Error in bnxSort Step

[GWheelerEB]

On attempting to run runBNG, I get an error where bnxSort fails to complete properly. Log information does not provide much that would help me get to the root of this problem. Tools and scripts are both installed and have executable permissions set for all files, and example files seem to work as intended. It seems I can get it to run if I reduce the genome size substantially, however a 5GBase genome is what I am expecting. The command I am attempting to run is:

./runBNG denovo -t ~/tools -s ~/scripts -b ~/Storage/BioNano/Assembly/Datasets/Q/Detect\ Molecules/Molecules.bnx -T 1400 -j 28 -z 5000 -o ~/Storage/BioNano/Output

The complete output I get is as follows:

========================================== De novo assembly starts =============================================
## Start date: Thu Jul 13 13:15:22 EDT 2017
## The bnx file is: /fs/project/PAS1172/BioNano/Assembly/Datasets/Q/Detect Molecules/Molecules.bnx
## The digested reference is: 
## The minimum molecule length is (Kb): 150
## The minimum label on a molecule is: 
## The path of BNG scripts folder is: /users/PAS1172/osu0330/scripts
## The path of BNG tools folder is: /users/PAS1172/osu0330/tools
## The number of threads is: 1400
## The number of jobs is: 28
## The number of iterations is: 5
## False Positive Density (/100Kb) [FP]: 1.5
## False Negative Rate (%/100) [FN]: 0.15
## ScalingSD (Kb^1/2) [sd]: 0.0
## SiteSD (Kb) [sf]: 0.2
## RelativeSD [sr]: 0.03
## The genome size (Mb) is: 5000
## The output directory is: /users/PAS1172/osu0330/Output

  Prerun Tests:
    0 ERRORS
    2 WARNINGS

  WARNING: Disabling SV detection (-V, default ON) because no reference supplied, or invalid.
  WARNING: Disabling alignment of molecules vs reference (-m, default ON) because no reference supplied, or invalid.

  Pipeline Version: $Id: SVModule.py 5134 2016-07-07 00:51:33Z wandrews $

  RefAligner Version: 5122

  Pipeline start time: Thu Jul 13 13:15:27 2017

Reading molecule stats from /users/PAS1172/osu0330/Output/all.bnx:
Molecule Stats:
N mols: 1087029
Total len (Mb): 237551.802
Avg len (kb)  :    218.533
Mol N50 (kb)  :    214.465
Lab (/100kb)  :      6.815

Sorting /users/PAS1172/osu0330/Output/all.bnx into /users/PAS1172/osu0330/Output/all_sorted
 Starting Multi-Threaded Process:
  SortBNX
  Running 1 jobs with 1 threads
   START   1:                        SortBNX,  1Thr,   1R,   1T,   0F,   0Q
   STOP    1:                        SortBNX,  1Thr,   0R,   1T,   1F,   0Q   0h 0.00m
 Finished Multi-Threaded Process:
  SortBNX

ERROR: sortBNX failed. Check: /users/PAS1172/osu0330/Output/all.bnx

  Pipeline end time: Thu Jul 13 13:15:32 2017
  Elapsed time: 0.08m; 0.00h; 0.00d

Warning/Error messages:
warning : Could not open file \"/users/PAS1172/osu0330/Output/all_sorted.stdout\" tries=0 exception=[Errno 2] No such file or directory: '/users/PAS1172/osu0330/Output/all_sorted.stdout'\n
error : job has not completed, see stdout=\"/users/PAS1172/osu0330/Output/all_sorted.stdout\"
critical : ERROR: sortBNX failed. Check: /users/PAS1172/osu0330/Output/all.bnx

Warning/Error summary:
    1 warning(s)
    1 critical(s)
    1 error(s)

Pipeline has completed with errors

## End date: Thu Jul 13 13:15:32 EDT 2017
===============================================================================================================`

[yyx8671]

Hi @GWheelerEB,

Thank you for the issue you raised. I found that I missed a "$" in Line 1254. The "site" should be "$site". You may change the code in your 'runBNG' or download the fixed version. Let me know if it works.

Cheers, Andy

[GWheelerEB]

Thanks a lot! It now seems to work as intended even when setting large expected genome size values.