set -e
true
true
/opt/software/SPAdes/3.15.3-GCC-11.2.0/bin/spades-hammer /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/corrected/configs/config.info
/opt/software/Python/3.9.6-GCCcore-11.2.0/bin/python /opt/software/SPAdes/3.15.3-GCC-11.2.0/share/spades/spades_pipeline/scripts/compress_all.py --input_file /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/corrected/corrected.yaml --ext_python_modules_home /opt/software/SPAdes/3.15.3-GCC-11.2.0/share/spades --max_threads 4 --output_dir /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/corrected --gzip_output
true
true
/opt/software/SPAdes/3.15.3-GCC-11.2.0/bin/spades-core /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/K21/configs/config.info
/opt/software/SPAdes/3.15.3-GCC-11.2.0/bin/spades-core /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/K33/configs/config.info
/opt/software/SPAdes/3.15.3-GCC-11.2.0/bin/spades-core /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/K55/configs/config.info
/opt/software/Python/3.9.6-GCCcore-11.2.0/bin/python /opt/software/SPAdes/3.15.3-GCC-11.2.0/share/spades/spades_pipeline/scripts/copy_files.py /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/K55/before_rr.fasta /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/before_rr.fasta /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/K55/assembly_graph_after_simplification.gfa /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/assembly_graph_after_simplification.gfa /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/K55/final_contigs.fasta /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/contigs.fasta /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/K55/first_pe_contigs.fasta /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/first_pe_contigs.fasta /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/K55/strain_graph.gfa /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/strain_graph.gfa /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/K55/scaffolds.fasta /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/scaffolds.fasta /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/K55/scaffolds.paths /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/scaffolds.paths /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/K55/assembly_graph_with_scaffolds.gfa /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/assembly_graph_with_scaffolds.gfa /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/K55/assembly_graph.fastg /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/assembly_graph.fastg /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/K55/final_contigs.paths /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/contigs.paths
true
/opt/software/Python/3.9.6-GCCcore-11.2.0/bin/python /opt/software/SPAdes/3.15.3-GCC-11.2.0/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/scaffolds.fasta --misc_dir /glfs/brick01/gv0/mramseylab/TnSeq_THP/snakemake/Snakemake_Training/01_genome/misc --threshold_for_breaking_scaffolds 3
true