[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.
