/home/bionano/tools/access/1.0/../../pipeline/1.0/Pipeline/1.0/pipelineCL.py -l /home/bionano/access/local/jobs/10229312/output -t /home/bionano/tools/access/1.0/../../pipeline/1.0/RefAligner/1.0 -C /home/bionano/tools/access/1.0/../../pipeline/1.0/Pipeline/1.0/clusterArguments_saphyr_supermicro.xml -b /home/bionano/access/local/jobs/10229312/RawMolecules.filtered.filtered.bnx -y -d -U -i 5 -F 1 -W 1 -c 1 -a /home/bionano/access/share/jobs/10229312/optArguments_nonhaplotype_noES_noCut_DLE1_saphyr.xml -r /home/bionano/access/share/jobs/10229312/Musa_Calcutta4_EXP_REFINEFINAL1.cmap -R 0.5 --compute-confidence non_human --species-reference other -f 0.08 -J 56 -j 56 -jp 48 -je 48 -Tn 56 -N 4 -json {"jobID":"jobs+10229312+startPipeline","toolsVer":"1.7.96","solveVer":"Solve3.7_03302022_283"} --docker -NoExtCharCheck -NoCheckFiles Informatics Report Version: 2.3.0 Tools Version: 1.7.96 Solve Version: Solve3.7_03302022_283 Pipeline Version: 3.7.1 RefAligner Version: 12642 Molecule Stats (/home/bionano/access/local/jobs/10229312/output/all.bnx): Total number of molecules: 663224 Total length (Mbp) : 329793.225 Average length (kbp) : 497.258 Molecule N50 (kbp) : 479.625 Label density (/100kb) : 18.786 Stage Summary: CharacterizeD_Assembly Number Genome Maps: 1975 Total Genome Map Length (Mbp): 1877.130 Mean Genome Map Length (Mbp): 0.950 Median Genome Map Length (Mbp): 0.540 Genome Map N50 (Mbp): 0.866 Total Reference Length (Mbp): 675.866 Total Genome Map Length / Reference Length : 2.777 Total number of aligned Genome Maps : 467 (0.24) Total Aligned Length (Mbp) : 285.193 Total Aligned Length / Reference Length: 0.422 Total Unique Aligned Length (Mbp) : 60.538 Total Unique Aligned Length / Reference Length: 0.090 Stage Summary: CharacterizeD_refineB1 Number Genome Maps: 1994 Total Genome Map Length (Mbp): 1714.997 Mean Genome Map Length (Mbp): 0.860 Median Genome Map Length (Mbp): 0.462 Genome Map N50 (Mbp): 0.743 Total Reference Length (Mbp): 675.866 Total Genome Map Length / Reference Length : 2.537 Total number of aligned Genome Maps : 578 (0.29) Total Aligned Length (Mbp) : 495.081 Total Aligned Length / Reference Length: 0.733 Total Unique Aligned Length (Mbp) : 187.388 Total Unique Aligned Length / Reference Length: 0.277 Stage Summary: CharacterizeD_Merge0 Number Genome Maps: 556 Total Genome Map Length (Mbp): 607.749 Mean Genome Map Length (Mbp): 1.093 Median Genome Map Length (Mbp): 0.177 Genome Map N50 (Mbp): 13.157 Total Reference Length (Mbp): 675.866 Total Genome Map Length / Reference Length : 0.899 Total number of aligned Genome Maps : 54 (0.10) Total Aligned Length (Mbp) : 198.314 Total Aligned Length / Reference Length: 0.293 Total Unique Aligned Length (Mbp) : 197.848 Total Unique Aligned Length / Reference Length: 0.293 Automatically determined noise parameters: NLV:7.805 PLV:5.005 bpp:481.12 readparameters:/home/bionano/access/local/jobs/10229312/output/contigs/auto_noise/autoNoise1.errbin res:3.061 sd:0.01777 sf:0.13051 sr:0.01939 Stage Summary: CharacterizeD_Assembly Number Genome Maps: 2310 Total Genome Map Length (Mbp): 2033.141 Mean Genome Map Length (Mbp): 0.880 Median Genome Map Length (Mbp): 0.544 Genome Map N50 (Mbp): 0.752 Total Reference Length (Mbp): 675.866 Total Genome Map Length / Reference Length : 3.008 Total number of aligned Genome Maps : 521 (0.23) Total Aligned Length (Mbp) : 317.338 Total Aligned Length / Reference Length: 0.470 Total Unique Aligned Length (Mbp) : 87.896 Total Unique Aligned Length / Reference Length: 0.130 Molecule Stats (/home/bionano/access/local/jobs/10229312/output/contigs/auto_noise/autoNoise1_rescaled.bnx): Total number of molecules: 619928 Total length (Mbp) : 296890.830 Average length (kbp) : 478.912 Molecule N50 (kbp) : 463.567 Label density (/100kb) : 16.585 Raw coverage of reference (X): 439.275 Molecules aligned to reference: Total number of aligned molecules : 174322 Fraction of aligned molecules : 0.281 Total molecule align length (Mbp) : 55124.0 Total reference align length (Mbp) : 55868.5 Effective coverage of reference (X): 82.662 Average aligned length (kbp) : 316.2 Fraction aligned length : 0.186 Average confidence : 22.3 Stage Summary: CharacterizeD_refineB1 Number Genome Maps: 2334 Total Genome Map Length (Mbp): 1829.707 Mean Genome Map Length (Mbp): 0.784 Median Genome Map Length (Mbp): 0.459 Genome Map N50 (Mbp): 0.625 Total Reference Length (Mbp): 675.866 Total Genome Map Length / Reference Length : 2.707 Total number of aligned Genome Maps : 612 (0.26) Total Aligned Length (Mbp) : 516.582 Total Aligned Length / Reference Length: 0.764 Total Unique Aligned Length (Mbp) : 202.483 Total Unique Aligned Length / Reference Length: 0.300 Stage Summary: CharacterizeD_Merge0 Number Genome Maps: 56 Total Genome Map Length (Mbp): 681.527 Mean Genome Map Length (Mbp): 12.170 Median Genome Map Length (Mbp): 2.939 Genome Map N50 (Mbp): 45.328 Total Reference Length (Mbp): 675.866 Total Genome Map Length / Reference Length : 1.008 Total number of aligned Genome Maps : 39 (0.70) Total Aligned Length (Mbp) : 210.744 Total Aligned Length / Reference Length: 0.312 Total Unique Aligned Length (Mbp) : 195.180 Total Unique Aligned Length / Reference Length: 0.289 Stage Summary: CharacterizeD_Merge1 Number Genome Maps: 50 Total Genome Map Length (Mbp): 680.369 Mean Genome Map Length (Mbp): 13.607 Median Genome Map Length (Mbp): 3.230 Genome Map N50 (Mbp): 47.040 Total Reference Length (Mbp): 675.866 Total Genome Map Length / Reference Length : 1.007 Total number of aligned Genome Maps : 37 (0.74) Total Aligned Length (Mbp) : 208.945 Total Aligned Length / Reference Length: 0.309 Total Unique Aligned Length (Mbp) : 196.484 Total Unique Aligned Length / Reference Length: 0.291 Stage Summary: CharacterizeD_Merge2 Number Genome Maps: 47 Total Genome Map Length (Mbp): 678.111 Mean Genome Map Length (Mbp): 14.428 Median Genome Map Length (Mbp): 3.231 Genome Map N50 (Mbp): 47.040 Total Reference Length (Mbp): 675.866 Total Genome Map Length / Reference Length : 1.003 Total number of aligned Genome Maps : 36 (0.77) Total Aligned Length (Mbp) : 210.095 Total Aligned Length / Reference Length: 0.311 Total Unique Aligned Length (Mbp) : 200.989 Total Unique Aligned Length / Reference Length: 0.297 Stage Summary: CharacterizeD_Merge3 Number Genome Maps: 46 Total Genome Map Length (Mbp): 677.823 Mean Genome Map Length (Mbp): 14.735 Median Genome Map Length (Mbp): 3.289 Genome Map N50 (Mbp): 47.040 Total Reference Length (Mbp): 675.866 Total Genome Map Length / Reference Length : 1.003 Total number of aligned Genome Maps : 36 (0.78) Total Aligned Length (Mbp) : 213.290 Total Aligned Length / Reference