Invalid xml file : optArguments_new.xml

[stephrom]

Dear,

I do get this error systematically when I run runBNG, for and xml file that should be made by runBNG i suppose. But when I want to look at this file, the file itself doesn't exists.

ERROR: Invalid xml file /scratch/popmet_tmp/BDG_205/BIONANO/refaln/optArguments_new.xml: StartTag: invalid element name, line 115, column 10 (line 115)

Stephane

the whole error log:

========================================== De novo assembly starts =============================================

Start date: Fri Aug 20 16:23:44 CEST 2021

The data generation platform is: irys

The bnx file is: /scratch/popmet_tmp/BDG_205/BIONANO/INRAE_Pnigra_BDG_Div7_raw.bnx

The digested reference is: polished_genome_CTTAAG_20kb_5labels.cmap

The minimum molecule length is (Kb): 100

The minimum label on a molecule is: 8

Maximum backbone intensity is: 0.6

The path to Bionano Solve folder is: /home/strom/bin/bionano/pipeline/Solve3.6.1_11162020

The path to Bionano RefAligner folder is: /home/strom/bin/bionano/pipeline/Solve3.6.1_11162020/RefAligner/11442.11643rel

The number of threads is: 8

Large jobs maximum memory (GB) is: 128

Small jobs maximum memory (GB) is: 8

The number of threads for each subjob is: 2

The number of iterations is: 5

False Positive Density (/100Kb) [FP]: 2.0

False Negative Rate (%/100) [FN]: 0.10

ScalingSD (Kb^1/2) [sd]: 0.0

SiteSD (Kb) [sf]: 0.1

RelativeSD [sr]: 0.03

The genome size (Mb) is: 420

The xml file is: /home/strom/bin/bionano/pipeline/Solve3.6.1_11162020/RefAligner/11442.11643rel/optArguments_nonhaplotype_irys.xml

The output directory is: refaln

Prerun Tests:
1 ERRORS
0 WARNINGS

Disabling autoNoise during rough Assembly

ERROR: Invalid xml file /scratch/popmet_tmp/BDG_205/BIONANO/refaln/optArguments_new.xml: StartTag: invalid element name, line 115, column 10 (line 115)

Pipeline Version: $Id: Multithreading.py 11646 2020-09-25 16:50:59Z Elam $

EXITING: See errors

End date: Fri Aug 20 16:23:47 CEST 2021

===============================================================================================================

[yuxuanyuan]

Hi @stephrom,

As you used the old bionano data, you may try runBNG v1.03, which can be found in Releases

The old bionano scripts and tools can be found at http://doi.org/10.5281/zenodo.4661675