Closed DrinnanSante closed 5 months ago
joshfactorial
commented
5 months ago the disable target regions thing I have not seen, but we have a fix for that divide by zero error in version 4.1.1. I would try that or the latest on main and see if that clears this up.
joshfactorial
commented
5 months ago Will be working on this as soon as time allows.
MTDouglas
commented
4 months ago I am having a very similar issue with the following
[neat_config.yml]: reference: references/nCoV-2019.reference.fasta read_len: 126 ploidy: 1 produce_bam: True produce_vcf: True paired_ended: True fragment_mean: 300 fragment_st_dev: 30 rng_seed: 12345
Running this command neat --no-log read-simulator -c neat_config.yml -o simulation/
And am getting the following error: `2024-05-08 12:41:08,572:INFO:neat.read_simulator.runner:Using configuration file neat_config.yml 2024-05-08 12:41:08,573:INFO:neat.read_simulator.runner:Saving output files to . 2024-05-08 12:41:08,573:INFO:neat.read_simulator.utils.options:Run Configuration... 2024-05-08 12:41:08,573:INFO:neat.read_simulator.utils.options:Input fasta:/references/nCoV-2019.reference.fasta 2024-05-08 12:41:08,573:INFO:neat.read_simulator.utils.options:Producing the following files:
2024-05-08 12:41:08,573:INFO:neat.read_simulator.utils.options:Single threading - 1 thread. 2024-05-08 12:41:08,574:INFO:neat.read_simulator.utils.options:Running in paired-ended mode. 2024-05-08 12:41:08,574:INFO:neat.read_simulator.utils.options:Generating fragment model based on mean=300.0, st dev=30.0 2024-05-08 12:41:08,574:INFO:neat.read_simulator.utils.options:Using a read length of 126 2024-05-08 12:41:08,574:INFO:neat.read_simulator.utils.options:Average coverage: 10 2024-05-08 12:41:08,574:INFO:neat.read_simulator.utils.options:Using default error model. 2024-05-08 12:41:08,574:INFO:neat.read_simulator.utils.options:Ploidy value: 1 2024-05-08 12:41:08,574:INFO:neat.read_simulator.utils.options:RNG seed value for run: 12345 2024-05-08 12:41:08,574:INFO:neat.read_simulator.runner:Reading Models... 2024-05-08 12:41:08,574:INFO:neat.read_simulator.runner:Reading references/nCoV-2019.reference.fasta. 2024-05-08 12:41:08,577:INFO:neat.read_simulator.runner:Beginning simulation. 2024-05-08 12:41:08,578:INFO:neat.read_simulator.runner:Generating variants for MN908947.3 2024-05-08 12:41:08,596:INFO:neat.read_simulator.utils.generate_variants:Finished generating random mutations in 0.00 minutes 2024-05-08 12:41:08,597:INFO:neat.read_simulator.utils.generate_variants:Added 25 mutations to MN908947.3 2024-05-08 12:41:08,597:INFO:neat.read_simulator.runner:Outputting temp vcf for MN908947.3 for later use 2024-05-08 12:41:08,597:INFO:neat.read_simulator.utils.local_file_writer:Finished outputting temp vcf/fasta 2024-05-08 12:41:08,597:INFO:neat.read_simulator.utils.generate_reads:Sampling reads... 2024-05-08 12:41:08,615:ERROR:neat:read-simulator failed, see the traceback below Traceback (most recent call last): File /.local/lib/python3.10/site-packages/neat/cli/cli.py", line 133, in main cmd(args) File /.local/lib/python3.10/site-packages/neat/cli/commands/read_simulator.py", line 47, in execute read_simulator_runner(arguments.config, arguments.output) File "/.local/lib/python3.10/site-packages/neat/read_simulator/runner.py", line 333, in read_simulator_runner generate_reads(local_reference, File "/.local/lib/python3.10/site-packages/neat/read_simulator/utils/generate_reads.py", line 441, in generate_reads _LOG.debug(f"Paired percentage = {len(paired_reads)/len(sam_read_order)}") ZeroDivisionError: division by zero ERROR: read-simulator failed, showing the last error Traceback (most recent call last): File "/.local/lib/python3.10/site-packages/neat/cli/cli.py", line 133, in main cmd(args) File "/.local/lib/python3.10/site-packages/neat/cli/commands/read_simulator.py", line 47, in execute read_simulator_runner(arguments.config, arguments.output) File "/.local/lib/python3.10/site-packages/neat/read_simulator/runner.py", line 333, in read_simulator_runner generate_reads(local_reference, File "/.local/lib/python3.10/site-packages/neat/read_simulator/utils/generate_reads.py", line 441, in generate_reads _LOG.debug(f"Paired percentage = {len(paired_reads)/len(sam_read_order)}") ZeroDivisionError: division by zero`
joshfactorial
commented
4 months ago Okay, we are working on this now!
