sortBNX failed

[MikeEHMatson]

Hello,
I think I am having a similar issue to the one described last year by GWheelerEB.

Trying to run command:

runBNG denovo -b mqr/MQR_table_rescaled.bnx -t $tools -s $scripts -T 16 -S 45 -j 16 -l 50 -z 50 -r $refCMAP -p 0.95 -n 0.09 -d -0.03 -f 0.22 -R 0.03 -o denovo
But getting:

========================================== De novo assembly starts =============================================
## Start date: Tue May 15 11:47:21 PDT 2018
## The bnx file is: /bigdata/judelsonlab/mmatson/usdaTemp/bionano/runBNG_reAnalyze/mqr/MQR_table_rescaled.bnx
## The digested reference is: /bigdata/judelsonlab/mmatson/usdaTemp/bionano/runBNG_reAnalyze/faCMAP/fa2cmap/11_12_run2_ff.fasta.cut_BspQI_20Kb_5labels.cmap
## The minimum molecule length is (Kb): 50
## The minimum label on a molecule is: 8
## Maximum backbone intensity is: 0.6
## The path of BNG scripts folder is: /bigdata/judelsonlab/mmatson/usdaTemp/bionano/scripts
## The path of BNG tools folder is: /bigdata/judelsonlab/mmatson/usdaTemp/bionano/tools
## The number of threads is: 16
## Large jobs maximum memory (GB) is: 128
## Small jobs maximum memory (GB) isL 45
## The number of threads for each subjob is: 16
## The number of iterations is: 5
## False Positive Density (/100Kb) [FP]: 0.95
## False Negative Rate (%/100) [FN]: 0.09
## ScalingSD (Kb^1/2) [sd]: -0.03
## SiteSD (Kb) [sf]: 0.22
## RelativeSD [sr]: 0.03
## The genome size (Mb) is: 50
## The output directory is: denovo

  Prerun Tests:
        0 ERRORS
        0 WARNINGS

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

  RefAligner Version: 5122
Pipeline start time: Tue May 15 11:47:22 2018

Reading molecule stats from /bigdata/judelsonlab/mmatson/usdaTemp/bionano/runBNG_reAnalyze/denovo/all.bnx:
Molecule Stats:
N mols: 469093
Total len (Mb):  45791.266
Avg len (kb)  :     97.617
Mol N50 (kb)  :     92.320
Lab (/100kb)  :     15.206

Sorting /bigdata/judelsonlab/mmatson/usdaTemp/bionano/runBNG_reAnalyze/denovo/all.bnx into /bigdata/judelsonlab/mmatson/usdaTemp/bionano/runBNG_reAnalyze/denovo/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: /bigdata/judelsonlab/mmatson/usdaTemp/bionano/runBNG_reAnalyze/denovo/all.bnx

  Pipeline end time: Tue May 15 11:47:25 2018
  Elapsed time: 0.05m; 0.00h; 0.00d

Warning/Error messages:
warning : Could not open file \"/bigdata/judelsonlab/mmatson/usdaTemp/bionano/runBNG_reAnalyze/denovo/all_sorted.stdout\" tries=0 exception=[Errno 2] No such file or directory: '/bigdata/judelsonlab/mmatson/usdaTemp/bionano/runBNG_reAnalyze/denovo/all_sorted.stdout'\n
error : job has not completed, see stdout=\"/bigdata/judelsonlab/mmatson/usdaTemp/bionano/runBNG_reAnalyze/denovo/all_sorted.stdout\"
critical : ERROR: sortBNX failed. Check: /bigdata/judelsonlab/mmatson/usdaTemp/bionano/runBNG_reAnalyze/denovo/all.bnx

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

Pipeline has completed with errors

Changing around some of the CPU or memory settings doesnt help, nor switching the input .bnx files (which are outputs of runBNG mqr) to the original, nonmodified, .bnx files changes the error.

Currently running the most recent release (1.03-cda06f4).

Thanks,
Mike

[yyx8671]

Hi Mike,

Can you please try '-B 0' in the de novo approach?

Cheers,
Andy

[MikeEHMatson]

Hi Andy,
That didn't seem to change anything, and the "sortBNX failed" message still appears.

Mike

[MikeEHMatson]

Hi Andy,
I'm still having the issue and was wondering if there were any other things I might be able to try.

Thanks,
Mike

[yyx8671]

Hi Mike,

Sorry for the delayed reply.

Did you get your bnx file from the Irys platform or the saphyr platform? I only tested the bnx files from the Irys platform and they worked well.

Did you try different parameters, such as the min molecule length? Looking through, it seems you used 50Kb and perhaps you have filtered many maps.

Cheers,
Andy

[MikeEHMatson]

Hi Andy,
I tried reducing the molecule length cutoff to 10kb, without success. I also tried eliminating the minimum memory requirements, and reducing the number of CPUs and jobs, both of which didn't seem to change anything. I also removed the "-B" option from the command, which appears to not be relevant to runBNG denovo anyway, though this also did not fix the error.

The bnx files are from an irys, and not a saphyr platform.

Mike

[yyx8671]

Hi Mike,
In the bnx sort step, the key parameters are: -l, -m and -B.
Can you please check the stats of your bnx file and adjust ' -l ' in the denovo step? May try 150 or 100.
Cheers,
Andy

[MikeEHMatson]

Hi Andy,
i have tried several different combinations of varying -l, -m, and -B, but they all still result in the same error. I am starting to suspect the input bnx file is to blame, as it was supplied as a single already-merged .bnx file.

While the mqr step has worked previously on this already-merged file (the denovo step is using that output, though using the original .bnx file still gives the sortBNX error), I ended up not filtering the original file because I got a similarly frustrating error when running

runBNG bnxfilter -b $bnx -t 16 -m 45 -r $refAligner -o filter -p filter_04

which gave
Opps! Your input '' is not an integer or smaller than 0. Please check!

Not sure what input I am missing there.

Mike

[yyx8671]

Hi Mike,

I found in the bnxfilter function, I made a typo error on Line 888. "minLen" should be "minlen" (runBNG has been updated). This error has no association with the denovo function. Not sure why it cannot be applied to your bnx file since you have already tried different settings.

You may try 'bnxmerge' to reorganise your bnx file with only one input. If the problem is still there, I'm afraid I cannot give a further help.

Cheers,
Andy

[yuezhao666]

Hi Mike,

Can you please try '-B 0' in the de novo approach?

Cheers,
Andy

Excuse me, I wonder what the "-B" (maximum backbone intensity) parameter mean. Could you please tell me?
Thanks a lot!

Best,
Joy

[xiaoquexingchen]

Hi @MikeEHMatson ,

I want to ask how you solved this problem before? I keep reporting this problem when I run it, and it has not been resolved. I hope to get your reply.
Thanks