TrimmomaticPE: Started with arguments:
 -phred33 -threads 8 -trimlog /home/sam/analyses/miseq-testing/trimmed/312_S13_L001.trimmomatic.log /home/sam/data/databases/silva/MiSeq_files_for_Gannet/312_S13_L001_R1_001.fastq.gz /home/sam/data/databases/silva/MiSeq_files_for_Gannet/312_S13_L001_R2_001.fastq.gz /home/sam/analyses/miseq-testing/trimmed/312_S13_L001.trimmed.paired.R1.fq /home/sam/analyses/miseq-testing/trimmed/312_S13_L001.trimmed.unpaired.R1.fq /home/sam/analyses/miseq-testing/trimmed/312_S13_L001.trimmed.paired.R2.fq /home/sam/analyses/miseq-testing/trimmed/312_S13_L001.trimmed.unpaired.R2.fq ILLUMINACLIP:/home/sam/programs/Trimmomatic-0.39/adapters/NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:8:10 MINLEN:100
Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Read Pairs: 163222 Both Surviving: 136783 (83.80%) Forward Only Surviving: 19366 (11.86%) Reverse Only Surviving: 95 (0.06%) Dropped: 6978 (4.28%)
TrimmomaticPE: Completed successfully