no align files in alignFolder

[wangzhennan14]

Hi, When I used runBNG to run denovo mode, there was an error as follow: ERROR: no align files in alignFolder /home/runBNG_denovo_ref/align Warning/Error messages: ('warning', 'Could not open file \"/home/runBNG_denovo_ref/align/exppairwise1of171.stdout\" tries=0 exception=[Errno 2] No such file or directory: \'/home/runBNG_denovo_ref/align/exppairwise1of171.stdout\'\n')

The command I ran was: runBNG denovo -t /home/bioSoft/tools/pipeline/Solve3.6_09252020/RefAligner/11442.11643rel/avx/ -s /home/Assembly/tools/pipeline/Solve3.6_09252020/ -b 01.runBNG_merged/runBNG_merged.bnx -T 80 -j 20 -z 1300 -o /home/runBNG_denovo_ref -r genome_DLE1_20kb_5labels.cmap -B 0 -P saphyr -l 100 -m 5 -a 1

I run denovo mode with the merge bnx file, the error also appeared. what is the matter? Could you help me to solve this problem? Thank you very much! wang

[yyx8671]

Hi @wangzhennan14,

I saw you changed some parameter settings rather than using the defaults. Do you have evidence to change these settings, such as '-B', '-m'? By the way, the '-a' setting may be not correct, as from my observation, the density for DLE would not be 1 for most species.

Cheers, Andy

[wangzhennan14]

Hi @yyx8671 , Then I used the example to ran runBNG and used the parameter as follow, ../runBNG denovo -t /home/bioSoft/Assembly/tools/pipeline/Solve3.6_09252020/RefAligner/11442.11643rel/ -b Molecules.bnx -T 100 -s /home/bioSoft/Assembly/tools/pipeline/Solve3.6_09252020/ -j 5 -z 100 -o /home/bioSoft/Assembly/runBNG/Examples/test And the error as follow, ERROR: no align files in alignFolder /home/bioSoft/Assembly/runBNG/Examples/test/align Warning/Error messages: ('warning', 'Found text in \"/home/bioSoft/Assembly/runBNG/Examples/test/all_sorted.stdout\" after \"END of output\"\n') ('warning', 'Found text in \"/home/bioSoft/Assembly/runBNG/Examples/test/all.stdout\" after \"END of output\"\n')

The parameter were default, but the error was same, did I set some thing wrong? Thank you!

Best wishes, wang

[yyx8671]

Sorry @wangzhennan14. I didn't update the test dataset. It was generated by the irys platform and digested by BspQI

[yyx8671]

Hi @Missandei-hcl,

Please be aware that the test OM file provided in 'runBNG' was generated using the irys platform with enzyme BspQI and the species is e.coli.

You may use -P irys -z 5 -e no to test.

[Missandei-hcl]

Hi @yyx8671 ,

I typed "./runBNG denovo -P irys -M yes -e no -t /home/len/tools/pipeline/Solve3.6.1_11162020/RefAligner/1.0 -s /home/len/tools/pipeline/Solve3.6.1_11162020 -b /root/runBNG-master/Examples/Molecules.bnx -r /root/runBNG-master/Examples/Test_BSPQI_20kb_5labels.cmap -T 2 -l 150 -j 1 -z 5 -o /root/runBNG-master/Examples "After the error is reported, the display is as follows

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

Start date: 2021年 04月 08日 星期四 21:18:46 CST The data generation platform is: irys The bnx file is: /root/runBNG-master/Examples/Molecules.bnx The digested reference is: /root/runBNG-master/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 utilities.checkExternalDependencies: which failed for dependency R

utilities.checkExternalDependencies: which failed for dependency Rscript

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

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

EXITING: See errors

How should I solve this problem? Is it because of the lack of the R installation package?I look forward to receiving your reply! Thank you very much!

Best wishes,

[yyx8671]

Hi @Missandei-hcl,

The test dataset was from e.coli, -M should be no. You may use python2 to run runBNG. R is mainly used to call CNVs and dual-enzyme scaffolding. For the denovo step, you may not need R.

[Missandei-hcl]

Hello! After I changed -M to No, the same error still appeared.How should I solve this problem?

./runBNG denovo -P irys -M no -e no -t /home/len/tools/pipeline/Solve3.6.1_11162020/RefAligner/11442.11643rel -s /home/len/tools/pipeline/Solve3.6.1_11162020 -b /root/runBNG-master/Examples/Molecules.bnx -r /root/runBNG-master/Examples/Test_BSPQI_20kb_5labels.cmap -T 2 -l 150 -j 1 -z 5 -o /root/runBNG-master/Examples

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

Start date: 2021年 04月 08日 星期四 22:07:02 CST The data generation platform is: irys The bnx file is: /root/runBNG-master/Examples/Molecules.bnx The digested reference is: /root/runBNG-master/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/11442.11643rel 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/11442.11643rel/optArguments_nonhaplotype_irys.xml The output directory is: /root/runBNG-master/Examples utilities.checkExternalDependencies: which failed for dependency R

utilities.checkExternalDependencies: which failed for dependency Rscript

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

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

EXITING: See errors

[yyx8671]

Hi @Missandei-hcl, from the log file, it seems Bionano scripts check if you have R installed.

Please read and follow the README and Manual files provided in runBNG to run this software and then you may have a better experience in using runBNG