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_22VTJNLT4_L5_1.fq.gz in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCP03/SCP03_MKRN250024229-1A_22VTJNLT4_L5_2.fq.gz out=TRIMMED/SCP03_MKRN250024229-1A_22VTJNLT4_L5_1.fastq out2=TRIMMED/SCP03_MKRN250024229-1A_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/SCP03_MKRN250024229-1A_22VTJNLT4_L5.bbduk2_stats.txt
Executing jgi.BBDuk2 [-Xmx4g, threads=8, in=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCP03/SCP03_MKRN250024229-1A_22VTJNLT4_L5_1.fq.gz, in2=/home/upload/files/PG_C._albicans_RNAseq/01.RawData/SCP03/SCP03_MKRN250024229-1A_22VTJNLT4_L5_2.fq.gz, out=TRIMMED/SCP03_MKRN250024229-1A_22VTJNLT4_L5_1.fastq, out2=TRIMMED/SCP03_MKRN250024229-1A_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/SCP03_MKRN250024229-1A_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: 	0.172 seconds.
Memory: max=4294m, free=4263m, used=31m

Input is being processed as paired
Started output streams:	0.040 seconds.
Processing time:   		118.398 seconds.

Input:                  	12499360 reads 		1874904000 bases.
QTrimmed:               	238496 reads (1.91%) 	45051089 bases (2.40%)
KTrimmed:               	131934 reads (1.06%) 	5523899 bases (0.29%)
Trimmed by overlap:     	63038 reads (0.50%) 	662714 bases (0.04%)
Low quality discards:   	0 reads (0.00%) 	0 bases (0.00%)
Total Removed:          	310886 reads (2.49%) 	51139555 bases (2.73%)
Result:                 	12188474 reads (97.51%) 	1823764445 bases (97.27%)

Time:   			118.655 seconds.
Reads Processed:      12499k 	105.34k reads/sec
Bases Processed:       1874m 	15.80m bases/sec