Length: 0.316 Total Unique Aligned Length (Mbp) : 203.552 Total Unique Aligned Length / Reference Length: 0.301 Stage Summary: CharacterizeD_Merge4 Number Genome Maps: 46 Total Genome Map Length (Mbp): 678.472 Mean Genome Map Length (Mbp): 14.749 Median Genome Map Length (Mbp): 3.289 Genome Map N50 (Mbp): 47.040 Total Reference Length (Mbp): 675.866 Total Genome Map Length / Reference Length : 1.004 Total number of aligned Genome Maps : 36 (0.78) Total Aligned Length (Mbp) : 211.383 Total Aligned Length / Reference Length: 0.313 Total Unique Aligned Length (Mbp) : 199.027 Total Unique Aligned Length / Reference Length: 0.294 Stage Summary: CharacterizeD_Merge5 Number Genome Maps: 44 Total Genome Map Length (Mbp): 678.777 Mean Genome Map Length (Mbp): 15.427 Median Genome Map Length (Mbp): 3.463 Genome Map N50 (Mbp): 47.040 Total Reference Length (Mbp): 675.866 Total Genome Map Length / Reference Length : 1.004 Total number of aligned Genome Maps : 36 (0.82) Total Aligned Length (Mbp) : 202.553 Total Aligned Length / Reference Length: 0.300 Total Unique Aligned Length (Mbp) : 189.555 Total Unique Aligned Length / Reference Length: 0.280 Stage Summary: CharacterizeF_refineFinal1 Number Genome Maps: 44 Total Genome Map Length (Mbp): 678.142 Mean Genome Map Length (Mbp): 15.412 Median Genome Map Length (Mbp): 3.470 Genome Map N50 (Mbp): 46.977 Total Reference Length (Mbp): 675.866 Total Genome Map Length / Reference Length : 1.003 Total number of aligned Genome Maps : 36 (0.82) Total Aligned Length (Mbp) : 195.745 Total Aligned Length / Reference Length: 0.290 Total Unique Aligned Length (Mbp) : 183.912 Total Unique Aligned Length / Reference Length: 0.272 SV detect: svdetect_exp_refineFinal1_sv Full SV summary: SV type : N : N/tot complex : 112 : 0.0952 deletion : 425 : 0.3611 deletion_tiny : 42 : 0.0357 duplication : 10 : 0.0085 duplication_inverted : 24 : 0.0204 end : 25 : 0.0212 insertion : 417 : 0.3543 insertion_tiny : 26 : 0.0221 inversion : 8 : 0.0068 inversion_partial : 14 : 0.0119 inversion_repeat : 6 : 0.0051 translocation_interchr : 66 : 0.0561 translocation_intrachr : 2 : 0.0017 Total number of SVs: 1177 Molecule Stats (/home/bionano/access/local/jobs/10229312/output/contigs/auto_noise/autoNoise1_rescaled.bnx): Raw coverage of assembly (X): 437.800 Molecules aligned to assembly: Total number of aligned molecules : 590057 Fraction of aligned molecules : 0.952 Total molecule align length (Mbp) : 226118.6 Total assembly align length (Mbp) : 227225.1 Effective coverage of assembly (X): 335.070 Average aligned length (kbp) : 383.2 Fraction aligned length : 0.762 Average confidence : 55.6 Filtered SV summary (Entries with low confidence for the SV calls, except duplications, are filtered out) SV type : N : N/tot deletion : 419 : 0.4496 duplication : 10 : 0.0107 duplication_inverted : 24 : 0.0258 insertion : 403 : 0.4324 inversion : 4 : 0.0043 inversion_partial : 4 : 0.0043 translocation_interchr : 66 : 0.0708 translocation_intrachr : 2 : 0.0021 Total number of SVs: 932 Clustered SV summary (SVs except translocation with >50% interval overlap and >80% size overlap are collapsed; translocation calls within 35kb are collapsed): Deletions : 410 Insertions : 387 Duplications : 7 Inversion breakpoints : 4 Interchr. translocation breakpoints: 65 Intrachr. translocation breakpoints: 2