"bbmap_SLOW" - Views: 225 · Hits: 225 - Type: Public

[email protected]:~/FUSARIUM/solexa/EthFoc11$ srun --partition=high --mem=24000 --time=72:00:00 --nodes=1 bbmap.sh usejni=f slow t=8 in1=EthFoc-11_1_clean.fq in2=EthFoc-11_2_clean.fq outm=EthFoc-11_Vs_ASM175734v1_mapped3.sam outu=EthFoc-11_Vs_ASM175734v1_UNmapped3.sam ref=GCA_001757345.1_ASM175734v1_genomic.fna mhist=EthFoc-11_Vs_ASM175734v1_BBmap_mhist3.txt qhist=EthFoc-11_Vs_ASM175734v1_BBmap_qhist3.txt qahist=EthFoc-11_Vs_ASM175734v1_BBmap_qahist3.txt
srun: job 13812483 queued and waiting for resources
srun: job 13812483 has been allocated resources
java -Djava.library.path=/share/apps/bio/bio/opt/bbmap-36.32/jni/ -ea -Xmx44505m -cp /share/apps/bio/bio/opt/bbmap-36.32/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 usejni=f slow t=8 in1=EthFoc-11_1_clean.fq in2=EthFoc-11_2_clean.fq outm=EthFoc-11_Vs_ASM175734v1_mapped3.sam outu=EthFoc-11_Vs_ASM175734v1_UNmapped3.sam ref=GCA_001757345.1_ASM175734v1_genomic.fna mhist=EthFoc-11_Vs_ASM175734v1_BBmap_mhist3.txt qhist=EthFoc-11_Vs_ASM175734v1_BBmap_qhist3.txt qahist=EthFoc-11_Vs_ASM175734v1_BBmap_qahist3.txt
Executing align2.BBMap [tipsearch=150, minhits=1, minratio=0.45, build=1, overwrite=true, fastareadlen=500, usejni=f, t=8, in1=EthFoc-11_1_clean.fq, in2=EthFoc-11_2_clean.fq, outm=EthFoc-11_Vs_ASM175734v1_mapped3.sam, outu=EthFoc-11_Vs_ASM175734v1_UNmapped3.sam, ref=GCA_001757345.1_ASM175734v1_genomic.fna, mhist=EthFoc-11_Vs_ASM175734v1_BBmap_mhist3.txt, qhist=EthFoc-11_Vs_ASM175734v1_BBmap_qhist3.txt, qahist=EthFoc-11_Vs_ASM175734v1_BBmap_qahist3.txt]

BBMap version 36.32
Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.450
Set threads to 8
Set match histogram output to EthFoc-11_Vs_ASM175734v1_BBmap_mhist3.txt
Set quality histogram output to EthFoc-11_Vs_ASM175734v1_BBmap_qhist3.txt
Set quality accuracy histogram output to EthFoc-11_Vs_ASM175734v1_BBmap_qahist3.txt
Retaining first best site only for ambiguous mappings.
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 [GCA_001757345.1_ASM175734v1_genomic.fna, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=false]

Set genScaffoldInfo=true
Writing chunk 1
Set genome to 1

Loaded Reference:	0.032 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:	9.376 seconds.
Analyzed Index:   	3.278 seconds.
Started output stream:	0.068 seconds.
Started output stream:	0.002 seconds.
Cleared Memory:    	0.227 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:             	16000
Minimum Score Ratio:  	0.45
Mapping Mode:         	normal
Reads Used:           	33192724	(4978908600 bases)

Mapping:          	6616.921 seconds.
Reads/sec:       	5016.34
kBases/sec:      	752.45


Pairing data:   	pct reads	num reads 	pct bases	   num bases

mated pairs:     	 61.2585% 	 10166677 	 61.2585% 	  3050003100
bad pairs:       	 10.0694% 	  1671150 	 10.0694% 	   501345000
insert size avg: 	  239.04


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

mapped:          	 76.3620% 	 12673315 	 76.3620% 	  1900997250
unambiguous:     	 75.2899% 	 12495383 	 75.2899% 	  1874307450
ambiguous:       	  1.0721% 	   177932 	  1.0721% 	    26689800
low-Q discards:  	  0.0000% 	        0 	  0.0000% 	           0

perfect best site:	 12.9554% 	  2150123 	 12.9554% 	   322518450
semiperfect site:	 12.9812% 	  2154402 	 12.9812% 	   323160300
rescued:         	  3.6438% 	   604744

Match Rate:      	      NA 	       NA 	 85.6864% 	  1778419704
Error Rate:      	 82.8777% 	 10503659 	 14.2007% 	   294734949
Sub Rate:        	 81.9037% 	 10380219 	  4.0463% 	    83981465
Del Rate:        	 12.5412% 	  1589429 	  8.4077% 	   174501595
Ins Rate:        	 19.8207% 	  2512013 	  1.7467% 	    36251889
N Rate:          	  1.5546% 	   197030 	  0.1129% 	     2344192


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

mapped:          	 75.8273% 	 12584577 	 75.8273% 	  1887686550
unambiguous:     	 74.7755% 	 12410005 	 74.7755% 	  1861500750
ambiguous:       	  1.0519% 	   174572 	  1.0519% 	    26185800
low-Q discards:  	  0.0019% 	      320 	  0.0019% 	       48000

perfect best site:	 11.1606% 	  1852254 	 11.1606% 	   277838100
semiperfect site:	 11.1840% 	  1856140 	 11.1840% 	   278421000
rescued:         	  4.5283% 	   751541

Match Rate:      	      NA 	       NA 	 84.2406% 	  1759587823
Error Rate:      	 85.0369% 	 10701690 	 15.6555% 	   327006034
Sub Rate:        	 84.1893% 	 10595010 	  4.3652% 	    91179643
Del Rate:        	 12.3038% 	  1548408 	  9.6267% 	   201078181
Ins Rate:        	 19.1519% 	  2410223 	  1.6636% 	    34748210
N Rate:          	  2.6385% 	   332043 	  0.1039% 	     2170874

Total time:     	6632.737 seconds.