"BBmapVs.Ref (super fast run, less sensitive)" - Views: 226 · Hits: 226 - Type: Public

[email protected]:~/FUSARIUM/solexa/EthFoc11$ srun --partition=high --mem=24000 --time=72:00:00 --nodes=1 bbmap.sh usejni=f usemodulo fast minid=0.9 maxindel=3 perfectmode=t bwr=0.16 bw=12 t=8 in1=EthFoc-11_1_clean.fq in2=EthFoc-11_2_clean.fq outm=EthFoc-11_Vs_ASM175734v1_mapped.sam outu=EthFoc-11_Vs_ASM175734v1_UNmapped.sam ref=GCA_001757345.1_ASM175734v1_genomic.fna mhist=EthFoc-11_Vs_ASM175734v1_BBmap_mhist.txt qhist=EthFoc-11_Vs_ASM175734v1_BBmap_qhist.txt qahist=EthFoc-11_Vs_ASM175734v1_BBmap_qahist.txt
srun: job 13810482 queued and waiting for resources
[srun: job 13810482 has been allocated resources
java -Djava.library.path=/share/apps/bio/bio/opt/bbmap-36.32/jni/ -ea -Xmx44525m -cp /share/apps/bio/bio/opt/bbmap-36.32/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 usejni=f usemodulo fast minid=0.9 maxindel=3 perfectmode=t bwr=0.16 bw=12 t=8 in1=EthFoc-11_1_clean.fq in2=EthFoc-11_2_clean.fq outm=EthFoc-11_Vs_ASM175734v1_mapped.sam outu=EthFoc-11_Vs_ASM175734v1_UNmapped.sam ref=GCA_001757345.1_ASM175734v1_genomic.fna mhist=EthFoc-11_Vs_ASM175734v1_BBmap_mhist.txt qhist=EthFoc-11_Vs_ASM175734v1_BBmap_qhist.txt qahist=EthFoc-11_Vs_ASM175734v1_BBmap_qahist.txt
Executing align2.BBMap [tipsearch=20, maxindel=80, minhits=2, bwr=0.18, bw=40, minratio=0.65, midpad=150, minscaf=50, quickmatch=t, rescuemismatches=15, rescuedist=800, maxsites=3, maxsites2=100, build=1, overwrite=true, fastareadlen=500, usejni=f, usemodulo, minid=0.9, maxindel=3, perfectmode=t, bwr=0.16, bw=12, t=8, in1=EthFoc-11_1_clean.fq, in2=EthFoc-11_2_clean.fq, outm=EthFoc-11_Vs_ASM175734v1_mapped.sam, outu=EthFoc-11_Vs_ASM175734v1_UNmapped.sam, ref=GCA_001757345.1_ASM175734v1_genomic.fna, mhist=EthFoc-11_Vs_ASM175734v1_BBmap_mhist.txt, qhist=EthFoc-11_Vs_ASM175734v1_BBmap_qhist.txt, qahist=EthFoc-11_Vs_ASM175734v1_BBmap_qahist.txt]

BBMap version 36.32
Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.650
Set threads to 8
Set match histogram output to EthFoc-11_Vs_ASM175734v1_BBmap_mhist.txt
Set quality histogram output to EthFoc-11_Vs_ASM175734v1_BBmap_qhist.txt
Set quality accuracy histogram output to EthFoc-11_Vs_ASM175734v1_BBmap_qahist.txt
Retaining first best site only for ambiguous mappings.
Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.816
Writing reference.
Executing dna.FastaToChromArrays2 [GCA_001757345.1_ASM175734v1_genomic.fna, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=50, midpad=150, startpad=8000, stoppad=8000, nodisk=false]

Set genScaffoldInfo=true
Writing chunk 1
Set genome to 1

Loaded Reference:	0.038 seconds.
Loading index for chunk 1-1, build 1
No index available; generating from reference genome: /home/aksrao/FUSARIUM/solexa/EthFoc11/ref/index/1/chr1_index_k13_c5_b1.block
Indexing threads started for block 0-1
Indexing threads finished for block 0-1
Generated Index:	5.969 seconds.
Analyzed Index:   	4.250 seconds.
Started output stream:	0.039 seconds.
Started output stream:	0.003 seconds.
Cleared Memory:    	0.472 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 8 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7

   ------------------   Results   ------------------   

Genome:                	1
Key Length:            	13
Max Indel:             	0
Minimum Score Ratio:  	1.0
Mapping Mode:         	perfect
Reads Used:           	33192724	(4978908600 bases)

Mapping:          	259.897 seconds.
Reads/sec:       	127714.70
kBases/sec:      	19157.21


Pairing data:   	pct reads	num reads 	pct bases	   num bases

mated pairs:     	  5.7547% 	   955079 	  5.7547% 	   286523700
bad pairs:       	  0.2265% 	    37597 	  0.2265% 	    11279100
insert size avg: 	  228.07


Read 1 data:      	pct reads	num reads 	pct bases	   num bases

mapped:          	 12.9524% 	  2149624 	 12.9524% 	   322443600
unambiguous:     	 12.9166% 	  2143690 	 12.9166% 	   321553500
ambiguous:       	  0.0358% 	     5934 	  0.0358% 	      890100
low-Q discards:  	  0.8665% 	   143808 	  0.8665% 	    21571200

perfect best site:	 12.9524% 	  2149624 	 12.9524% 	   322443600
semiperfect site:	 12.9524% 	  2149624 	 12.9524% 	   322443600
rescued:         	  0.0001% 	       10

Match Rate:      	      NA 	       NA 	100.0000% 	   322443600
Error Rate:      	  0.0000% 	        0 	  0.0000% 	           0
Sub Rate:        	  0.0000% 	        0 	  0.0000% 	           0
Del Rate:        	  0.0000% 	        0 	  0.0000% 	           0
Ins Rate:        	  0.0000% 	        0 	  0.0000% 	           0
N Rate:          	  0.0000% 	        0 	  0.0000% 	           0


Read 2 data:      	pct reads	num reads 	pct bases	   num bases

mapped:          	 11.1580% 	  1851830 	 11.1580% 	   277774500
unambiguous:     	 11.1260% 	  1846518 	 11.1260% 	   276977700
ambiguous:       	  0.0320% 	     5312 	  0.0320% 	      796800
low-Q discards:  	  1.9668% 	   326410 	  1.9668% 	    48961500

perfect best site:	 11.1580% 	  1851830 	 11.1580% 	   277774500
semiperfect site:	 11.1580% 	  1851830 	 11.1580% 	   277774500
rescued:         	  0.0000% 	        8

Match Rate:      	      NA 	       NA 	100.0000% 	   277774500
Error Rate:      	  0.0000% 	        0 	  0.0000% 	           0
Sub Rate:        	  0.0000% 	        0 	  0.0000% 	           0
Del Rate:        	  0.0000% 	        0 	  0.0000% 	           0
Ins Rate:        	  0.0000% 	        0 	  0.0000% 	           0
N Rate:          	  0.0000% 	        0 	  0.0000% 	           0

Total time:     	272.051 seconds.