Error in the "autoNoise0" stage while doing de novo assembly of Bionano data

Question

[Ritu]

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.

Answer 1

[BFisher]

I came to the same problem, but cannot find any solution by google. May my experience help someone. It may be that your python subprocess.Popen cannot find the command on your system. Type print(jobArgs) before line 822 of the file: [path]/tools/pipeline/1.0/Pipeline/1.0/Multithreading.py,
Just like this:

print(jobArgs)
super(SingleJob, self).__init__(jobArgs, stdout=stdout, stderr=stderr)
self.startTime = time.time()
self.isRunning = True

Check the commands on you system and

yum install [the command for centos]