problem with NanoPreprocess
MSajek opened this issue · 2 comments
I try to run nanopreprocess.nf and have the following error:
N E X T F L O W ~ version 19.04.0
Launching nanopreprocess.nf [cheesy_boyd] - revision: dd396dfd00
╔╦╗┌─┐┌─┐┌┬┐┌─┐┬─┐ ┌─┐┌─┐ ╔═╗╔═╗╦═╗╔═╗╔═╗
║║║├─┤└─┐ │ ├┤ ├┬┘ │ │├┤ ╠═╝║ ║╠╦╝║╣ ╚═╗
╩ ╩┴ ┴└─┘ ┴ └─┘┴└─ └─┘└ ╩ ╚═╝╩╚═╚═╝╚═╝
====================================================
BIOCORE@CRG Preprocessing of Nanopore direct RNA - N F ~ version 0.1
kit : SQK-RNA002
flowcell : FLO-MIN106
fast5 : /home/programs/master_of_pores/NanoPreprocess/test/*.fast5
reference : /media/dysk3/marcin/L2nanopore/gencode.v38.transcripts.fa
annotation :
ref_type : transcriptome
seq_type : RNA
output : /media/dysk3/marcin/L2nanopore/0hr/testOut
qualityqc : 5
granularity :
basecaller : guppy
basecaller_opt : --cpu_threads_per_caller 45
GPU : OFF
demultiplexing : guppy
demultiplexing_opt : -m pAmps-final-actrun_newdata_nanopore_UResNet20v2_model.030.h5
demulti_fast5 : OFF
filter :
filter_opt :
mapper : minimap2
mapper_opt : -ax map-ont -t 45
map_type : spliced
counter : NO
counter_opt :
downsampling :
variant_caller : NO
variant_opt :
email :
Skipping the email
executor > local (2)
[a2/40f906] process > testInput [ 0%] 0 of 1
[fe/14252e] process > logBaseCalling [100%] 1 of 1 ✔
: Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 3.4.5+fb1fbfb
executor > local (2)
[a2/40f906] process > testInput [100%] 1 of 1 ✔
[fe/14252e] process > logBaseCalling [100%] 1 of 1 ✔
: Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 3.4.5+fb1fbfb
FLO-MIN106 SQK-RNA002 rna_r9.4.1_70bps_hac
ERROR ~ For input string: "multi-read"
-- Check script 'nanopreprocess.nf' at line: 177 or see '.nextflow.log' file for more details
I run basic command:
nextflow run nanopreprocess.nf -with-docker
I know that fast5 files are ok, because everything works fine when I use guppy/minimap2/other software alone.
Thank you for help
Hi, can you try the little dataset we include in the repo, please?
Hi, is this issue solved?