UnsubmittedJobs Problem while running 'runBNG denovo'

[onkar2470]

Hi, I am running 'runBNG denovo' command to covert my raw .bnx file into .cmap file (i.e. Rough Assembly) on a server But while processing sortBNX job, i am encountering UInsubmittedJobs problem. Job is not being submitted Trying to run command: ./runBNG denovo -b RawMolecules.bnx -t /Solve3.5.1_01142020/RefAligner/1.0/avx2/ -s /Solve3.5.1_01142020/Pipeline/1.0/ -T 30 -j 15 -l 180 -z 480 -o denovo2

But getting: The number of threads for each subjob is: 15 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: 480 The output directory is: denovo2

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.

Tools Version: N/A Solve Version: N/A Pipeline Version: 10322 RefAligner Version: 10436

Assembly ID: 100

Pipeline start time: Fri Mar 20 00:17:09 2020

checkScanScaling: autoNoise= False Not performing autoNoise (see -y): setting doScanScale = False, hence not using _rescaled.bnx for BNX splits Executing stage number 1 : AutoNoise + SplitBNX

Molecule Stats (/bionano/denovo2/all.bnx): Total number of molecules: Total length (Mbp) : Average length (kbp) :
Molecule N50 (kbp) :
Label density (/100kb) :

Sorting bionano/denovo2/all.bnx into bionano/denovo2/all_sorted Starting Multi-Threaded Process: SortBNX Running 1 jobs with 30 threads, sleepTime=0.02 SortBNX: jobName= SortBNX: not on cluster: availableThreads= 30, sJob.maxThreads= 47 (skipping) SortBNX: waited 1800.0 seconds for job completion: UnsubmittedJobs= 1, ActiveJobs= 0, FinishedJobs= 0 SortBNX: jobName= SortBNX: not on cluster: availableThreads= 30, sJob.maxThreads= 47 (skipping) SortBNX: waited 3600.0 seconds for job completion: UnsubmittedJobs= 1, ActiveJobs= 0, FinishedJobs= 0

Am I missing some parameter? Please help Thanx, Onkar

[yuxuanyuan]

Hi @onkar2470 ,

Thanks for using 'runBNG'. I noticed this issue when using the latest Bionano scripts. The current 'runBNG' is suitable for the old IrysSolve scripts instead of the BionanoSolve scripts.

You may consider adding more options in 'runBNG' at line 1404 or 1408 to customise the number of threads used for each subjob, as the new BionanoSolve is designed for the Saphyr workstation/cluster. Please also note that the xml file has been changed as well.

If you are in a hurry to run your jobs, please consider using 'pipelineCL.py' directly from Solve3.xxx. I'm rewriting a 'runBNG_saphyr' script, but it will take a while.

Cheers, Andy

[onkar2470]

Hi Andy, I appreciate your quick reply I have used 'pipelineCL.py' directly also from Solve3.5.1 and used optArguments_haplotype_saphyr.xml with -R parameter but getting same problem My data generated using Saphyr

Should I use the previous version of Solve?

Thanx, Onkar

[yuxuanyuan]

Hi Onkar,

I haven't tested the Saphyr data using the old pipeline as at the time of writing 'runBNG' we had no such data. You may try the old scripts, but I cannot guarantee the accuracy of the result.

For the xml file, please ensure you require a haplotype phased assembly or not. You may try to set '-j', '-je', '-jp', '-J', ' -TJ' and '-Te' to run your job (for instance setting 6 for all) when using 'pipelineCL.py'.

Please let me know if it works.

Cheers, Andy

[onkar2470]

Hi Andy, I set '-j', '-je', '-jp', '-J', ' -TJ' and '-Te' all these parameters to 6 as you suggested and its working!!! This command is running Hope it will run without interruption Thank you so much for your help and such a quick response