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/SCP01/SCP01_MKRN250024227-1A_22VNWKLT4_L6_1.fq.gz in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCP01/SCP01_MKRN250024227-1A_22VNWKLT4_L6_2.fq.gz out=TRIMMED/SCP01_MKRN250024227-1A_22VNWKLT4_L6_1.fastq out2=TRIMMED/SCP01_MKRN250024227-1A_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/SCP01_MKRN250024227-1A_22VNWKLT4_L6.bbduk2_stats.txt
Executing jgi.BBDuk2 [-Xmx4g, threads=8, in=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCP01/SCP01_MKRN250024227-1A_22VNWKLT4_L6_1.fq.gz, in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCP01/SCP01_MKRN250024227-1A_22VNWKLT4_L6_2.fq.gz, out=TRIMMED/SCP01_MKRN250024227-1A_22VNWKLT4_L6_1.fastq, out2=TRIMMED/SCP01_MKRN250024227-1A_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/SCP01_MKRN250024227-1A_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=4273m, used=21m

Added 216529 kmers; time: 	0.138 seconds.
Memory: max=4294m, free=4262m, used=32m

Input is being processed as paired
Started output streams:	0.026 seconds.
Processing time:   		71.369 seconds.

Input:                  	29366520 reads 		4404978000 bases.
QTrimmed:               	466421 reads (1.59%) 	94202525 bases (2.14%)
KTrimmed:               	518914 reads (1.77%) 	26775050 bases (0.61%)
Trimmed by overlap:     	179746 reads (0.61%) 	2127728 bases (0.05%)
Low quality discards:   	0 reads (0.00%) 	0 bases (0.00%)
Total Removed:          	723322 reads (2.46%) 	122773197 bases (2.79%)
Result:                 	28643198 reads (97.54%) 	4282204803 bases (97.21%)

Time:   			71.576 seconds.
Reads Processed:      29366k 	410.29k reads/sec
Bases Processed:       4404m 	61.54m bases/sec
