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/SCE02/SCE02_MKRN250024225-1A_22VNWKLT4_L6_1.fq.gz in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCE02/SCE02_MKRN250024225-1A_22VNWKLT4_L6_2.fq.gz out=TRIMMED/SCE02_MKRN250024225-1A_22VNWKLT4_L6_1.fastq out2=TRIMMED/SCE02_MKRN250024225-1A_22VNWKLT4_L6_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/SCE02_MKRN250024225-1A_22VNWKLT4_L6.bbduk2_stats.txt
Executing jgi.BBDuk2 [-Xmx4g, threads=8, in=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCE02/SCE02_MKRN250024225-1A_22VNWKLT4_L6_1.fq.gz, in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCE02/SCE02_MKRN250024225-1A_22VNWKLT4_L6_2.fq.gz, out=TRIMMED/SCE02_MKRN250024225-1A_22VNWKLT4_L6_1.fastq, out2=TRIMMED/SCE02_MKRN250024225-1A_22VNWKLT4_L6_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/SCE02_MKRN250024225-1A_22VNWKLT4_L6.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: 	0.155 seconds.
Memory: max=4294m, free=4264m, used=30m

Input is being processed as paired
Started output streams:	0.029 seconds.
Processing time:   		78.249 seconds.

Input:                  	31538882 reads 		4730832300 bases.
QTrimmed:               	544202 reads (1.73%) 	107807239 bases (2.28%)
KTrimmed:               	476810 reads (1.51%) 	21841169 bases (0.46%)
Trimmed by overlap:     	198624 reads (0.63%) 	1979112 bases (0.04%)
Low quality discards:   	0 reads (0.00%) 	0 bases (0.00%)
Total Removed:          	780740 reads (2.48%) 	131434947 bases (2.78%)
Result:                 	30758142 reads (97.52%) 	4599397353 bases (97.22%)

Time:   			78.468 seconds.
Reads Processed:      31538k 	401.93k reads/sec
Bases Processed:       4730m 	60.29m bases/sec
