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trim_task_list.txt
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skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep3/5_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./5x/rep3/5_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep1/5_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./5x/rep1/5_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./5x/rep2/5_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./5x/rep2/5_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep3/3_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./3x/rep3/3_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep1/3_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./3x/rep1/3_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./3x/rep2/3_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./3x/rep2/3_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep2/4_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./4x/rep2/4_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep1/4_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./4x/rep1/4_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./4x/rep3/4_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./4x/rep3/4_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep1/10_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./10x/rep1/10_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep2/10_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./10x/rep2/10_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./10x/rep3/10_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./10x/rep3/10_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep3/7_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./7x/rep3/7_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep1/7_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./7x/rep1/7_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./7x/rep2/7_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./7x/rep2/7_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep1/8_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./8x/rep1/8_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep2/8_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./8x/rep2/8_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./8x/rep3/8_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./8x/rep3/8_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep3/6_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./6x/rep3/6_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep2/6_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./6x/rep2/6_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./6x/rep1/6_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./6x/rep1/6_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep2/9_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./9x/rep2/9_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep1/9_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./9x/rep1/9_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01396-L1_S11_L008_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01396-L1_S11_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01392-L1_S7_L005_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01392-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01401-L1_S4_L003_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01401-L1_S4_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01403-L1_S6_L003_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01403-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01406-L1_S9_L006_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01406-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01391-L1_S6_L004_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01391-L1_S6_L004_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01399-L1_S2_L001_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01399-L1_S2_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01400-L1_S3_L001_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01400-L1_S3_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01402-L1_S5_L003_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01402-L1_S5_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01395-L1_S10_L007_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01395-L1_S10_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01398-L1_S1_L001_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01398-L1_S1_L001_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01405-L1_S8_L006_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01405-L1_S8_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01406-L1_S9_L005_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01406-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01399-L1_S2_L002_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01399-L1_S2_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01397-L1_S12_L008_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01397-L1_S12_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01392-L1_S7_L006_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01392-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01405-L1_S8_L005_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01405-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01400-L1_S3_L002_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01400-L1_S3_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01398-L1_S1_L002_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01398-L1_S1_L002_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01394-L1_S9_L006_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01394-L1_S9_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01404-L1_S7_L006_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01404-L1_S7_L006_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01396-L1_S11_L007_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01396-L1_S11_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01391-L1_S6_L003_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01391-L1_S6_L003_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01395-L1_S10_L008_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01395-L1_S10_L008_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01393-L1_S8_L005_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01393-L1_S8_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01397-L1_S12_L007_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01397-L1_S12_L007_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01394-L1_S9_L005_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01394-L1_S9_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01404-L1_S7_L005_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01404-L1_S7_L005_shuffled.fastq.pair2.fastq
skewer -m PE -q 30 -l 54 -n -z -t 8 --quiet ./9x/rep3/9_H01393-L1_S8_L006_shuffled.fastq.pair1.fastq ./9x/rep3/9_H01393-L1_S8_L006_shuffled.fastq.pair2.fastq