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

Question

[akainth]

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

Answer 1

[akainth]

This issue is resolved upon installation of latest NanoSim.

Answer 2

[Mensur Dlakic]

I don't use this program, but this line caught my eye:

-i : training ONT real reads, must be fasta files

It appears that the script wants fasta file, and you are providing fastq.

[akainth]

Hi, Thanks for looking into that and pointing out the requirement of fasta file. I did try fasta files as well but got the same error.