/home/bionano/tools/access/1.0/../../pipeline/1.0/Pipeline/1.0/pipelineCL.py -l /home/bionano/access/local/jobs/10228508/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/10228508/RawMolecules.filtered.bnx -y -d -U -i 5 -F 1 -W 1 -c 1 -a /home/bionano/access/share/jobs/10228508/optArguments_nonhaplotype_noES_noCut_DLE1_saphyr.xml -r /home/bionano/access/share/jobs/10228508/b73_v4_DLE-1_0kb_0labels.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+10228508+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/10228508/output/all.bnx):
Total number of molecules: 859750
Total length (Mbp)       : 357491.903
Average length (kbp)     :    415.809
Molecule N50 (kbp)       :    402.801
Label density (/100kb)   :     17.758

Stage Summary: CharacterizeD_Assembly
Number Genome Maps: 4801
Total Genome Map Length  (Mbp): 3185.699
Mean Genome Map Length   (Mbp):    0.664
Median Genome Map Length (Mbp):    0.499
Genome Map N50           (Mbp):    0.586
Total Reference Length   (Mbp): 2134.249
Total Genome Map Length / Reference Length :    1.493
Total number of aligned Genome Maps    : 0 (0.00)
Total Aligned Length (Mbp)             :    0.000
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.000
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_refineB1
Number Genome Maps: 4821
Total Genome Map Length  (Mbp): 2794.568
Mean Genome Map Length   (Mbp):    0.580
Median Genome Map Length (Mbp):    0.424
Genome Map N50           (Mbp):    0.482
Total Reference Length   (Mbp): 2134.249
Total Genome Map Length / Reference Length :    1.309
Total number of aligned Genome Maps    : 0 (0.00)
Total Aligned Length (Mbp)             :    0.000
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.000
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_Merge0
Number Genome Maps: 265
Total Genome Map Length  (Mbp):  625.889
Mean Genome Map Length   (Mbp):    2.362
Median Genome Map Length (Mbp):    0.184
Genome Map N50           (Mbp):   21.021
Total Reference Length   (Mbp): 2134.249
Total Genome Map Length / Reference Length :    0.293
Total number of aligned Genome Maps    : 0 (0.00)
Total Aligned Length (Mbp)             :    0.000
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.000
Total Unique Aligned Length / Reference Length:    0.000

Automatically determined noise parameters:
NLV:7.988
PLV:5.011
bpp:502.09
readparameters:/home/bionano/access/local/jobs/10228508/output/contigs/auto_noise/autoNoise1.errbin
res:2.933
sd:0.02473
sf:0.14845
sr:0.02577

Molecule Stats (/home/bionano/access/local/jobs/10228508/output/contigs/auto_noise/autoNoise1_rescaled.bnx):
Total number of molecules: 843447
Total length (Mbp)       : 348184.966
Average length (kbp)     :    412.812
Molecule N50 (kbp)       :    400.682
Label density (/100kb)   :     17.288
Raw coverage of reference (X):    163.142

Molecules aligned to reference:
Total number of aligned molecules  :      6824
Fraction of aligned molecules      :         0.008
Total molecule align length (Mbp)  :       781.2
Total reference align length (Mbp) :       802.8
Effective coverage of reference (X):         0.376
Average aligned length (kbp)       :       114.5
Fraction aligned length            :         0.002
Average confidence                 :        11.8

