set -e
true
/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/bin/spades-hammer /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/corrected/configs/config.info
/usr/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/scripts/compress_all.py --input_file /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/corrected/corrected.yaml --ext_python_modules_home /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades --max_threads 60 --output_dir /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/corrected --gzip_output
true
true
/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/bin/spades-core /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/K21/configs/config.info
/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/bin/spades-core /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/K33/configs/config.info
/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/bin/spades-core /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/K55/configs/config.info
/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/bin/spades-core /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/K77/configs/config.info
/usr/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/scripts/copy_files.py /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/K77/before_rr.fasta /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/before_rr.fasta /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/K77/final_contigs.fasta /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/contigs.fasta /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/K77/first_pe_contigs.fasta /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/first_pe_contigs.fasta /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/K77/scaffolds.fasta /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/scaffolds.fasta /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/K77/scaffolds.paths /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/scaffolds.paths /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/K77/assembly_graph_with_scaffolds.gfa /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/assembly_graph_with_scaffolds.gfa /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/K77/assembly_graph.fastg /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/assembly_graph.fastg /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/K77/final_contigs.paths /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/contigs.paths
true
/usr/bin/python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/scaffolds.fasta --misc_dir /srv/scratch/marinovg/SPAdes-3.14-L1397-Sphacelaria_sp_gDNA/misc --threshold_for_breaking_scaffolds 3
true