[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_phix174_mapped.sam outu=EthFoc-11_Vs_phix174_UNmapped.sam ref=phix174_ill.ref.fa mhist=EthFoc-11_Vs_phix174_BBmap_mhist.txt qhist=EthFoc-11_Vs_phix174_BBmap_qhist.txt qahist=EthFoc-11_Vs_phix174_BBmap_qahist.txt
srun: job 13810615 queued and waiting for resources
srun: job 13810615 has been allocated resources
java -Djava.library.path=/share/apps/bio/bio/opt/bbmap-36.32/jni/ -ea -Xmx44023m -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_phix174_mapped.sam outu=EthFoc-11_Vs_phix174_UNmapped.sam ref=phix174_ill.ref.fa mhist=EthFoc-11_Vs_phix174_BBmap_mhist.txt qhist=EthFoc-11_Vs_phix174_BBmap_qhist.txt qahist=EthFoc-11_Vs_phix174_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_phix174_mapped.sam, outu=EthFoc-11_Vs_phix174_UNmapped.sam, ref=phix174_ill.ref.fa, mhist=EthFoc-11_Vs_phix174_BBmap_mhist.txt, qhist=EthFoc-11_Vs_phix174_BBmap_qhist.txt, qahist=EthFoc-11_Vs_phix174_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_phix174_BBmap_mhist.txt
Set quality histogram output to EthFoc-11_Vs_phix174_BBmap_qhist.txt
Set quality accuracy histogram output to EthFoc-11_Vs_phix174_BBmap_qahist.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: 1.950 seconds.
Analyzed Index: 3.210 seconds.
Started output stream: 0.032 seconds.
Started output stream: 0.001 seconds.
Cleared Memory: 0.164 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: 162.742 seconds.
Reads/sec: 203958.59
kBases/sec: 30593.79
Pairing data: pct reads num reads pct bases num bases
mated pairs: 0.0033% 554 0.0033% 166200
bad pairs: 0.0000% 8 0.0000% 2400
insert size avg: 357.41
Read 1 data: pct reads num reads pct bases num bases
mapped: 0.0114% 1887 0.0114% 283050
unambiguous: 0.0114% 1887 0.0114% 283050
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: 0.0114% 1887 0.0114% 283050
rescued: 0.0000% 0
Match Rate: NA NA 100.0000% 283050
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: 0.0050% 838 0.0050% 125700
unambiguous: 0.0050% 838 0.0050% 125700
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: 0.0050% 838 0.0050% 125700
rescued: 0.0000% 0
Match Rate: NA NA 100.0000% 125700
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: 168.473 seconds.
