"BBmapVs.phix174 (fast run, better sensitivity)" - Views: 229 · Hits: 229 - 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 semiperfectmode=t t=8 in1=EthFoc-11_1_clean.fq in2=EthFoc-11_2_clean.fq outm=EthFoc-11_Vs_phix174_mapped2.sam outu=EthFoc-11_Vs_phix174_UNmapped2.sam ref=phix174_ill.ref.fa mhist=EthFoc-11_Vs_phix174_BBmap_mhist2.txt qhist=EthFoc-11_Vs_phix174_BBmap_qhist2.txt qahist=EthFoc-11_Vs_phix174_BBmap_qahist2.txt
srun: job 13810699 queued and waiting for resources
srun: job 13810699 has been allocated resources
java -Djava.library.path=/share/apps/bio/bio/opt/bbmap-36.32/jni/ -ea -Xmx44486m -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 semiperfectmode=t t=8 in1=EthFoc-11_1_clean.fq in2=EthFoc-11_2_clean.fq outm=EthFoc-11_Vs_phix174_mapped2.sam outu=EthFoc-11_Vs_phix174_UNmapped2.sam ref=phix174_ill.ref.fa mhist=EthFoc-11_Vs_phix174_BBmap_mhist2.txt qhist=EthFoc-11_Vs_phix174_BBmap_qhist2.txt qahist=EthFoc-11_Vs_phix174_BBmap_qahist2.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, semiperfectmode=t, t=8, in1=EthFoc-11_1_clean.fq, in2=EthFoc-11_2_clean.fq, outm=EthFoc-11_Vs_phix174_mapped2.sam, outu=EthFoc-11_Vs_phix174_UNmapped2.sam, ref=phix174_ill.ref.fa, mhist=EthFoc-11_Vs_phix174_BBmap_mhist2.txt, qhist=EthFoc-11_Vs_phix174_BBmap_qhist2.txt, qahist=EthFoc-11_Vs_phix174_BBmap_qahist2.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_phix174_BBmap_mhist2.txt
Set quality histogram output to EthFoc-11_Vs_phix174_BBmap_qhist2.txt
Set quality accuracy histogram output to EthFoc-11_Vs_phix174_BBmap_qahist2.txt
Retaining first best site only for ambiguous mappings.
Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.816
NOTE:	Deleting contents of ref/genome/1 because reference is specified and overwrite=true
NOTE:	Deleting contents of ref/index/1 because reference is specified and overwrite=true
Writing reference.
Executing dna.FastaToChromArrays2 [phix174_ill.ref.fa, 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:	0.004 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_c16_b1.block
Indexing threads started for block 0-1
Indexing threads finished for block 0-1
Generated Index:	2.003 seconds.
Analyzed Index:   	3.030 seconds.
Started output stream:	0.028 seconds.
Started output stream:	0.033 seconds.
Cleared Memory:    	0.142 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:  	0.45
Mapping Mode:         	semiperfect
Reads Used:           	33192724	(4978908600 bases)

Mapping:          	74.573 seconds.
Reads/sec:       	445105.70
kBases/sec:      	66765.85


Pairing data:   	pct reads	num reads 	pct bases	   num bases

mated pairs:     	  0.0035% 	      583 	  0.0035% 	      174900
bad pairs:       	  0.0002% 	       29 	  0.0002% 	        8700
insert size avg: 	  356.84


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

mapped:          	  0.0118% 	     1956 	  0.0118% 	      293400
unambiguous:     	  0.0118% 	     1956 	  0.0118% 	      293400
ambiguous:       	  0.0000% 	        0 	  0.0000% 	           0
low-Q discards:  	  0.8665% 	   143808 	  0.8665% 	    21571200

perfect best site:	  0.0114% 	     1887 	  0.0114% 	      283050
semiperfect site:	  0.0118% 	     1956 	  0.0118% 	      293400
rescued:         	  0.0000% 	        0

Match Rate:      	      NA 	       NA 	 99.0518% 	      290618
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:          	  3.5276% 	       69 	  0.9482% 	        2782


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

mapped:          	  0.0052% 	      870 	  0.0052% 	      130500
unambiguous:     	  0.0052% 	      870 	  0.0052% 	      130500
ambiguous:       	  0.0000% 	        0 	  0.0000% 	           0
low-Q discards:  	  1.9668% 	   326410 	  1.9668% 	    48961500

perfect best site:	  0.0050% 	      838 	  0.0050% 	      125700
semiperfect site:	  0.0052% 	      870 	  0.0052% 	      130500
rescued:         	  0.0000% 	        0

Match Rate:      	      NA 	       NA 	 99.0383% 	      129245
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:          	  3.6782% 	       32 	  0.9617% 	        1255

Total time:     	80.215 seconds.