set -e
true
true
/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/bin/spades-hammer /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/corrected/configs/config.info
/users/marinovg/miniconda3/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/share/spades/spades_pipeline/scripts/compress_all.py --input_file /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/corrected/corrected.yaml --ext_python_modules_home /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/share/spades --max_threads 16 --output_dir /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/corrected --not_used_yaml_file /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/corrected/dont_correct.yaml --gzip_output
true
true
/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/bin/spades-core /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/K21/configs/config.info
/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/bin/spades-core /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/K33/configs/config.info
/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/bin/spades-core /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/K55/configs/config.info
/users/marinovg/miniconda3/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/share/spades/spades_pipeline/scripts/copy_files.py /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/K55/before_rr.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/before_rr.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/K55/assembly_graph_after_simplification.gfa /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/assembly_graph_after_simplification.gfa /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/K55/final_contigs.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/contigs.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/K55/first_pe_contigs.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/first_pe_contigs.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/K55/strain_graph.gfa /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/strain_graph.gfa /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/K55/scaffolds.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/scaffolds.fasta /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/K55/scaffolds.paths /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/scaffolds.paths /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/K55/assembly_graph_with_scaffolds.gfa /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/assembly_graph_with_scaffolds.gfa /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/K55/assembly_graph.fastg /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/assembly_graph.fastg /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/K55/final_contigs.paths /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/contigs.paths
true
/users/marinovg/miniconda3/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/scaffolds.fasta --misc_dir /oak/stanford/groups/akundaje/marinovg/Stanford_bootcamp/2017/2023-07-11-YAC/SPAdes-3.15.4-YAC-V2/misc --threshold_for_breaking_scaffolds 3
true