set -e
true
true
/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.0-Linux/bin/spades-hammer /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/corrected/configs/config.info
/share/software/user/open/python/2.7.13/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.0-Linux/share/spades/spades_pipeline/scripts/compress_all.py --input_file /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/corrected/corrected.yaml --ext_python_modules_home /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.0-Linux/share/spades --max_threads 20 --output_dir /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/corrected --gzip_output
true
true
/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.0-Linux/bin/spades-core /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/K21/configs/config.info
/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.0-Linux/bin/spades-core /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/K33/configs/config.info
/share/software/user/open/python/2.7.13/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.0-Linux/share/spades/spades_pipeline/scripts/copy_files.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/K33/before_rr.fasta /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/before_rr.fasta /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/K33/assembly_graph_after_simplification.gfa /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/assembly_graph_after_simplification.gfa /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/K33/final_contigs.fasta /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/contigs.fasta /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/K33/first_pe_contigs.fasta /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/first_pe_contigs.fasta /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/K33/strain_graph.gfa /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/strain_graph.gfa /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/K33/scaffolds.fasta /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/scaffolds.fasta /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/K33/scaffolds.paths /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/scaffolds.paths /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/K33/assembly_graph_with_scaffolds.gfa /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/assembly_graph_with_scaffolds.gfa /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/K33/assembly_graph.fastg /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/assembly_graph.fastg /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/K33/final_contigs.paths /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/contigs.paths
true
/share/software/user/open/python/2.7.13/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.0-Linux/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/scaffolds.fasta --misc_dir /oak/stanford/groups/akundaje/marinovg/ENCODE4/ATAC/2021-01-21-ATAC-seq-assembly/SPAdes-3.15-Squirrel_monkey_ID_2655_Sample2418/misc --threshold_for_breaking_scaffolds 3
true