/home/bionano/tools/access/1.0/../../pipeline/1.0/Pipeline/1.0/pipelineCL.py -l /home/bionano/access/local/jobs/10230251/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/10230251/RawMolecules.filtered.bnx -y -d -U -i 5 -F 1 -W 1 -c 1 -a /home/bionano/access/share/jobs/10230251/optArguments_nonhaplotype_noES_noCut_DLE1_saphyr.xml -r /home/bionano/access/share/jobs/10230251/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+10230251+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/10230251/output/all.bnx):
Total number of molecules: 783488
Total length (Mbp)       : 280921.525
Average length (kbp)     :    358.552
Molecule N50 (kbp)       :    344.538
Label density (/100kb)   :     17.989

Stage Summary: CharacterizeD_Assembly
Number Genome Maps: 1825
Total Genome Map Length  (Mbp): 2106.349
Mean Genome Map Length   (Mbp):    1.154
Median Genome Map Length (Mbp):    0.426
Genome Map N50           (Mbp):   18.174
Total Reference Length   (Mbp):  675.866
Total Genome Map Length / Reference Length :    3.117
Total number of aligned Genome Maps    : 2 (0.00)
Total Aligned Length (Mbp)             :    0.199
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.199
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_refineB1
Number Genome Maps: 1877
Total Genome Map Length  (Mbp): 1997.249
Mean Genome Map Length   (Mbp):    1.064
Median Genome Map Length (Mbp):    0.362
Genome Map N50           (Mbp):   18.295
Total Reference Length   (Mbp):  675.866
Total Genome Map Length / Reference Length :    2.955
Total number of aligned Genome Maps    : 3 (0.00)
Total Aligned Length (Mbp)             :    0.377
Total Aligned Length / Reference Length:    0.001
Total Unique Aligned Length (Mbp)      :    0.227
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_Merge0
Number Genome Maps: 799
Total Genome Map Length  (Mbp): 1167.809
Mean Genome Map Length   (Mbp):    1.462
Median Genome Map Length (Mbp):    0.256
Genome Map N50           (Mbp):   13.188
Total Reference Length   (Mbp):  675.866
Total Genome Map Length / Reference Length :    1.728
Total number of aligned Genome Maps    : 1 (0.00)
Total Aligned Length (Mbp)             :    0.151
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.151
Total Unique Aligned Length / Reference Length:    0.000

Automatically determined noise parameters:
NLV:11.663
PLV:6.119
bpp:504.33
readparameters:/home/bionano/access/local/jobs/10230251/output/contigs/auto_noise/autoNoise1.errbin
res:2.92
sd:0.02943
sf:0.14877
sr:0.0242

Stage Summary: CharacterizeD_Assembly
Number Genome Maps: 1882
Total Genome Map Length  (Mbp): 2151.336
Mean Genome Map Length   (Mbp):    1.143
Median Genome Map Length (Mbp):    0.447
Genome Map N50           (Mbp):   15.478
Total Reference Length   (Mbp):  675.866
Total Genome Map Length / Reference Length :    3.183
Total number of aligned Genome Maps    : 1 (0.00)
Total Aligned Length (Mbp)             :    0.071
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.071
Total Unique Aligned Length / Reference Length:    0.000

Molecule Stats (/home/bionano/access/local/jobs/10230251/output/contigs/auto_noise/autoNoise1_rescaled.bnx):
Total number of molecules: 737618
Total length (Mbp)       : 253231.426
Average length (kbp)     :    343.310
Molecule N50 (kbp)       :    333.568
Label density (/100kb)   :     15.673
Raw coverage of reference (X):    374.677

Molecules aligned to reference:
Total number of aligned molecules  :      1355
Fraction of aligned molecules      :         0.002
Total molecule align length (Mbp)  :       170.4
Total reference align length (Mbp) :       174.6
Effective coverage of reference (X):         0.258
Average aligned length (kbp)       :       125.8
Fraction aligned length            :         0.001
Average confidence                 :        12.7