Stage Summary: CharacterizeD_Assembly
Number Genome Maps: 3847
Total Genome Map Length  (Mbp): 2667.758
Mean Genome Map Length   (Mbp):    0.693
Median Genome Map Length (Mbp):    0.493
Genome Map N50           (Mbp):    0.603
Total Reference Length   (Mbp): 2134.249
Total Genome Map Length / Reference Length :    1.250
Total number of aligned Genome Maps    : 0 (0.00)
Total Aligned Length (Mbp)             :    0.000
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.000
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_refineB1
Number Genome Maps: 3880
Total Genome Map Length  (Mbp): 2357.419
Mean Genome Map Length   (Mbp):    0.608
Median Genome Map Length (Mbp):    0.419
Genome Map N50           (Mbp):    0.488
Total Reference Length   (Mbp): 2134.249
Total Genome Map Length / Reference Length :    1.105
Total number of aligned Genome Maps    : 0 (0.00)
Total Aligned Length (Mbp)             :    0.000
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.000
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_Merge0
Number Genome Maps: 51
Total Genome Map Length  (Mbp):  677.505
Mean Genome Map Length   (Mbp):   13.284
Median Genome Map Length (Mbp):    2.673
Genome Map N50           (Mbp):   41.523
Total Reference Length   (Mbp): 2134.249
Total Genome Map Length / Reference Length :    0.317
Total number of aligned Genome Maps    : 0 (0.00)
Total Aligned Length (Mbp)             :    0.000
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.000
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_Merge1
Number Genome Maps: 37
Total Genome Map Length  (Mbp):  675.805
Mean Genome Map Length   (Mbp):   18.265
Median Genome Map Length (Mbp):    6.477
Genome Map N50           (Mbp):   45.641
Total Reference Length   (Mbp): 2134.249
Total Genome Map Length / Reference Length :    0.317
Total number of aligned Genome Maps    : 0 (0.00)
Total Aligned Length (Mbp)             :    0.000
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.000
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_Merge2
Number Genome Maps: 36
Total Genome Map Length  (Mbp):  676.329
Mean Genome Map Length   (Mbp):   18.787
Median Genome Map Length (Mbp):    6.473
Genome Map N50           (Mbp):   47.580
Total Reference Length   (Mbp): 2134.249
Total Genome Map Length / Reference Length :    0.317
Total number of aligned Genome Maps    : 0 (0.00)
Total Aligned Length (Mbp)             :    0.000
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.000
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_Merge3
Number Genome Maps: 36
Total Genome Map Length  (Mbp):  677.014
Mean Genome Map Length   (Mbp):   18.806
Median Genome Map Length (Mbp):    6.552
Genome Map N50           (Mbp):   47.580
Total Reference Length   (Mbp): 2134.249
Total Genome Map Length / Reference Length :    0.317
Total number of aligned Genome Maps    : 0 (0.00)
Total Aligned Length (Mbp)             :    0.000
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.000
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_Merge4
Number Genome Maps: 36
Total Genome Map Length  (Mbp):  677.291
Mean Genome Map Length   (Mbp):   18.814
Median Genome Map Length (Mbp):    6.628
Genome Map N50           (Mbp):   47.580
Total Reference Length   (Mbp): 2134.249
Total Genome Map Length / Reference Length :    0.317
Total number of aligned Genome Maps    : 0 (0.00)
Total Aligned Length (Mbp)             :    0.000
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.000
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_Merge5
Number Genome Maps: 36
Total Genome Map Length  (Mbp):  677.756
Mean Genome Map Length   (Mbp):   18.827
Median Genome Map Length (Mbp):    6.706
Genome Map N50           (Mbp):   47.580
Total Reference Length   (Mbp): 2134.249
Total Genome Map Length / Reference Length :    0.318
Total number of aligned Genome Maps    : 0 (0.00)
Total Aligned Length (Mbp)             :    0.000
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.000
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeF_refineFinal1
Number Genome Maps: 38
Total Genome Map Length  (Mbp):  675.866
Mean Genome Map Length   (Mbp):   17.786
Median Genome Map Length (Mbp):    5.531
Genome Map N50           (Mbp):   47.435
Total Reference Length   (Mbp): 2134.249
Total Genome Map Length / Reference Length :    0.317
Total number of aligned Genome Maps    : 0 (0.00)
Total Aligned Length (Mbp)             :    0.000
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.000
Total Unique Aligned Length / Reference Length:    0.000

SV detect: svdetect_exp_refineFinal1_sv
Full SV summary:
Total number of SVs: 0

Molecule Stats (/home/bionano/access/local/jobs/10228508/output/contigs/auto_noise/autoNoise1_rescaled.bnx):
Raw coverage of assembly (X):    515.169

Molecules aligned to assembly:
Total number of aligned molecules  :    792116
Fraction of aligned molecules      :         0.939
Total molecule align length (Mbp)  :    267575.6
Total  assembly align length (Mbp) :    269128.4
Effective coverage of  assembly (X):       398.198
Average aligned length (kbp)       :       337.8
Fraction aligned length            :         0.768
Average confidence                 :        46.6

Filtered SV summary (Entries with low confidence for the SV calls, except duplications, are filtered out)
Total number of SVs: 0

Clustered SV summary (SVs except translocation with >50% interval overlap and >80% size overlap are collapsed; translocation calls within 35kb are collapsed):
Deletions                          :    0
Insertions                         :    0
Duplications                       :    0
Inversion breakpoints              :    0
Interchr. translocation breakpoints:    0
Intrachr. translocation breakpoints:    0