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config_sbatch.json
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{
"sbatch_general": {
"account": "b2010008",
"wrapper_script": "/proj/b2010008/bin/sbatch_job"
},
"schedule_default": {
"days": 0,
"hours": 0,
"minutes": 5,
"partition": "core",
"cores": "1",
"extra_parameters": ""
},
"schedule_short": {
"days": 0,
"hours": 0,
"minutes": 15,
"partition": "core",
"cores": "1",
"extra_parameters": ""
},
"schedule_two_cores_medium": {
"days": 0,
"hours": 12,
"minutes": 0,
"partition": "core",
"cores": "2",
"extra_parameters": ""
},
"schedule_all": "schedule_default",
"schedule_concoct_cutup_10K_all": "schedule_default",
"schedule_concoct_map_10K_all": "schedule_default",
"schedule_concoct_inputtable_10K_all": "schedule_default",
"schedule_concoct_cutup_10K": {
"days": 0,
"hours": 0,
"minutes": 5,
"partition": "core",
"cores": "1",
"extra_parameters": ""
},
"schedule_concoct_generate_coverage_table_10K": "schedule_two_cores_medium",
"schedule_concoct_run_10K": {
"days": 3,
"hours": 0,
"minutes": 0,
"partition": "core",
"cores": "11",
"extra_parameters": ""
},
"schedule_concoct_run_10K_all": "schedule_default",
"schedule_bowtie2_index": {
"days": 0,
"hours": 2,
"minutes": 0,
"partition": "core",
"cores": "1",
"extra_parameters": ""
},
"schedule_bowtie2_map": {
"days": 2,
"hours": 0,
"minutes": 0,
"partition": "core",
"cores": "1",
"extra_parameters": ""
},
"schedule_bowtie2_map_fasta": {
"days": 1,
"hours": 0,
"minutes": 0,
"partition": "core",
"cores": "4",
"extra_parameters": ""
},
"schedule_remove_mark_duplicates": {
"days": 1,
"hours": 0,
"minutes": 0,
"partition": "core",
"cores": "6",
"extra_parameters": ""
},
"schedule_bedtools_coverage": {
"days": 0,
"hours": 6,
"minutes": 0,
"partition": "core",
"cores": "1",
"extra_parameters": ""
},
"schedule_bam_sort": {
"days": 0,
"hours": 12,
"minutes": 0,
"partition": "core",
"cores": "1",
"extra_parameters": ""
},
"schedule_rpsblast_run": {
"days": 1,
"hours": 0,
"minutes": 0,
"partition": "core",
"cores": "14",
"extra_parameters": ""
},
"schedule_hmmer_run": {
"days": 1,
"hours": 0,
"minutes": 0,
"partition": "core",
"cores": "16",
"extra_parameters": ""
},
"schedule_trimmomatic_pe": {
"days": 0,
"hours": 12,
"minutes": 0,
"partition": "node",
"cores": "16",
"extra_parameters": ""
},
"schedule_ray_assembly": {
"days": 1,
"hours": 0,
"minutes": 0,
"partition": "node",
"cores": "64",
"extra_parameters": ""
},
"schedule_merge_newbler": {
"days": 1,
"hours": 0,
"minutes": 0,
"partition": "node",
"cores": "8",
"extra_parameters": ""
},
"schedule_fastqc": "schedule_bowtie2_index",
"schedule_create_read_symlink": "schedule_short",
"schedule_ray_assembly_all": "schedule_short",
"schedule_merge_newbler_all": "schedule_short",
"schedule_fastqc_all": "schedule_short",
"schedule_trimmomatic_all": "schedule_short",
"schedule_rpsblast_run_all": "schedule_default",
"schedule_hmmer_run_all": "schedule_default",
"schedule_prodigal_run": "schedule_bedtools_coverage",
"schedule_prodigal_run_all": "schedule_default",
"schedule_bam_sort_name": "schedule_bam_sort",
"schedule_bam_index": "schedule_short",
"schedule_sam_to_bam": "schedule_short",
"schedule_bam_stats": "schedule_short",
"schedule_fasta_dict": "schedule_short",
"schedule_fasta_index": "schedule_short",
"schedule_bam_measure_insert_size": "schedule_bowtie2_map",
"schedule_sample_merge": "schedule_bowtie2_map",
"schedule_concoct_eval_cog_table": "schedule_bedtools_coverage",
"schedule_concoct_eval_cog_plot": "schedule_short",
"schedule_concoct_eval_cog_plot_all": "schedule_short",
"schedule_concoct_eval_cog_plot_merged": "schedule_short",
"schedule_concoct_eval_all": "schedule_short",
"schedule_merge_concoct_results": "schedule_short",
"schedule_concoct_eval_cog_table_merged": "schedule_bedtools_coverage",
"schedule_concoct_extract_approved_scg_bins_all_merged": "schedule_short",
"schedule_concoct_extract_approved_scg_bins_merged": "schedule_short",
"schedule_concoct_dnadiff_dist_matrix_merged": "schedule_trimmomatic_pe",
"schedule_concoct_dnadiff_dist_matrix": "schedule_trimmomatic_pe",
"schedule_concoct_dnadiff_dist_matrix_mags": "schedule_trimmomatic_pe",
"schedule_concoct_cutup_gz_10K": "schedule_concoct_cutup_10K",
"schedule_build_index_all": "schedule_short",
"schedule_map_10K_all_first": "schedule_short",
"schedule_prokka_extended_run": "schedule_two_cores_medium",
"schedule_prokka_extended_run_rpsblast": "schedule_two_cores_medium",
"schedule_prokka_extended_output": "schedule_short",
"schedule_prokka_extended_all": "schedule_short",
"schedule_prokka_extended_get_prokka_annotation": "schedule_short",
"schedule_prokka_extended_collate_annotations": "schedule_short",
"schedule_prokka_extended_summarize_all": "schedule_short"
}