Stage Summary: CharacterizeD_refineB1
Number Genome Maps: 1918
Total Genome Map Length  (Mbp): 2032.658
Mean Genome Map Length   (Mbp):    1.060
Median Genome Map Length (Mbp):    0.380
Genome Map N50           (Mbp):   17.381
Total Reference Length   (Mbp):  675.866
Total Genome Map Length / Reference Length :    3.007
Total number of aligned Genome Maps    : 4 (0.00)
Total Aligned Length (Mbp)             :    0.459
Total Aligned Length / Reference Length:    0.001
Total Unique Aligned Length (Mbp)      :    0.232
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_Merge0
Number Genome Maps: 112
Total Genome Map Length  (Mbp): 1285.110
Mean Genome Map Length   (Mbp):   11.474
Median Genome Map Length (Mbp):    1.916
Genome Map N50           (Mbp):   43.186
Total Reference Length   (Mbp):  675.866
Total Genome Map Length / Reference Length :    1.901
Total number of aligned Genome Maps    : 2 (0.02)
Total Aligned Length (Mbp)             :    0.231
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.231
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_Merge1
Number Genome Maps: 92
Total Genome Map Length  (Mbp): 1290.858
Mean Genome Map Length   (Mbp):   14.031
Median Genome Map Length (Mbp):    2.341
Genome Map N50           (Mbp):   45.503
Total Reference Length   (Mbp):  675.866
Total Genome Map Length / Reference Length :    1.910
Total number of aligned Genome Maps    : 1 (0.01)
Total Aligned Length (Mbp)             :    0.160
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.160
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_Merge2
Number Genome Maps: 91
Total Genome Map Length  (Mbp): 1294.103
Mean Genome Map Length   (Mbp):   14.221
Median Genome Map Length (Mbp):    2.353
Genome Map N50           (Mbp):   45.663
Total Reference Length   (Mbp):  675.866
Total Genome Map Length / Reference Length :    1.915
Total number of aligned Genome Maps    : 2 (0.02)
Total Aligned Length (Mbp)             :    0.232
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.232
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_Merge3
Number Genome Maps: 88
Total Genome Map Length  (Mbp): 1295.591
Mean Genome Map Length   (Mbp):   14.723
Median Genome Map Length (Mbp):    2.501
Genome Map N50           (Mbp):   45.820
Total Reference Length   (Mbp):  675.866
Total Genome Map Length / Reference Length :    1.917
Total number of aligned Genome Maps    : 2 (0.02)
Total Aligned Length (Mbp)             :    0.232
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.232
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_Merge4
Number Genome Maps: 87
Total Genome Map Length  (Mbp): 1297.620
Mean Genome Map Length   (Mbp):   14.915
Median Genome Map Length (Mbp):    2.408
Genome Map N50           (Mbp):   45.978
Total Reference Length   (Mbp):  675.866
Total Genome Map Length / Reference Length :    1.920
Total number of aligned Genome Maps    : 2 (0.02)
Total Aligned Length (Mbp)             :    0.232
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.232
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeD_Merge5
Number Genome Maps: 82
Total Genome Map Length  (Mbp): 1296.662
Mean Genome Map Length   (Mbp):   15.813
Median Genome Map Length (Mbp):    3.211
Genome Map N50           (Mbp):   46.139
Total Reference Length   (Mbp):  675.866
Total Genome Map Length / Reference Length :    1.919
Total number of aligned Genome Maps    : 2 (0.02)
Total Aligned Length (Mbp)             :    0.232
Total Aligned Length / Reference Length:    0.000
Total Unique Aligned Length (Mbp)      :    0.232
Total Unique Aligned Length / Reference Length:    0.000

Stage Summary: CharacterizeF_refineFinal1
Number Genome Maps: 85
Total Genome Map Length  (Mbp): 1296.079
Mean Genome Map Length   (Mbp):   15.248
Median Genome Map Length (Mbp):    2.918
Genome Map N50           (Mbp):   46.108
Total Reference Length   (Mbp):  675.866
Total Genome Map Length / Reference Length :    1.918
Total number of aligned Genome Maps    : 38 (0.45)
Total Aligned Length (Mbp)             :  140.247
Total Aligned Length / Reference Length:    0.208
Total Unique Aligned Length (Mbp)      :  129.113
Total Unique Aligned Length / Reference Length:    0.191

SV detect: svdetect_exp_refineFinal1_sv
Full SV summary:
                 SV type :   N : N/tot
                 complex :   24 : 0.0294
                deletion :  306 : 0.3745
           deletion_tiny :   34 : 0.0416
             duplication :    4 : 0.0049
                     end :   24 : 0.0294
               insertion :  345 : 0.4223
          insertion_tiny :   42 : 0.0514
               inversion :    9 : 0.0110
        inversion_paired :    2 : 0.0024
       inversion_partial :   10 : 0.0122
        inversion_repeat :    1 : 0.0012
  translocation_interchr :   15 : 0.0184
  translocation_intrachr :    1 : 0.0012
Total number of SVs: 817

Molecule Stats (/home/bionano/access/local/jobs/10230251/output/contigs/auto_noise/autoNoise1_rescaled.bnx):
Raw coverage of assembly (X):    195.383

Molecules aligned to assembly:
Total number of aligned molecules  :    656111
Fraction of aligned molecules      :         0.889
Total molecule align length (Mbp)  :    192338.7
Total  assembly align length (Mbp) :    193205.7
Effective coverage of  assembly (X):       149.069
Average aligned length (kbp)       :       293.1
Fraction aligned length            :         0.760
Average confidence                 :        36.3

Filtered SV summary (Entries with low confidence for the SV calls, except duplications, are filtered out)
                 SV type :   N : N/tot
                deletion :  288 : 0.4608
             duplication :    4 : 0.0064
               insertion :  309 : 0.4944
               inversion :    3 : 0.0048
        inversion_paired :    2 : 0.0032
       inversion_partial :    3 : 0.0048
  translocation_interchr :   15 : 0.0240
  translocation_intrachr :    1 : 0.0016
Total number of SVs: 625

Clustered SV summary (SVs except translocation with >50% interval overlap and >80% size overlap are collapsed; translocation calls within 35kb are collapsed):
Deletions                          :  283
Insertions                         :  309
Duplications                       :    4
Inversion breakpoints              :    4
Interchr. translocation breakpoints:   15
Intrachr. translocation breakpoints:    1