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AppliedBioinformatics / runBNG

An easy way to run BioNano genomic analysis
MIT License
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runBNG: line 1752: bionano/tools/pipeline/Solve3.6.1_11162020/RefAligner/11442.11643rel: Is a directory #29

Closed olechnwin closed 3 years ago

olechnwin commented 3 years ago

Hello, I ran into this error that looks like it can't find the RefAligner folder. I was using the same RefAligner folder path that I used for runBNG denovo that ran successfully. Can you please help me fix this? Thank you!

~/opt/runBNG/runBNG compare \
        -R      ~/opt/bionano/tools/pipeline/Solve3.6.1_11162020/RefAligner/1.0 \
        -r      ~/Data/A673_bionano/runBNG_rslt/hg19_DLE1_20kb_5labels.cmap \
        -q  ~/Data/A673_bionano/runBNG_rslt/contigs/exp_refineFinal1/EXP_REFINEFINAL1.cmap \
        -t      $SLURM_CPUS_PER_TASK \
        -z      3200 \
        -m  800 \
        -p      EXP_REFINEFINAL1_aligned_to_hg19_DLE1_20kb_5labels \
        -o      ~/Data/A673_bionano/runBNG_rslt
/home/opt/runBNG/runBNG compare -R /home/opt/bionano/tools/pipeline/Solve3.6.1_11162020/RefAligner/1.0 -r /home/Data/A673_bionano/runBNG_rslt/hg19_DLE1_20kb_5labels.cmap -q /home/Data/A673_bionano/runBNG_rslt/contigs/exp_refineFinal1/EXP_REFINEFINAL1.cmap -t 20 -z 3200 -m 800 -p EXP_REFINEFINAL1_aligned_to_hg19_DLE1_20kb_5labels -o /home/Data/A673_bionano/runBNG_rslt
========================================== comparison starts =============================================
## Start date: Fri Apr 16 11:48:04 EDT 2021
## The ref cmap file is: /home/Data/A673_bionano/runBNG_rslt/hg19_DLE1_20kb_5labels.cmap
## The qry cmap file is: /home/Data/A673_bionano/runBNG_rslt/contigs/exp_refineFinal1/EXP_REFINEFINAL1.cmap
## The genome size (Mb) is: 3200
## The Binano RefAligner is: /home/opt/bionano/tools/pipeline/Solve3.6.1_11162020/RefAligner/11442.11643rel
## The maximum threads is: 20
## The maximum RAM (Gb) is: 800
## The output file names are: /home/Data/A673_bionano/runBNG_rslt/EXP_REFINEFINAL1_aligned_to_hg19_DLE1_20kb_5labels*

/home/opt/runBNG/runBNG: line 1752: /home/opt/bionano/tools/pipeline/Solve3.6.1_11162020/RefAligner/11442.11643rel: Is a directory
yuxuanyuan commented 3 years ago

Hi @olechnwin, in runBNG compare '-R' should be followed by the full path to RefAligner (not the folder containing RefAligner). Please check '-help' before running.

olechnwin commented 3 years ago

Hi @yuxuanyuan, Thank you so much for your quick reply. I actually checked the 'runBNG compare -h' before running but totally misunderstood the wording. Sorry about that.