I am trying to do de novo assembly of Bionano data. Bionano Pipeline tools and Access server have been installed on a Virtual Machine running Ubuntu 18.04. When I run it with the Bionano data-set downloaded from Genome in a Bottle (all.bnx from ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/BioNano/), the pipeline runs fine. But with my dataset, it gives an error in the "autoNoise0" stage.

The Terminal output ends with the following:

  Prerun Tests:
        0 ERRORS
        0 WARNINGS

Tools Version: N/A
Solve Version: N/A
Pipeline Version: 7981
RefAligner Version: 7989

  Pipeline start time: Wed May 15 11:06:07 2019

checkScanScaling: autoNoise= True
Executing stage number 1 : AutoNoise + SplitBNX

Molecule Stats (/home/bionano/gis_exp/ref_map/all.bnx):
Total number of molecules: 3877274
Total length (Mbp)       : 480326.722
Average length (kbp)     :    123.883
Molecule N50 (kbp)       :    245.752
Label density (/100kb)   :     16.096

Sorting /home/bionano/gis_exp/ref_map/all.bnx into /home/bionano/gis_exp/ref_map/all_sorted
minlen adjusted to 135 for bnx_sort because scan scaling enabled (original minlen is 150)
 Starting Multi-Threaded Process:
  SortBNX
  Running 1 jobs with 1 threads, sleepTime=0.05
   START    1:                        SortBNX,   1 Thr,    1 R,    1 T,    0 F,    0 Q
   STOP     1:                        SortBNX,   1 Thr,    0 R,    1 T,    1 F,    0 Q  TotalTime= 0h 0.50m  RunTime= 0h 0.50m  CPUload=160% host=NA
 Finished Multi-Threaded Process:
  SortBNX

autoNoise0
 Starting Multi-Threaded Process:
  Autonoise0
 Running 1 jobs with 1 threads, sleepTime=0.05
   START    1:                     Autonoise0,   1 Thr,    1 R,    1 T,    0 F,    0 Q
   STOP     1:                     Autonoise0,   1 Thr,    0 R,    1 T,    1 F,    0 Q  TotalTime= 0h 0.20m  RunTime= 0h 0.20m  CPUload=99% host=NA Command exited with non-zero status 1
 Finished Multi-Threaded Process:
  Autonoise0

ERROR: AutoNoise0 failed. Check: /home/bionano/gis_exp/ref_map/contigs/auto_noise/autoNoise0.stdout

autoNoise0.stdout is as follows:

WARNING: -RepeatMask with -RepeatRec requires -extend 1 or -extend 2 (using -extend 1)

Reading input maps from /home/bionano/gis_exp/ref_map/all_sorted.bnx

After applying -maxEnd 90.0000 -bpp 500.0000 -mres 0.90000000 -minSNR 0.0000 to /home/bionano/gis_exp/ref_map/all_sorted.bnx : maps=0, sites=0, length= 0.000 kb (avg= -nan kb, label density= 0.000 /100kb, N50= 0.0000 Mb):wtime=0.006038

WARNING: no maps in 1 -i input files

Generating -i input map statistics in /home/bionano/gis_exp/ref_map/molecule_stats.txt

Read 0 Maps from 1 file /home/bionano/gis_exp/ref_map/all_sorted.bnx : total maps=0, sites=0, length=0.000 kb (avg=-nan kb, label density = 0.000 /100kb, N50= 0.0000 Mb):wall time=0.006213

Read 24 reference maps from 1 input files :total maps=24, sites=554371, length=3088269.832 kb (avg=128677.910 kb, Label Density=17.951/100kb)

kmax=5,average Kmax[I]=0.539

1:score_init():Insufficient -i map data:nummaps=0,total sites=0,total length=0.000
enter code here

My script is as follows:

DATA=/home/bionano/gis_exp/data/RawMolecules-M002C-800K.bnx
#DATA=/home/bionano/gis_exp/data/all.bnx
BNTOOLSDIR=/home/bionano/tools/pipeline/Solve3.3_10252018
PLINEDIR=$BNTOOLSDIR/Pipeline/10252018
REFALNDIR=$BNTOOLSDIR/RefAligner/7915.7989rel
OUTDIR=/home/bionano/gis_exp/ref_map
NUMTH=2
HUMANREF=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

python2 $PLINEDIR/pipelineCL.py -T $NUMTH -j $NUMTH -N 1 -i 5 -y \
-b $DATA -l $OUTDIR -t $REFALNDIR -a $REFALNDIR/optArguments_haplotype_irys.xml -r $BNTOOLSDIR/RefGenome/hg38_DLE1_0kb_0labels.cmap

Could someone kindly guide me what might be wrong in the run with my own datbase.