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bcgsc / NanoSim

Nanopore sequence read simulator
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Please specify the training reads and its reference genome! #191

Closed kainth-amoldeep closed 1 year ago

kainth-amoldeep commented 1 year ago

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 -rg 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 have also tried feeding fasta files instead of fastq but still get the same error. Please help. Thanks
kmnip commented 1 year ago

The command looks okay to me.

Can you report the version you are using?

python read_analysis.py -v

I am suspecting that you have installed an old version of NanoSim. The option descriptions you posted don't match those in the current version.

kainth-amoldeep commented 1 year ago

Hi, you are right; my conda installation somehow installed an old version of NanoSim. I proceeded to directly download the latest version (3.0) and ran the command again. It seems to be working now. Thanks a lot for reaching out.

kmnip commented 1 year ago

@kainth-amoldeep That's great to hear! I am closing this issue now. Please create another issue if you have any more problems.