TrimmomaticPE: Started with arguments: -threads 8 /output/Preprocessing/MT.R1.fq /output/Preprocessing/MT.R2.fq /output/Preprocessing/MT.R1.trimmed.fq /output/Preprocessing/MT.SE1.trimmed.fq /output/Preprocessing/MT.R2.trimmed.fq /output/Preprocessing/MT.SE2.trimmed.fq ILLUMINACLIP:/databases/adapters/TruSeq2-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:1:3 MINLEN:40 MAXINFO:40:0.5 Using PrefixPair: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT' Using Long Clipping Sequence: 'TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC' Using Long Clipping Sequence: 'TTTTTTTTTTCAAGCAGAAGACGGCATACGA' Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT' Using Long Clipping Sequence: 'AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG' Using Long Clipping Sequence: 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT' Using Long Clipping Sequence: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' ILLUMINACLIP: Using 1 prefix pairs, 6 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Quality encoding detected as phred33 Input Read Pairs: 16493393 Both Surviving: 13230357 (80.22%) Forward Only Surviving: 2660201 (16.13%) Reverse Only Surviving: 66935 (0.41%) Dropped: 535900 (3.25%) TrimmomaticPE: Completed successfully TrimmomaticPE: Started with arguments: -threads 8 /output/Preprocessing/MG.R1.fq /output/Preprocessing/MG.R2.fq /output/Preprocessing/MG.R1.trimmed.fq /output/Preprocessing/MG.SE1.trimmed.fq /output/Preprocessing/MG.R2.trimmed.fq /output/Preprocessing/MG.SE2.trimmed.fq ILLUMINACLIP:/databases/adapters/TruSeq2-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:1:3 MINLEN:40 MAXINFO:40:0.5 Using PrefixPair: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT' Using Long Clipping Sequence: 'TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC' Using Long Clipping Sequence: 'TTTTTTTTTTCAAGCAGAAGACGGCATACGA' Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT' Using Long Clipping Sequence: 'AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG' Using Long Clipping Sequence: 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT' Using Long Clipping Sequence: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' ILLUMINACLIP: Using 1 prefix pairs, 6 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Quality encoding detected as phred33 Input Read Pairs: 14699402 Both Surviving: 13108258 (89.18%) Forward Only Surviving: 949045 (6.46%) Reverse Only Surviving: 250721 (1.71%) Dropped: 391378 (2.66%) TrimmomaticPE: Completed successfully