136/scratch/WhyardData/NextFlow/Output
qualityqc : 5
granularity :
basecaller : guppy
basecaller_opt :
GPU : ON
demultiplexing : guppy
demultiplexing_opt :
demulti_fast5 :
filter : nanofilt
filter_opt :
mapper : minimap2
mapper_opt : -uf -k14
map_type : spliced
counter : YES
counter_opt :
downsampling :
variant_caller : YES
variant_opt :
email : rober136@myumanitoba.ca
"""`
See the attached .txt file for the output. I see no errors, it says the execution status is ok, yet it's not putting anything in the Output folder I specified. I have tried running this with and without the Output folder being created ahead of time.
If I look at the NanoPreProcess/work folder, I can find the QC reports it does look like it's run successfully. Any idea what's going on?
Closing the issue. I see that this version of MoP is depreciated and am now looking into MoP2.