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AppliedBioinformatics / runBNG

An easy way to run BioNano genomic analysis
MIT License
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AttributeError: 'NoneType' object has no attribute 'endswith' #28

Closed olechnwin closed 3 years ago

olechnwin commented 3 years ago

Hello,

I have an error when running the following command:

~/opt/runBNG/runBNG denovo \
        -t      ~/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 \
        -M      yes \
        -a      9 \
        -T      $((SLURM_CPUS_PER_TASK-2)) \
        -j      2 \
        -z      3137 \
        -m      3 \
        -r      ~/Data/A673_bionano/runBNG_rslt/hg19_DLE1_20kb_5labels.cmap \
        -o      ~/Data/A673_bionano/runBNG_rslt

These are the last warning/error messages:

Warning summary:
    983 warning(s)

WARNING: missing cnv file: /home/Data/A673_bionano/runBNG_rslt/contigs/alignmolvref/copynumber/cnv_calls_exp.txt

Starting smap2vcf script:
python /home/opt/bionano/tools/pipeline/Solve3.6.1_11162020/Pipeline/11162020/Analysis/vcf_converter/bionano_vcf_converter.py -s /home/Data/A673_bionano/runBNG_rslt/contigs/exp_refineFinal1_sv/merged_smaps/exp_refineFinal1_merged_filter_inversions.smap -x /home/Data/A673_bionano/runBNG_rslt/contigs/exp_refineFinal1_sv/merged_smaps/exp_refineFinal1_merged.xmap -r /home/Data/A673_bionano/runBNG_rslt/contigs/exp_refineFinal1_sv/merged_smaps/exp_refineFinal1_merged_r.cmap -o /home/Data/A673_bionano/runBNG_rslt/contigs/exp_refineFinal1_sv/merged_smaps/exp_refineFinal1_merged_filter_inversions -a hg19_DLE1_20kb_5labels.cmap -b False -m 0

Traceback (most recent call last):
  File "/home/opt/bionano/tools/pipeline/Solve3.6.1_11162020/Pipeline/1.0/pipelineCL.py", line 52, in <module>
    dnpipeline.run(conf)
  File "/home/opt/bionano/tools/pipeline/Solve3.6.1_11162020/Pipeline/11162020/Pipeline.py", line 2129, in run
    self.finalizePipeline(conf, ers)
  File "/home/opt/bionano/tools/pipeline/Solve3.6.1_11162020/Pipeline/11162020/Pipeline.py", line 2895, in finalizePipeline
    self.smap2vcf(conf)
  File "/home/opt/bionano/tools/pipeline/Solve3.6.1_11162020/Pipeline/11162020/Pipeline.py", line 2885, in smap2vcf
    log = os.path.join(conf.clusterLogDir, stageName + ".log")
  File "/usr/lib64/python2.7/posixpath.py", line 77, in join
    elif path == '' or path.endswith('/'):
AttributeError: 'NoneType' object has no attribute 'endswith'
Python Exception : 'NoneType' object has no attribute 'endswith'
Exception stack trace:

I am attaching the full log for more info. runbng_denovo_391392.txt

Thank you again for your help.

yuxuanyuan commented 3 years ago

Hi @olechnwin,

I didn't test the CNV calling function in this. Maybe i need to disable it or set an option in the next update.

From the log file, it seems this is a warning and you can still get your denovo assembly file at /home/Data/A673_bionano/runBNG_rslt/contigs/exp_refineFinal1/EXP_REFINEFINAL1.cmap

olechnwin commented 3 years ago

Hi @yuxuanyuan.

Thanks for your reply. Ahh...so it's doing CNV as well. I didn't realize I already have my denovo assembly. Thanks!