java -Djava.library.path=/home/michael/pieranski/bbmap/jni/ -ea -Xmx4g -Xms4g -cp /home/michael/pieranski/bbmap/current/ jgi.BBDuk2 -Xmx4g threads=8 in=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCE01/SCE01_MKRN250024224-1A_22VTJNLT4_L5_1.fq.gz in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCE01/SCE01_MKRN250024224-1A_22VTJNLT4_L5_2.fq.gz out=TRIMMED/SCE01_MKRN250024224-1A_22VTJNLT4_L5_1.fastq out2=TRIMMED/SCE01_MKRN250024224-1A_22VTJNLT4_L5_2.fastq qtrim=w trimq=20 maq=10 rref=bbmap/resources/adapters.fa k=23 mink=11 hdist=1 tbo tpe minlength=100 removeifeitherbad=t overwrite=t stats=STATUS/SCE01_MKRN250024224-1A_22VTJNLT4_L5.bbduk2_stats.txt
Executing jgi.BBDuk2 [-Xmx4g, threads=8, in=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCE01/SCE01_MKRN250024224-1A_22VTJNLT4_L5_1.fq.gz, in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCE01/SCE01_MKRN250024224-1A_22VTJNLT4_L5_2.fq.gz, out=TRIMMED/SCE01_MKRN250024224-1A_22VTJNLT4_L5_1.fastq, out2=TRIMMED/SCE01_MKRN250024224-1A_22VTJNLT4_L5_2.fastq, qtrim=w, trimq=20, maq=10, rref=bbmap/resources/adapters.fa, k=23, mink=11, hdist=1, tbo, tpe, minlength=100, removeifeitherbad=t, overwrite=t, stats=STATUS/SCE01_MKRN250024224-1A_22VTJNLT4_L5.bbduk2_stats.txt]

BBDuk2 version 37.02
Set threads to 8
maskMiddle was disabled because useShortKmers=true
k=23
mink=11
hamming distance=1
right-ktrimming using 1 reference.
quality-trimming right end to Q20

Initial:
Memory: max=4294m, free=4274m, used=20m

Added 216529 kmers; time: 	0.149 seconds.
Memory: max=4294m, free=4262m, used=32m

Input is being processed as paired
Started output streams:	0.026 seconds.
Processing time:   		33.336 seconds.

Input:                  	13198776 reads 		1979816400 bases.
QTrimmed:               	259701 reads (1.97%) 	48426427 bases (2.45%)
KTrimmed:               	249122 reads (1.89%) 	12372832 bases (0.62%)
Trimmed by overlap:     	98662 reads (0.75%) 	900696 bases (0.05%)
Low quality discards:   	0 reads (0.00%) 	0 bases (0.00%)
Total Removed:          	359652 reads (2.72%) 	61489527 bases (3.11%)
Result:                 	12839124 reads (97.28%) 	1918326873 bases (96.89%)

Time:   			33.547 seconds.
Reads Processed:      13198k 	393.44k reads/sec
Bases Processed:       1979m 	59.02m bases/sec
