TrimmomaticPE: Started with arguments:
 -phred33 -threads 28 -trimlog /gscratch/scrubbed/samwhite/outputs/20221026-rhodes-marine_mammals-16s-silva-138-99-seqs-515-806/trimmed/Pos_S88_L001.trimmomatic.log /gscratch/srlab/sam/data/databases/silva/MiSeq_files_for_Gannet/Pos_S88_L001_R1_001.fastq.gz /gscratch/srlab/sam/data/databases/silva/MiSeq_files_for_Gannet/Pos_S88_L001_R2_001.fastq.gz /gscratch/scrubbed/samwhite/outputs/20221026-rhodes-marine_mammals-16s-silva-138-99-seqs-515-806/trimmed/Pos_S88_L001.trimmed.paired.R1.fq /gscratch/scrubbed/samwhite/outputs/20221026-rhodes-marine_mammals-16s-silva-138-99-seqs-515-806/trimmed/Pos_S88_L001.trimmed.unpaired.R1.fq /gscratch/scrubbed/samwhite/outputs/20221026-rhodes-marine_mammals-16s-silva-138-99-seqs-515-806/trimmed/Pos_S88_L001.trimmed.paired.R2.fq /gscratch/scrubbed/samwhite/outputs/20221026-rhodes-marine_mammals-16s-silva-138-99-seqs-515-806/trimmed/Pos_S88_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
java.io.FileNotFoundException: /home/sam/programs/Trimmomatic-0.39/adapters/NexteraPE-PE.fa (No such file or directory)
	at java.base/java.io.FileInputStream.open0(Native Method)
	at java.base/java.io.FileInputStream.open(FileInputStream.java:216)
	at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
	at org.usadellab.trimmomatic.fasta.FastaParser.parse(FastaParser.java:54)
	at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:110)
	at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:71)
	at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32)
	at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)
	at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:552)
	at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)
Input Read Pairs: 61940 Both Surviving: 61846 (99.85%) Forward Only Surviving: 3 (0.00%) Reverse Only Surviving: 24 (0.04%) Dropped: 67 (0.11%)
TrimmomaticPE: Completed successfully