2024-12-11 11:11:01,309:INFO:neat.common.logging:writing log to: neat4/1733915460.8927002_NEAT.log
2024-12-11 11:11:01,309:INFO:neat.read_simulator.runner:Using configuration file config.yml
2024-12-11 11:11:01,311:INFO:neat.read_simulator.runner:Saving output files to .
2024-12-11 11:11:01,315:INFO:neat.read_simulator.utils.options:Run Configuration...
2024-12-11 11:11:01,315:INFO:neat.read_simulator.utils.options:Input fasta: refs/Mycobacterium_tuberculosis_H37Rv.fasta
2024-12-11 11:11:01,316:INFO:neat.read_simulator.utils.options:Producing the following files:
	- neat4/test_vcf_r1.fastq.gz
	- neat4/test_vcf_r2.fastq.gz

2024-12-11 11:11:01,316:INFO:neat.read_simulator.utils.options:Single threading - 1 thread.
2024-12-11 11:11:01,316:INFO:neat.read_simulator.utils.options:Using a read length of 150
2024-12-11 11:11:01,316:INFO:neat.read_simulator.utils.options:Generating fragments based on mean=300, stand. dev=30
2024-12-11 11:11:01,316:INFO:neat.read_simulator.utils.options:Running in paired-ended mode.
2024-12-11 11:11:01,316:INFO:neat.read_simulator.utils.options:Average coverage: 5
2024-12-11 11:11:01,317:INFO:neat.read_simulator.utils.options:Using default error model.
2024-12-11 11:11:01,317:INFO:neat.read_simulator.utils.options:Ploidy value: 2
2024-12-11 11:11:01,317:INFO:neat.read_simulator.utils.options:Vcf of variants to include: test_dir_new/variants.vcf
2024-12-11 11:11:01,317:INFO:neat.read_simulator.utils.options:RNG seed value for run: 8732147021153953
2024-12-11 11:11:01,317:INFO:neat.read_simulator.runner:Reading Models...
2024-12-11 11:11:01,318:INFO:neat.read_simulator.runner:Reading refs/Mycobacterium_tuberculosis_H37Rv.fasta.
2024-12-11 11:11:01,425:INFO:neat.read_simulator.runner:Reading input VCF: test_dir_new/variants.vcf.
2024-12-11 11:11:01,425:INFO:neat.read_simulator.utils.vcf_func:Parsing input vcf test_dir_new/variants.vcf
2024-12-11 11:11:03,319:INFO:neat.read_simulator.utils.vcf_func:Found 17 variants in input VCF.
2024-12-11 11:11:03,320:INFO:neat.read_simulator.utils.vcf_func:Skipped 0 variants because of multiples at the same location
2024-12-11 11:11:03,320:INFO:neat.read_simulator.utils.vcf_func:Skipped 0 variants because of a mismatch between Ref and reference.
2024-12-11 11:11:03,672:INFO:neat.read_simulator.runner:Beginning simulation.
2024-12-11 11:11:03,788:INFO:neat.read_simulator.runner:Generating variants for ChrI
2024-12-11 11:11:03,902:INFO:neat.read_simulator.utils.generate_variants:Finished generating random mutations in 0.00 minutes
2024-12-11 11:11:03,903:INFO:neat.read_simulator.utils.generate_variants:Added 0 mutations to ChrI
2024-12-11 11:11:03,903:INFO:neat.read_simulator.utils.generate_reads:Sampling reads...
2024-12-11 11:11:05,695:ERROR:neat:read-simulator failed, see the traceback below
Traceback (most recent call last):
  File "/home/matt/anaconda3/envs/neat4/lib/python3.10/site-packages/neat/cli/cli.py", line 131, in main
    cmd(args)
  File "/home/matt/anaconda3/envs/neat4/lib/python3.10/site-packages/neat/cli/commands/read_simulator.py", line 47, in execute
    read_simulator_runner(arguments.config, arguments.output)
  File "/home/matt/anaconda3/envs/neat4/lib/python3.10/site-packages/neat/read_simulator/runner.py", line 313, in read_simulator_runner
    read1_fastq_paired, read1_fastq_single, read2_fastq_paired, read2_fastq_single = generate_reads(
  File "/home/matt/anaconda3/envs/neat4/lib/python3.10/site-packages/neat/read_simulator/utils/generate_reads.py", line 345, in generate_reads
    read_1.finalize_read_and_write(
  File "/home/matt/anaconda3/envs/neat4/lib/python3.10/site-packages/neat/read_simulator/utils/read.py", line 344, in finalize_read_and_write
    self.read_quality_string = "".join([chr(x + quality_offset) for x in self.quality_array])
  File "/home/matt/anaconda3/envs/neat4/lib/python3.10/site-packages/neat/read_simulator/utils/read.py", line 344, in <listcomp>
    self.read_quality_string = "".join([chr(x + quality_offset) for x in self.quality_array])
TypeError: can only concatenate str (not "int") to str