Comments (4)
NanoSim is able to deal with multiple entries in a fasta file and it should work fine for small reference genomes, just take longer to generate a proper read length. Could you send me your reference plasmid fasta file so I can test on it? Thanks!
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I send the file to your bcgsc.ca mail address.
I did some more testing and it seems that every reference over ~40kb works but with ~20kb or less it always crashes for me. However, if I use --perfect, it works just fine. The problem probably lies within mutate_read.
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I found a solution: specifying the "max_len" as the length of the reference contigs.
Seems like it was trying to create reads longer than the reference?
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Oh, I see. NanoSim will try to mimic the length distribution as the training profile. So if your reference genome is smaller than the empirical length distribution, it may not able to find the right length for each read. Specifying the max_len
is the solution and probably you don't mind the simulated read length doesn't mach the profile given the reference size.
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Related Issues (20)
- Stuck at simulation stage HOT 4
- simulator.py genome FileNotFoundError: [Errno 2] No such file or directory: 'training_model_profile' HOT 1
- NanoSim for tuning Minimap2 parameters? HOT 2
- Models for newer versions of Guppy with sup basecalls HOT 3
- Options / suggestions for how to simulate nCats data? HOT 1
- Support for Dorado? HOT 2
- IndexError: list index out of range HOT 4
- Installation error HOT 4
- How to find reference genome for pre-trained models HOT 2
- Coverage breadth following metagenome characterization HOT 2
- Can't install Nanosim HOT 2
- Questions about the usage and processing of the expression profile HOT 1
- Failure in using Nanosim for transcriptome (ValueError: file does not contain alignment data)
- Reading the simulated_aligned_reads HOT 3
- Stuck at the simulation step HOT 5
- gzip intermediate fastq files
- Effect of `-b` in metagenome mode HOT 5
- Variation in relative abundances of simulated Zymo mock microbes HOT 1
- output different replicates of a sample HOT 1
- No such file or directory: 'training_ht_length.pkl' HOT 4
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