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AppliedBioinformatics / runBNG

An easy way to run BioNano genomic analysis
MIT License
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Irys data with splitbnx error #40

Open Johnsonzcode opened 1 year ago

Johnsonzcode commented 1 year ago

Dear @yyx8671 Than you for your integration of Bionnao software. When I run with runBNG v1.3 and old Bionano packages as you mentioned in here, it seems the all.bnx will be replaced with a very small file size. There are 5050 files like align/exppairwise2559of5050.stdout It shows

# hostname=pbsnode01
# $ cd /storage-02/zhaoqiangsen/genome_asm/mallard/50k_ctg_hic_scafed_filled_bionano_cor; /storage-01/poultrylab1/zhaoqiangsen/software/runBNG/bionano/tools/RefAligner -first -1 -i /storage-02/zhaoqiangsen/genome_asm/mallard/50k_ctg_hic_scafed_filled_bionano_cor/all_30_of_100.bnx -i /storage-02/zhaoqiangsen/genome_asm/mallard/50k_ctg_hic_scafed_filled_bionano_cor/all_94_of_100.bnx -o /storage-02/zhaoqiangsen/genome_asm/mallard/50k_ctg_hic_scafed_filled_bionano_cor/align/exppairwise2559of5050 -usecolor 1 -FP 1.66 -FN 0.08 -sd -0.02 -sf 0.13 -sr 0.02 -res 3.3 -T 8.33333e-09 -maxmem 100 -minlen 150 -minsites 8 -MaxIntensity 0.6 -usecolor 1 -maxsites 200 -mres 0.9 -usecolor 1 -A 5 -S 1 -MaxSE 0.5 -outlier 0.0001 -outlierMax 40. -endoutlier 0 -RepeatMask 2 0.01 -RepeatRec 0.7 0.6 1.4 -PVres 2 -alignscore -maptype 0 -HSDrange 1.0 -hashoffset 1 -f -hashgen 5 3 2.2 1.2 0.05 3.0 1 1 1 -hash -nosplit 2 -align_format 1 -stdout -stderr -maxthreads 10 -XmapStatRead /storage-02/zhaoqiangsen/genome_asm/mallard/50k_ctg_hic_scafed_filled_bionano_cor/molecule_stats.txt
# CompileDir= /home/users3/tanantharaman/branches/4794/4794.5122/4794.5122 CompileCmd=/opt/gcc-4.9.2TSAN/bin/g++ -fopenmp -Ofast -fno-associative-math -mavx -mfpmath=sse -DUSE_PFLOAT=1 -DUSE_RFLOAT=1 -DUSE_SSE=1 -I/home/users/tanantharaman/amdlibm-3-0-2/include -DREPLACE_WITH_AMDLIBM -DUSE_STATIC -flto -DRELEASE=1 -lrt -L/home/users/tanantharaman/amdlibm-3-0-2/lib/static -lamdlibm -L/opt/gcc-4.9.2TSAN/lib64 -s -static SVNversion=5122 $Header: http://svn.bnm.local:81/svn/Informatics/RefAligner/branches/4794/RefAligner.cpp 4916 2016-05-10 18:12:38Z kbhakta $
# FLAGS: USE_SSE=1 USE_AVX=1 USE_MIC=0 USE_PFLOAT=1 USE_RFLOAT=1 DEBUG=1 VERB=1
WARNING: -RepeatMask with -RepeatRec requires -extend 1 or -extend 2 (using -extend 1)
Reading input maps from /storage-02/zhaoqiangsen/genome_asm/mallard/50k_ctg_hic_scafed_filled_bionano_cor/all_30_of_100.bnx ... /storage-02/zhaoqiangsen/genome_asm/mallard/50k_ctg_hic_scafed_filled_bionano_cor/all_94_of_100.bnx (2 files)
input_bnx:Failed to read input file /storage-02/zhaoqiangsen/genome_asm/mallard/50k_ctg_hic_scafed_filled_bionano_cor/all_30_of_100.bnx (1'th of 2 files)

How could I solve it ?

Best Johnson