/home/jcatchen/research/hg/chromonomer/chromonomer -p /home/jcatchen/research/chromonomer_paper/nco/genetic_map/20160830_rockcod_consensus.tsv -s /home/jcatchen/research/chromonomer_paper/nco/aligned/nco_markers_vs_nco.bam -a /home/jcatchen/research/chromonomer_paper/nco/genome/GCA_000735185.1_NC01_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp -o /home/jcatchen/research/chromonomer_paper/nco/chrr/20190908_nco/ --fasta /home/jcatchen/research/chromonomer_paper/nco/genome/GCA_000735185.1_NC01_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna --scaffold_prefix NCO --data_version 20190908_nco --description Chromonomer 1.10; rockcod consensus map assembly. /home/jcatchen/research/hg/chromonomer/chromonomer version 1.10 executed 2019-09-10 14:36:44 3847 scaffolds in the linkage map, from 2803 original scaffolds. Splits Num Scaffolds 0 2533 1 163 2 54 3 26 4 8 5 6 6 1 7 2 8 1 9 1 12 1 20 1 27 1 45 1 77 1 134 1 139 1 142 1 6394 markers in the final map; 1436 inconsistent markers excluded. Chromosome lengths: LG1: 39117920bp LG10: 31489328bp LG11: 29831625bp LG2: 41074319bp LG3: 38712909bp LG4: 39904351bp LG5: 33168792bp LG6: 43849810bp LG7: 36010389bp LG8: 34862490bp LG9: 31456939bp Total length: 399478872bp Unmodified genome sequence FASTA: 636595335bp. Integrated genome sequence FASTA: Wrote 399862472bp of integrated sequence [383600bp scaffold join gaps]; 236032685bp of unplaced sequences; 635895157bp total length.