set -e
true
true
/net/clusterhn.cluster.com/opt/software/SPAdes/3.15.2-GCC-10.2.0/bin/spades-hammer /data/mramseylab/Soralis/spades_out/corrected/configs/config.info
/opt/software/Python/3.8.6-GCCcore-10.2.0/bin/python /net/clusterhn.cluster.com/opt/software/SPAdes/3.15.2-GCC-10.2.0/share/spades/spades_pipeline/scripts/compress_all.py --input_file /data/mramseylab/Soralis/spades_out/corrected/corrected.yaml --ext_python_modules_home /net/clusterhn.cluster.com/opt/software/SPAdes/3.15.2-GCC-10.2.0/share/spades --max_threads 10 --output_dir /data/mramseylab/Soralis/spades_out/corrected --gzip_output
true
true
/net/clusterhn.cluster.com/opt/software/SPAdes/3.15.2-GCC-10.2.0/bin/spades-core /data/mramseylab/Soralis/spades_out/K21/configs/config.info
/net/clusterhn.cluster.com/opt/software/SPAdes/3.15.2-GCC-10.2.0/bin/spades-core /data/mramseylab/Soralis/spades_out/K33/configs/config.info
/net/clusterhn.cluster.com/opt/software/SPAdes/3.15.2-GCC-10.2.0/bin/spades-core /data/mramseylab/Soralis/spades_out/K55/configs/config.info
/net/clusterhn.cluster.com/opt/software/SPAdes/3.15.2-GCC-10.2.0/bin/spades-core /data/mramseylab/Soralis/spades_out/K77/configs/config.info
/opt/software/Python/3.8.6-GCCcore-10.2.0/bin/python /net/clusterhn.cluster.com/opt/software/SPAdes/3.15.2-GCC-10.2.0/share/spades/spades_pipeline/scripts/copy_files.py /data/mramseylab/Soralis/spades_out/K77/before_rr.fasta /data/mramseylab/Soralis/spades_out/before_rr.fasta /data/mramseylab/Soralis/spades_out/K77/assembly_graph_after_simplification.gfa /data/mramseylab/Soralis/spades_out/assembly_graph_after_simplification.gfa /data/mramseylab/Soralis/spades_out/K77/final_contigs.fasta /data/mramseylab/Soralis/spades_out/contigs.fasta /data/mramseylab/Soralis/spades_out/K77/first_pe_contigs.fasta /data/mramseylab/Soralis/spades_out/first_pe_contigs.fasta /data/mramseylab/Soralis/spades_out/K77/strain_graph.gfa /data/mramseylab/Soralis/spades_out/strain_graph.gfa /data/mramseylab/Soralis/spades_out/K77/scaffolds.fasta /data/mramseylab/Soralis/spades_out/scaffolds.fasta /data/mramseylab/Soralis/spades_out/K77/scaffolds.paths /data/mramseylab/Soralis/spades_out/scaffolds.paths /data/mramseylab/Soralis/spades_out/K77/assembly_graph_with_scaffolds.gfa /data/mramseylab/Soralis/spades_out/assembly_graph_with_scaffolds.gfa /data/mramseylab/Soralis/spades_out/K77/assembly_graph.fastg /data/mramseylab/Soralis/spades_out/assembly_graph.fastg /data/mramseylab/Soralis/spades_out/K77/final_contigs.paths /data/mramseylab/Soralis/spades_out/contigs.paths
true
/opt/software/Python/3.8.6-GCCcore-10.2.0/bin/python /net/clusterhn.cluster.com/opt/software/SPAdes/3.15.2-GCC-10.2.0/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /data/mramseylab/Soralis/spades_out/scaffolds.fasta --misc_dir /data/mramseylab/Soralis/spades_out/misc --threshold_for_breaking_scaffolds 3
true