NanoSim Error “Please specify the training reads and its reference genome!”

NanoSim Error “Please specify the training reads and its reference genome!”

1

Hi, I installed nanosim using conda install -c bioconda nanosim and then tried to run the read characterization using
read_analysis.py transcriptome -i training_reads.fastq -r reference_genome.fa -rt reference_transcriptome.fa -annot reference_annotation.gtf -o training.

However, I get the following error:

Please specify the training reads and its reference genome!
./read_analysis.py
:
-h : print usage message
-i : training ONT real reads, must be fasta files
-r : reference genome of the training reads
-a : Aligner to be used: minimap2 or LAST, default=”minimap2
-m : User can provide their own alignment file, with maf or sam extension, can be omitted
-b : number of bins (for development), default = 20
-t : number of threads for LAST alignment, default = 1
-o : The prefix of output file, default = “training’
–no_model_fit : Skip the model fitting step

I am sure that the path to the respective files (training_reads and reference_genome) is correct. I tried to provide the input files as absolute as well as relative path but the error remains same. Please help. Thanks


NanoSim


RNA-seq


LongRead

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