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/SCP02/SCP02_MKRN250024228-1A_22VTJNLT4_L5_1.fq.gz in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCP02/SCP02_MKRN250024228-1A_22VTJNLT4_L5_2.fq.gz out=TRIMMED/SCP02_MKRN250024228-1A_22VTJNLT4_L5_1.fastq out2=TRIMMED/SCP02_MKRN250024228-1A_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/SCP02_MKRN250024228-1A_22VTJNLT4_L5.bbduk2_stats.txt
Executing jgi.BBDuk2 [-Xmx4g, threads=8, in=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCP02/SCP02_MKRN250024228-1A_22VTJNLT4_L5_1.fq.gz, in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCP02/SCP02_MKRN250024228-1A_22VTJNLT4_L5_2.fq.gz, out=TRIMMED/SCP02_MKRN250024228-1A_22VTJNLT4_L5_1.fastq, out2=TRIMMED/SCP02_MKRN250024228-1A_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/SCP02_MKRN250024228-1A_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: 	0.160 seconds.
Memory: max=4294m, free=4263m, used=31m

Input is being processed as paired
Started output streams:	0.032 seconds.
Processing time:   		93.162 seconds.

Input:                  	38381124 reads 		5757168600 bases.
QTrimmed:               	787035 reads (2.05%) 	148755991 bases (2.58%)
KTrimmed:               	510124 reads (1.33%) 	23722438 bases (0.41%)
Trimmed by overlap:     	226506 reads (0.59%) 	2721522 bases (0.05%)
Low quality discards:   	0 reads (0.00%) 	0 bases (0.00%)
Total Removed:          	1053588 reads (2.75%) 	174697065 bases (3.03%)
Result:                 	37327536 reads (97.25%) 	5582471535 bases (96.97%)

Time:   			93.398 seconds.
Reads Processed:      38381k 	410.94k reads/sec
Bases Processed:       5757m 	61.64m bases/sec
