yuxuanyuan
commented
3 years ago 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
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
===============================================================================================================