Extract Large samples.

[HenrikSpiegel]

Increased sample sizes:

• [x] download all ids from assembly database for Bifilobacterium, facalibacterium, E.col
• [x] Downsample to 100 random ids from each
• [x] Download via Asker script
• [x] Generate relevant camisim files (set novelty category= new_species) as to not find NCBI_taxid.

Clustering:

• [x] Run MCL on current dataset ( to set it up)
• [x] Run on larger sample.

[HenrikSpiegel]

Also run antismash.

Remember to increase allowed runtimes.

[HenrikSpiegel]

Error in some encoding.

/services/tools/camisim/1.3/scripts/ComunityDesign/communitydesign.py:95: SyntaxWarning: "is" with a literal. Did you mean "=="? if not self.validate_characters(self.id) or self.id is '': /services/tools/camisim/1.3/scripts/ComunityDesign/communitydesign.py:98: SyntaxWarning: "is" with a literal. Did you mean "=="? if not self.validate_characters(self.mode) or self.mode is '': 2022-12-01 17:14:14 INFO: [MetagenomeSimulationPipeline] Metagenome simulation starting 2022-12-01 17:14:14 INFO: [MetagenomeSimulationPipeline] Validating Genomes 2022-12-01 17:14:14 INFO: [MetadataReader] Reading file: '/home/projects/dtu_00009/people/henspi/git/Screener/data/simulated_data_large/camisim/id_map.tsv' 2022-12-01 17:14:14 ERROR: [MetagenomeSimulationPipeline] 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte in line 49 2022-12-01 17:14:14 INFO: [MetagenomeSimulationPipeline] Metagenome simulation aborted Traceback (most recent call last): File "/home/projects/dtu_00009/people/henspi/git/Screener/scripts/camisim_describe_run.py", line 47, in df = generate_simulation_overview(args.directory) File "/home/projects/dtu_00009/people/henspi/git/Screener/scripts/camisim_describe_run.py", line 20, in generate_simulation_overview for line in open(fp_map, "r"): FileNotFoundError: [Errno 2] No such file or directory: '/home/projects/dtu_00009/people/henspi/git/Screener/data/simulated_data_large/camisim/0_1GB/internal/genome_locations.tsv'

Perhaps we can ensure utf-8 encoding when writing to .csv