set -e
true
true
/usr/local/bin/spades-core /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/K127/configs/config.info
/usr/bin/python /usr/local/share/spades/spades_pipeline/scripts/copy_files.py /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/K127/before_rr.fasta /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/before_rr.fasta /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/K127/assembly_graph_after_simplification.gfa /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/assembly_graph_after_simplification.gfa /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/K127/final_contigs.fasta /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/contigs.fasta /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/K127/first_pe_contigs.fasta /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/first_pe_contigs.fasta /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/K127/strain_graph.gfa /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/strain_graph.gfa /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/K127/scaffolds.fasta /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/scaffolds.fasta /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/K127/scaffolds.paths /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/scaffolds.paths /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/K127/assembly_graph_with_scaffolds.gfa /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/assembly_graph_with_scaffolds.gfa /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/K127/assembly_graph.fastg /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/assembly_graph.fastg /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/K127/final_contigs.paths /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/contigs.paths
true
/usr/bin/python /usr/local/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/scaffolds.fasta --misc_dir /mnt/DGK_KLIF/data/klif/reads-for-assembly/trainingsets2/StaphPseudintermedius/pGCA_000009585.1_ASM958v1_genomic/misc --threshold_for_breaking_scaffolds 3
true