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/SCP03/SCP03_MKRN250024229-1A_22VNWKLT4_L6_1.fq.gz in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCP03/SCP03_MKRN250024229-1A_22VNWKLT4_L6_2.fq.gz out=TRIMMED/SCP03_MKRN250024229-1A_22VNWKLT4_L6_1.fastq out2=TRIMMED/SCP03_MKRN250024229-1A_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/SCP03_MKRN250024229-1A_22VNWKLT4_L6.bbduk2_stats.txt
Executing jgi.BBDuk2 [-Xmx4g, threads=8, in=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCP03/SCP03_MKRN250024229-1A_22VNWKLT4_L6_1.fq.gz, in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCP03/SCP03_MKRN250024229-1A_22VNWKLT4_L6_2.fq.gz, out=TRIMMED/SCP03_MKRN250024229-1A_22VNWKLT4_L6_1.fastq, out2=TRIMMED/SCP03_MKRN250024229-1A_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/SCP03_MKRN250024229-1A_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: 	0.157 seconds.
Memory: max=4294m, free=4262m, used=32m

Input is being processed as paired
Started output streams:	0.026 seconds.
Processing time:   		90.513 seconds.

Input:                  	35975120 reads 		5396268000 bases.
QTrimmed:               	576159 reads (1.60%) 	116423013 bases (2.16%)
KTrimmed:               	381806 reads (1.06%) 	15929723 bases (0.30%)
Trimmed by overlap:     	181424 reads (0.50%) 	1918100 bases (0.04%)
Low quality discards:   	0 reads (0.00%) 	0 bases (0.00%)
Total Removed:          	815946 reads (2.27%) 	134001525 bases (2.48%)
Result:                 	35159174 reads (97.73%) 	5262266475 bases (97.52%)

Time:   			90.739 seconds.
Reads Processed:      35975k 	396.47k reads/sec
Bases Processed:       5396m 	59.47m bases/sec
