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/SCE03/SCE03_MKRN250024226-1A_22VTJNLT4_L5_1.fq.gz in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCE03/SCE03_MKRN250024226-1A_22VTJNLT4_L5_2.fq.gz out=TRIMMED/SCE03_MKRN250024226-1A_22VTJNLT4_L5_1.fastq out2=TRIMMED/SCE03_MKRN250024226-1A_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/SCE03_MKRN250024226-1A_22VTJNLT4_L5.bbduk2_stats.txt
Executing jgi.BBDuk2 [-Xmx4g, threads=8, in=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCE03/SCE03_MKRN250024226-1A_22VTJNLT4_L5_1.fq.gz, in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCE03/SCE03_MKRN250024226-1A_22VTJNLT4_L5_2.fq.gz, out=TRIMMED/SCE03_MKRN250024226-1A_22VTJNLT4_L5_1.fastq, out2=TRIMMED/SCE03_MKRN250024226-1A_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/SCE03_MKRN250024226-1A_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=4263m, used=31m

Input is being processed as paired
Started output streams:	0.032 seconds.
Processing time:   		94.771 seconds.

Input:                  	14319590 reads 		2147938500 bases.
QTrimmed:               	229016 reads (1.60%) 	42629646 bases (1.98%)
KTrimmed:               	217366 reads (1.52%) 	12026514 bases (0.56%)
Trimmed by overlap:     	81402 reads (0.57%) 	862990 bases (0.04%)
Low quality discards:   	0 reads (0.00%) 	0 bases (0.00%)
Total Removed:          	325258 reads (2.27%) 	55262652 bases (2.57%)
Result:                 	13994332 reads (97.73%) 	2092675848 bases (97.43%)

Time:   			94.990 seconds.
Reads Processed:      14319k 	150.75k reads/sec
Bases Processed:       2147m 	22.61m bases/sec
