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_22VNWKLT4_L6_1.fq.gz in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCE03/SCE03_MKRN250024226-1A_22VNWKLT4_L6_2.fq.gz out=TRIMMED/SCE03_MKRN250024226-1A_22VNWKLT4_L6_1.fastq out2=TRIMMED/SCE03_MKRN250024226-1A_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/SCE03_MKRN250024226-1A_22VNWKLT4_L6.bbduk2_stats.txt
Executing jgi.BBDuk2 [-Xmx4g, threads=8, in=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCE03/SCE03_MKRN250024226-1A_22VNWKLT4_L6_1.fq.gz, in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCE03/SCE03_MKRN250024226-1A_22VNWKLT4_L6_2.fq.gz, out=TRIMMED/SCE03_MKRN250024226-1A_22VNWKLT4_L6_1.fastq, out2=TRIMMED/SCE03_MKRN250024226-1A_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/SCE03_MKRN250024226-1A_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: 	0.150 seconds.
Memory: max=4294m, free=4264m, used=30m

Input is being processed as paired
Started output streams:	0.031 seconds.
Processing time:   		68.431 seconds.

Input:                  	27044482 reads 		4056672300 bases.
QTrimmed:               	402629 reads (1.49%) 	80746140 bases (1.99%)
KTrimmed:               	439602 reads (1.63%) 	24579810 bases (0.61%)
Trimmed by overlap:     	160232 reads (0.59%) 	1633092 bases (0.04%)
Low quality discards:   	0 reads (0.00%) 	0 bases (0.00%)
Total Removed:          	629210 reads (2.33%) 	106496088 bases (2.63%)
Result:                 	26415272 reads (97.67%) 	3950176212 bases (97.37%)

Time:   			68.647 seconds.
Reads Processed:      27044k 	393.97k reads/sec
Bases Processed:       4056m 	59.09m bases/sec