From: MTDouglas @.> Sent: Wednesday, May 8, 2024 11:44 AM To: ncsa/NEAT @.> Cc: Allen, Josh @.>; Assign @.> Subject: Re: [ncsa/NEAT] Division by zero / cant disable target regions with discard (Issue #102)
I am having a very similar issue with the following
[neat_config.yml]: reference: references/nCoV-2019.reference.fasta read_len: 126 ploidy: 1 produce_bam: True produce_vcf: True paired_ended: True fragment_mean: 300 fragment_st_dev: 30 rng_seed: 12345
Running this command neat --no-log read-simulator -c neat_config.yml -o simulation/
And am getting the following error: `2024-05-08 12:41:08,572:INFO:neat.read_simulator.runner:Using configuration file neat_config.yml 2024-05-08 12:41:08,573:INFO:neat.read_simulator.runner:Saving output files to . 2024-05-08 12:41:08,573:INFO:neat.read_simulator.utils.options:Run Configuration... 2024-05-08 12:41:08,573:INFO:neat.read_simulator.utils.options:Input fasta:/references/nCoV-2019.reference.fasta 2024-05-08 12:41:08,573:INFO:neat.read_simulator.utils.options:Producing the following files:
2024-05-08 12:41:08,573:INFO:neat.read_simulator.utils.options:Single threading - 1 thread. 2024-05-08 12:41:08,574:INFO:neat.read_simulator.utils.options:Running in paired-ended mode. 2024-05-08 12:41:08,574:INFO:neat.read_simulator.utils.options:Generating fragment model based on mean=300.0, st dev=30.0 2024-05-08 12:41:08,574:INFO:neat.read_simulator.utils.options:Using a read length of 126 2024-05-08 12:41:08,574:INFO:neat.read_simulator.utils.options:Average coverage: 10 2024-05-08 12:41:08,574:INFO:neat.read_simulator.utils.options:Using default error model. 2024-05-08 12:41:08,574:INFO:neat.read_simulator.utils.options:Ploidy value: 1 2024-05-08 12:41:08,574:INFO:neat.read_simulator.utils.options:RNG seed value for run: 12345 2024-05-08 12:41:08,574:INFO:neat.read_simulator.runner:Reading Models... 2024-05-08 12:41:08,574:INFO:neat.read_simulator.runner:Reading references/nCoV-2019.reference.fasta. 2024-05-08 12:41:08,577:INFO:neat.read_simulator.runner:Beginning simulation. 2024-05-08 12:41:08,578:INFO:neat.read_simulator.runner:Generating variants for MN908947.3 2024-05-08 12:41:08,596:INFO:neat.read_simulator.utils.generate_variants:Finished generating random mutations in 0.00 minutes 2024-05-08 12:41:08,597:INFO:neat.read_simulator.utils.generate_variants:Added 25 mutations to MN908947.3 2024-05-08 12:41:08,597:INFO:neat.read_simulator.runner:Outputting temp vcf for MN908947.3 for later use 2024-05-08 12:41:08,597:INFO:neat.read_simulator.utils.local_file_writer:Finished outputting temp vcf/fasta 2024-05-08 12:41:08,597:INFO:neat.read_simulator.utils.generate_reads:Sampling reads... 2024-05-08 12:41:08,615:ERROR:neat:read-simulator failed, see the traceback below Traceback (most recent call last): File /.local/lib/python3.10/site-packages/neat/cli/cli.py", line 133, in main cmd(args) File /.local/lib/python3.10/site-packages/neat/cli/commands/read_simulator.py", line 47, in execute read_simulator_runner(arguments.config, arguments.output) File "/.local/lib/python3.10/site-packages/neat/read_simulator/runner.py", line 333, in read_simulator_runner generate_reads(local_reference, File "/.local/lib/python3.10/site-packages/neat/read_simulator/utils/generate_reads.py", line 441, in generate_reads _LOG.debug(f"Paired percentage = {len(paired_reads)/len(sam_read_order)}") ZeroDivisionError: division by zero ERROR: read-simulator failed, showing