yuxuanyuan
commented
2 years ago Hi @Julia-zhulinying,
From Bionano Solve 3.7, Bionano Genomics has changed the python version from python2 to python3. I havent got a time to update runBNG to be compatible. If you're in a rush, you may try to use Bionano Solve 3.5.
Let me know if you have any problems in running this.
Hello! Yuxuan, @yuxuanyuan I have issues running runBNG compare. All the Bionano Solve tools files are treated with chmod -R 777. Below is the running result. It seems still have issues with RefAligner, but I couldn't figure it out. Please help! Thanks!
$ runBNG compare -R /data/zhul7/runBNG/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12542rel/RefAligner -r /data/zhul7/runBNG/tools/pipeline/Solve3.7_03302022_283/RefGenome/hg38_DLE1_0kb_0labels.cmap -q /data/zhul7/bionano220729/1_RX_20K/output/contigs/exp_refineFinal1/1_RX_20K.cmap -z 3209286105 -o /data/zhul7/bionano220729/align -p align_1_RX_20K -t 16 -m 50 ========================================== comparison starts =============================================
Start date: Tue Aug 2 15:10:04 EDT 2022
The ref cmap file is: /gpfs/gsfs11/users/zhul7/runBNG/tools/pipeline/Solve3.7_03302022_283/RefGenome/hg38_DLE1_0kb_0labels.cmap
The qry cmap file is: /gpfs/gsfs11/users/zhul7/bionano220729/1_RX_20K/output/contigs/exp_refineFinal1/1_RX_20K.cmap
The genome size (Mb) is: 3209286105
The Binano RefAligner is: /gpfs/gsfs11/users/zhul7/runBNG/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12542rel/RefAligner
The maximum threads is: 16
The maximum RAM (Gb) is: 50
The output file names are: /data/zhul7/bionano220729/align/align_1_RX_20K*
Current binary /gpfs/gsfs11/users/zhul7/runBNG/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12542rel/RefAligner compiled with SSE3=1, AVX=1, AVX2=1, AVX512=0 /proc/cpuinfo: avx512= 0, znver2= 1: model name : AMD EPYC 7543 32-Core Processor builtin_cpu_supports(avx2)= 1024, GNUC= 9 builtin_cpu_is(znver2)= 0 WARNING: host cn4327 supports AMD Zen2 : switching to better binary execname=/gpfs/gsfs11/users/zhul7/runBNG/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12542rel,q=/RefAligner,p= Trying alternate binary: /gpfs/gsfs11/users/zhul7/runBNG/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12542rel/amd2/RefAligner Current binary /gpfs/gsfs11/users/zhul7/runBNG/tools/pipeline/Solve3.7_03302022_283/RefAligner/12432.12542rel/amd2/RefAligner compiled with SSE3=1, AVX=1, AVX2=1, AVX512=0 /proc/cpuinfo: avx512= 0, znver2= 1: model name : AMD EPYC 7543 32-Core Processor builtin_cpu_supports(avx2)= 1024, GNUC= 9 builtin_cpu_is(znver2)= 0 Appending stdout to /data/zhul7/bionano220729/align/align_1_RX_20K.stdout Appending stderr to /data/zhul7/bionano220729/align/align_1_RX_20K.stdout /data/zhul7/runBNG/runBNG: line 1756: 41181 Bus error "$RefA" -f -ref "$ref" -i "$qry" -o "$outDir_full" -maxthreads "$maxthreads" -output-veto-filter _intervals.txt$ -res 2.9 -FP 0.6 -FN 0.06 -sf 0.20 -sd 0.0 -sr 0.01 -extend 1 -outlier 0.0001 -endoutlier 0.001 -PVendoutlier -deltaX 12 -deltaY 12 -xmapchim 12 -hashgen 5 7 2.4 1.5 0.05 5.0 1 1 1 -hash -hashdelta 50 -mres 1e-3 -hashMultiMatch 100 -insertThreads 4 -nosplit 2 -biaswt 0 -T "$pv" -S -1000 -indel -PVres 2 -rres 0.9 -MaxSE 0.5 -HSDrange 1.0 -outlierBC -xmapUnique 12 -AlignRes 2. -outlierExtend 12 24 -Kmax 12 -f -maxmem "$maxmem" -BestRef 1 -stdout -stderr 1>&1
End date: Tue Aug 2 15:10:12 EDT 2022
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