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AppliedBioinformatics / runBNG

An easy way to run BioNano genomic analysis
MIT License
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error cannot open auto_noise #30

Closed olechnwin closed 3 years ago

olechnwin commented 3 years ago

Hello, I am using runBNG hybrid with the following command:

/opt/runBNG/runBNG hybrid \
        -R      /opt/bionano/tools/pipeline/Solve3.6.1_11162020/RefAligner/1.0 \
        -s      /opt/bionano/tools/pipeline/Solve3.6.1_11162020 \
        -b      /Data/A673_bionano/EwingSarcoma_November2019/EwingsSarcoma_Solve3.4_pipeline_results/output/all.bnx \
        -r      /Data/A673_pacbio/sequel_fasta/4-quiver/cns_output/fc_phase_pipeline/output/cns_p.phased.1.fasta \
        -f      /Data/A673_bionano/runBNG_rslt/contigs/exp_refineFinal1/EXP_REFINEFINAL1.cmap \
        -x      /opt/bionano/tools/pipeline/1.0/HybridScaffold/1.0/hybridScaffold_DLE1_config.xml \
        -t      $((SLURM_CPUS_PER_TASK-2)) \
        -B      2 \
        -N      2 \
        -M     1200 \
        -o      /Data/A673_bionano/runBNG_rslt/hybrid

It was running for a while but then the following error appeared:

Beginning alignment molecules to Bionano genome maps (auto noise)
Running command: python2.7 /opt/bionano/tools/pipeline/Solve3.6.1_11162020/Pipeline/11162020/pipelineCL.py -x -y -T 38 -j 38 -l /Data/A673_bionano/runBNG_rslt/hybrid/auto_noise -t /opt/bionano/tools/pipeline/Solve3.6.1_11162020/RefAligner/11442.11643rel/ -b /Data/A673_bionano/EwingSarcoma_November2019/EwingsSarcoma_Solve3.4_pipeline_results/output/all.bnx -r /Data/A673_bionano/runBNG_rslt/hybrid/assignAlignType/cut_conflicts/EXP_REFINEFINAL1_bppAdjust_cut.cmap -a /opt/bionano/tools/pipeline/Solve3.6.1_11162020/HybridScaffold/11162020/hybridScaffold_DLE1_config.xml
ERROR: Cannot open /Data/A673_bionano/runBNG_rslt/hybrid/auto_noise/contigs/auto_noise/autoNoise1.stdout: No such file or directory

Can you please let me what I need to do? Thank you!

yyx8671 commented 3 years ago

Hi @olechnwin，Which runBNG version did you use?

olechnwin commented 3 years ago

Hi @yyx8671,

I'm using runBNG version 2.0.1

/opt/runBNG/runBNG -h

------------------------------------------------------------------------------------------------------
Program:  runBNG
Version:  2.0.1
Author:   Yuxuan Yuan (yuxuan.yuan@outlook.com)
yuxuanyuan commented 3 years ago

Hi @olechnwin, sorry for the late reply. For -x <int> the xml file used to produce the final assembled cmap file, you may use the xml file from your denovo assembly folder (exp_optArguments.xml), it's not hybridScaffold_DLE1_config.xml.

olechnwin commented 3 years ago

That's okay. Thank you very much for your clarification.

olechnwin commented 3 years ago

Hi @yuxuanyuan, I've changed the -x to exp_optArguments.xml but still got the same error:

ERROR: Cannot open /Data/A673_bionano/runBNG_rslt/hybrid/auto_noise/contigs/auto_noise/autoNoise1.stdout: No such file or directory
ERROR: ERROR: Alignment of molecules to BioNano genome maps and hybrid scaffolds cannot be completed

Here is the command I used:

~/opt/runBNG/runBNG hybrid \
        -R      ~/opt/bionano/tools/pipeline/Solve3.6.1_11162020/RefAligner/1.0 \
        -s      ~/opt/bionano/tools/pipeline/Solve3.6.1_11162020 \
        -b      ~/Data/A673_bionano/EwingSarcoma_November2019/EwingsSarcoma_Solve3.4_pipeline_results/output/all.bnx \
        -r      ~/Data/A673_pacbio/sequel_fasta/4-quiver/cns_output/fc_phase_pipeline/output/cns_p.phased.1.fasta \
        -f      ~/Data/A673_bionano/runBNG_rslt/contigs/exp_refineFinal1/EXP_REFINEFINAL1.cmap \
        -x      ~/Data/A673_bionano/runBNG_rslt/exp_optArguments.xml \
        -t      $((SLURM_CPUS_PER_TASK-2)) \
        -B      2 \
        -N      2 \
        -M      1200 \
        -o      ~/Data/A673_bionano/runBNG_rslt/hybrid

I am attaching the entire message. runbng_hybrid_505460.txt Thank you!

yuxuanyuan commented 3 years ago

Hi @olechnwin,

I don't have enough time to investigate this at the moment, but you may check /Data/A673_bionano/runBNG_rslt/hybrid/hybrid_scaffolds and the hybrid assembly should be ready in your folder

*__HYBRID_SCAFFOLD.agp
*_HYBRID_SCAFFOLD.fasta
*_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta
olechnwin commented 3 years ago

Hi @yuxuanyuan,

Thank you for your reply. I do have the hybrid assembly, but I was hoping to get a zip output file that can be imported to bionano access for visualization. Do you have any suggestion on how to visualize the result? Thank you!

yuxuanyuan commented 3 years ago

Hi @olechnwin,

IrysView, MapOptics and OMTools are good alternatives to help visualise the result.

olechnwin commented 3 years ago

Hi @yuxuanyuan,

Thank you so much for your suggestions. I will look into those tools.