the last error Traceback (most recent call last): File "/.local/lib/python3.10/site-packages/neat/cli/cli.py", line 133, in main cmd(args) File "/.local/lib/python3.10/site-packages/neat/cli/commands/read_simulator.py", line 47, in execute read_simulator_runner(arguments.config, arguments.output) File "/.local/lib/python3.10/site-packages/neat/read_simulator/runner.py", line 333, in read_simulator_runner generate_reads(local_reference, File "/.local/lib/python3.10/site-packages/neat/read_simulator/utils/generate_reads.py", line 441, in generate_reads _LOG.debug(f"Paired percentage = {len(paired_reads)/len(sam_read_order)}") ZeroDivisionError: division by zero`
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running basic read-simulate, config file matches example but with different reference, bolded what I think are the important lines, if I am doing something wrong please let me know!
2024-04-16 21:33:27,144:INFO:neat.read_simulator.runner:Beginning simulation. 2024-04-16 21:33:27,181:INFO:neat.read_simulator.runner:Generating variants for 7e24d142adc2427d_1 2024-04-16 21:33:29,652:INFO:neat.read_simulator.utils.generate_variants:Finished generating random mutations in 0.04 minutes 2024-04-16 21:33:29,652:INFO:neat.read_simulator.utils.generate_variants:Added 2899 mutations to 7e24d142adc2427d_1 2024-04-16 21:33:29,652:INFO:neat.read_simulator.runner:Outputting temp vcf for 7e24d142adc2427d1 for later use 2024-04-16 21:33:29,659:INFO:neat.read_simulator.utils.local_file_writer:2899 variants excluded because of target regions with discard off-target enabled_ 2024-04-16 21:33:29,659:INFO:neat.read_simulator.utils.local_file_writer:Finished outputting temp vcf/fasta 2024-04-16 21:33:29,659:INFO:neat.read_simulator.utils.generate_reads:Sampling reads... 2024-04-16 21:33:31,649:ERROR:neat:read-simulator failed, see the traceback below Traceback (most recent call last): File "/home/drinnan/miniconda3/envs/neat/lib/python3.10/site-packages/neat/cli/cli.py", line 133, in main cmd(args) File "/home/drinnan/miniconda3/envs/neat/lib/python3.10/site-packages/neat/cli/commands/read_simulator.py", line 47, in execute read_simulator_runner(arguments.config, arguments.output) File "/home/drinnan/miniconda3/envs/neat/lib/python3.10/site-packages/neat/read_simulator/runner.py", line 333, in read_simulator_runner generate_reads(local_reference, File "/home/drinnan/miniconda3/envs/neat/lib/python3.10/site-packages/neat/read_simulator/utils/generate_reads.py", line 441, in generate_reads __LOG.debug(f"Paired percentage = {len(paired_reads)/len(sam_readorder)}") ZeroDivisionError: division by zero ERROR: read-simulator failed, showing the last error Traceback (most recent call last): File "/home/drinnan/miniconda3/envs/neat/lib/python3.10/site-packages/neat/cli/cli.py", line 133, in main cmd(args) File "/home/drinnan/miniconda3/envs/neat/lib/python3.10/site-packages/neat/cli/commands/read_simulator.py", line 47, in execute read_simulator_runner(arguments.config, arguments.output) File "/home/drinnan/miniconda3/envs/neat/lib/python3.10/site-packages/neat/read_simulator/runner.py", line 333, in read_simulator_runner generate_reads(local_reference, File "/home/drinnan/miniconda3/envs/neat/lib/python3.10/site-packages/neat/read_simulator/utils/generate_reads.py", line 441, in generate_reads _LOG.debug(f"Paired percentage = {len(paired_reads)/len(sam_read_order)}") ZeroDivisionError: division by zero