yyx8671
commented
3 years ago It seems there is someting wrong with the optArguments_nonhaplotype_irys.xml file provided by Bionano Genomics in version 3.6 and 3.6.1. You may use Bionano Solve v3.5.1 to complete your task.
Here are my tests.
Bionano Solve v3.6.1
$ python ~/Tools/bionano/tools/pipeline/Solve3.6.1_11162020/Pipeline/1.0/pipelineCL.py \
-R -w -d -U -T 4 -j 4 -je 4 -jp 4 -J 4 -TJ 4 -Te 4 -Tp 4 -i 5 -B 0 \
-t ~/Tools/bionano/tools/pipeline/Solve3.6.1_11162020/RefAligner/1.0 \
-a ~/Tools/bionano/tools/pipeline/Solve3.6.1_11162020/RefAligner/1.0/optArguments_nonhaplotype_irys.xml \
-l denovo -b ~/Tools/runBNG/Examples/Molecules.bnx -r fa2cmap/Test_BSPQI_20kb_5labels.cmap
Prerun Tests:
1 ERRORS
0 WARNINGS
Disabling autoNoise during rough Assembly
ERROR: Invalid xml file /home/yyuan/Tools/bionano/tools/pipeline/Solve3.6.1_11162020/RefAligner/1.0/optArguments_nonhaplotype_irys.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 errorsBionano Solve v3.6
$ python ~/Tools/bionano/tools/pipeline/Solve3.6_09252020/Pipeline/1.0/pipelineCL.py \
-R -w -d -U -T 4 -j 4 -je 4 -jp 4 -J 4 -TJ 4 -Te 4 -Tp 4 -i 5 -B 0 \
-t ~/Tools/bionano/tools/pipeline/Solve3.6.1_11162020/RefAligner/1.0 \
-a ~/Tools/bionano/tools/pipeline/Solve3.6_09252020/RefAligner/1.0/optArguments_nonhaplotype_irys.xml \
-l denovo -b ~/Tools/runBNG/Examples/Molecules.bnx -r fa2cmap/Test_BSPQI_20kb_5labels.cmap
Prerun Tests:
1 ERRORS
0 WARNINGS
Disabling autoNoise during rough Assembly
ERROR: Invalid xml file /home/yyuan/Tools/bionano/tools/pipeline/Solve3.6_09252020/RefAligner/1.0/optArguments_nonhaplotype_irys.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 errorsBionano Solve v3.5.1
$ python ~/Tools/bionano/Solve3.5.1_01142020/Pipeline/1.0/pipelineCL.py \
-R -w -d -U -T 4 -j 4 -je 4 -jp 4 -J 4 -TJ 4 -Te 4 -Tp 4 -i 5 -B 0 \
-t ~/Tools/bionano/tools/pipeline/Solve3.6.1_11162020/RefAligner/1.0 \
-a ~/Tools/bionano/Solve3.5.1_01142020/RefAligner/1.0/optArguments_nonhaplotype_irys.xml \
-l denovo -b ~/Tools/runBNG/Examples/Molecules.bnx -r fa2cmap/Test_BSPQI_20kb_5labels.cmap
Prerun Tests:
0 ERRORS
0 WARNINGS
Tools Version: N/A
Solve Version: N/A
Pipeline Version: 10322
RefAligner Version: 11643
Assembly ID: 581
Pipeline start time: Fri Apr 9 16:10:13 2021
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 (/home/yyuan/Tools/runBNG/Examples/denovo/all.bnx):
Total number of molecules: 7326
Total length (Mbp) : 1595.095
Average length (kbp) : 217.731
Molecule N50 (kbp) : 236.401
Label density (/100kb) : 11.015
Missandei-hcl
xiaoquexingchen
Hello! I typed "./runBNG denovo -P irys -H no -M no -e no -c yes -E yes -t /home/len/tools/pipeline/Solve3.6.1_11162020/RefAligner/1.0 -s /home/len /tools/pipeline/Solve3.6.1_11162020 -b /root/Examples/Molecules.bnx -r /root/Examples/Test_BSPQI_20kb_5labels.cmap -T 2 -l 150 -m 8 -B 0.6 -j 1 -i 5 -z 5 -o /root/runBNG-master/Examples", the operation error is as follows, I have been stuck with this problem for a long time, I don't know how to solve it, I hope to get your help, thank you very much!
./runBNG denovo -P irys -H no -M no -e no -c yes -E yes -t /home/len/tools/pipeline/Solve3.6.1_11162020/RefAligner/1.0 -s /home/len/tools/pipeline/Solve3.6.1_11162020 -b /root/Examples/Molecules.bnx -r /root/Examples/Test_BSPQI_20kb_5labels.cmap -T 2 -l 150 -m 8 -B 0.6 -j 1 -i 5 -z 5 -o /root/runBNG-master/Examples ========================================== De novo assembly starts =============================================
Start date: 2021年 04月 09日 星期五 15:06:31 CST The data generation platform is: irys The bnx file is: /root/Examples/Molecules.bnx The digested reference is: /root/Examples/Test_BSPQI_20kb_5labels.cmap The minimum molecule length is (Kb): 150 The minimum label on a molecule is: 8 Maximum backbone intensity is: 0.6 The path to Bionano Solve folder is: /home/len/tools/pipeline/Solve3.6.1_11162020 The path to Bionano RefAligner folder is: /home/len/tools/pipeline/Solve3.6.1_11162020/RefAligner/1.0 The number of threads is: 2 Large jobs maximum memory (GB) is: 128 Small jobs maximum memory (GB) is: 8 The number of threads for each subjob is: 1 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]: 0.15 RelativeSD [sr]: 0.03 The genome size (Mb) is: 5 The xml file is: /home/len/tools/pipeline/Solve3.6.1_11162020/RefAligner/1.0/optArguments_nonhaplotype_irys.xml The output directory is: /root/runBNG-master/Examples Prerun Tests: 1 ERRORS 0 WARNINGS
Disabling autoNoise during rough Assembly
ERROR: Invalid xml file /root/runBNG-master/Examples/optArguments_new.xml: StartTag: invalid element name, line 115, column 10