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Error with reference when running NEAT #132

@yaroslovakia

Description

@yaroslovakia

Describe the bug
I am trying to generate synthetic bam file using NEAT and it crashes with error "AttributeError: 'NoneType' object has no attribute 'reference_id'".

To Reproduce
That's what I am running:

[content of config.yml]
reference: /home/references/hg38/hg38.fa
read_len: 150
produce_bam: True
produce_vcf: False
paired_ended: True
coverage: 30
fragment_mean: 300
fragment_st_dev: 30
target_bed: /home/tables/regions.bed

neat read-simulator -c config.yml -o ~/synthetic_seq/neat

Expected behavior
Generation of bam file using my reference.

Screenshots
ref_error_screenshot

Desktop (please complete the following information):

  • OS: Linux
  • Version: 4.0

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