Sample command CF01-CM01-Zygote_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF01-CM01-Zygote_R1_001.fastq.gz --in2 CF01-CM01-Zygote_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF01-CM01-Zygote_R1_001.fastp-trim.20220827.report.html --json CF01-CM01-Zygote_R1_001.fastp-trim.20220827.report.json --out1 CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz --out2 CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz CF01-CM02-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF01-CM02-Larvae_R1_001.fastq.gz --in2 CF01-CM02-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF01-CM02-Larvae_R1_001.fastp-trim.20220827.report.html --json CF01-CM02-Larvae_R1_001.fastp-trim.20220827.report.json --out1 CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz CF02-CM02-Zygote_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF02-CM02-Zygote_R1_001.fastq.gz --in2 CF02-CM02-Zygote_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF02-CM02-Zygote_R1_001.fastp-trim.20220827.report.html --json CF02-CM02-Zygote_R1_001.fastp-trim.20220827.report.json --out1 CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz --out2 CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz CF03-CM03-Zygote_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF03-CM03-Zygote_R1_001.fastq.gz --in2 CF03-CM03-Zygote_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF03-CM03-Zygote_R1_001.fastp-trim.20220827.report.html --json CF03-CM03-Zygote_R1_001.fastp-trim.20220827.report.json --out1 CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz --out2 CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz CF03-CM04-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF03-CM04-Larvae_R1_001.fastq.gz --in2 CF03-CM04-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF03-CM04-Larvae_R1_001.fastp-trim.20220827.report.html --json CF03-CM04-Larvae_R1_001.fastp-trim.20220827.report.json --out1 CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz CF03-CM05-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF03-CM05-Larvae_R1_001.fastq.gz --in2 CF03-CM05-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF03-CM05-Larvae_R1_001.fastp-trim.20220827.report.html --json CF03-CM05-Larvae_R1_001.fastp-trim.20220827.report.json --out1 CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz CF04-CM04-Zygote_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF04-CM04-Zygote_R1_001.fastq.gz --in2 CF04-CM04-Zygote_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF04-CM04-Zygote_R1_001.fastp-trim.20220827.report.html --json CF04-CM04-Zygote_R1_001.fastp-trim.20220827.report.json --out1 CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz --out2 CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz CF05-CM02-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF05-CM02-Larvae_R1_001.fastq.gz --in2 CF05-CM02-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF05-CM02-Larvae_R1_001.fastp-trim.20220827.report.html --json CF05-CM02-Larvae_R1_001.fastp-trim.20220827.report.json --out1 CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz CF05-CM05-Zygote_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF05-CM05-Zygote_R1_001.fastq.gz --in2 CF05-CM05-Zygote_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF05-CM05-Zygote_R1_001.fastp-trim.20220827.report.html --json CF05-CM05-Zygote_R1_001.fastp-trim.20220827.report.json --out1 CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz --out2 CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz CF06-CM01-Zygote_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF06-CM01-Zygote_R1_001.fastq.gz --in2 CF06-CM01-Zygote_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF06-CM01-Zygote_R1_001.fastp-trim.20220827.report.html --json CF06-CM01-Zygote_R1_001.fastp-trim.20220827.report.json --out1 CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz --out2 CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz CF06-CM02-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF06-CM02-Larvae_R1_001.fastq.gz --in2 CF06-CM02-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF06-CM02-Larvae_R1_001.fastp-trim.20220827.report.html --json CF06-CM02-Larvae_R1_001.fastp-trim.20220827.report.json --out1 CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz CF07-CM02-Zygote_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF07-CM02-Zygote_R1_001.fastq.gz --in2 CF07-CM02-Zygote_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF07-CM02-Zygote_R1_001.fastp-trim.20220827.report.html --json CF07-CM02-Zygote_R1_001.fastp-trim.20220827.report.json --out1 CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz --out2 CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz CF08-CM03-Zygote_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF08-CM03-Zygote_R1_001.fastq.gz --in2 CF08-CM03-Zygote_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF08-CM03-Zygote_R1_001.fastp-trim.20220827.report.html --json CF08-CM03-Zygote_R1_001.fastp-trim.20220827.report.json --out1 CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz --out2 CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz CF08-CM04-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF08-CM04-Larvae_R1_001.fastq.gz --in2 CF08-CM04-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF08-CM04-Larvae_R1_001.fastp-trim.20220827.report.html --json CF08-CM04-Larvae_R1_001.fastp-trim.20220827.report.json --out1 CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz CF08-CM05-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 CF08-CM05-Larvae_R1_001.fastq.gz --in2 CF08-CM05-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html CF08-CM05-Larvae_R1_001.fastp-trim.20220827.report.html --json CF08-CM05-Larvae_R1_001.fastp-trim.20220827.report.json --out1 CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz EF01-EM01-Zygote_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF01-EM01-Zygote_R1_001.fastq.gz --in2 EF01-EM01-Zygote_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF01-EM01-Zygote_R1_001.fastp-trim.20220827.report.html --json EF01-EM01-Zygote_R1_001.fastp-trim.20220827.report.json --out1 EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz --out2 EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz EF02-EM02-Zygote_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF02-EM02-Zygote_R1_001.fastq.gz --in2 EF02-EM02-Zygote_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF02-EM02-Zygote_R1_001.fastp-trim.20220827.report.html --json EF02-EM02-Zygote_R1_001.fastp-trim.20220827.report.json --out1 EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz --out2 EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz EF03-EM03-Zygote_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF03-EM03-Zygote_R1_001.fastq.gz --in2 EF03-EM03-Zygote_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF03-EM03-Zygote_R1_001.fastp-trim.20220827.report.html --json EF03-EM03-Zygote_R1_001.fastp-trim.20220827.report.json --out1 EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz --out2 EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz EF03-EM04-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF03-EM04-Larvae_R1_001.fastq.gz --in2 EF03-EM04-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF03-EM04-Larvae_R1_001.fastp-trim.20220827.report.html --json EF03-EM04-Larvae_R1_001.fastp-trim.20220827.report.json --out1 EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz EF03-EM05-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF03-EM05-Larvae_R1_001.fastq.gz --in2 EF03-EM05-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF03-EM05-Larvae_R1_001.fastp-trim.20220827.report.html --json EF03-EM05-Larvae_R1_001.fastp-trim.20220827.report.json --out1 EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz EF04-EM04-Zygote_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF04-EM04-Zygote_R1_001.fastq.gz --in2 EF04-EM04-Zygote_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF04-EM04-Zygote_R1_001.fastp-trim.20220827.report.html --json EF04-EM04-Zygote_R1_001.fastp-trim.20220827.report.json --out1 EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz --out2 EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz EF04-EM05-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF04-EM05-Larvae_R1_001.fastq.gz --in2 EF04-EM05-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF04-EM05-Larvae_R1_001.fastp-trim.20220827.report.html --json EF04-EM05-Larvae_R1_001.fastp-trim.20220827.report.json --out1 EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz EF05-EM01-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF05-EM01-Larvae_R1_001.fastq.gz --in2 EF05-EM01-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF05-EM01-Larvae_R1_001.fastp-trim.20220827.report.html --json EF05-EM01-Larvae_R1_001.fastp-trim.20220827.report.json --out1 EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz EF05-EM05-Zygote_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF05-EM05-Zygote_R1_001.fastq.gz --in2 EF05-EM05-Zygote_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF05-EM05-Zygote_R1_001.fastp-trim.20220827.report.html --json EF05-EM05-Zygote_R1_001.fastp-trim.20220827.report.json --out1 EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz --out2 EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz EF05-EM06-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF05-EM06-Larvae_R1_001.fastq.gz --in2 EF05-EM06-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF05-EM06-Larvae_R1_001.fastp-trim.20220827.report.html --json EF05-EM06-Larvae_R1_001.fastp-trim.20220827.report.json --out1 EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz EF06-EM01-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF06-EM01-Larvae_R1_001.fastq.gz --in2 EF06-EM01-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF06-EM01-Larvae_R1_001.fastp-trim.20220827.report.html --json EF06-EM01-Larvae_R1_001.fastp-trim.20220827.report.json --out1 EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz EF06-EM02-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF06-EM02-Larvae_R1_001.fastq.gz --in2 EF06-EM02-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF06-EM02-Larvae_R1_001.fastp-trim.20220827.report.html --json EF06-EM02-Larvae_R1_001.fastp-trim.20220827.report.json --out1 EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz EF06-EM06-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF06-EM06-Larvae_R1_001.fastq.gz --in2 EF06-EM06-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF06-EM06-Larvae_R1_001.fastp-trim.20220827.report.html --json EF06-EM06-Larvae_R1_001.fastp-trim.20220827.report.json --out1 EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz EF07-EM01-Zygote_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF07-EM01-Zygote_R1_001.fastq.gz --in2 EF07-EM01-Zygote_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF07-EM01-Zygote_R1_001.fastp-trim.20220827.report.html --json EF07-EM01-Zygote_R1_001.fastp-trim.20220827.report.json --out1 EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz --out2 EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz EF07-EM03-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF07-EM03-Larvae_R1_001.fastq.gz --in2 EF07-EM03-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF07-EM03-Larvae_R1_001.fastp-trim.20220827.report.html --json EF07-EM03-Larvae_R1_001.fastp-trim.20220827.report.json --out1 EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz EF08-EM03-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF08-EM03-Larvae_R1_001.fastq.gz --in2 EF08-EM03-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF08-EM03-Larvae_R1_001.fastp-trim.20220827.report.html --json EF08-EM03-Larvae_R1_001.fastp-trim.20220827.report.json --out1 EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz EF08-EM04-Larvae_R1_001 /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 EF08-EM04-Larvae_R1_001.fastq.gz --in2 EF08-EM04-Larvae_R2_001.fastq.gz --detect_adapter_for_pe --thread 40 --html EF08-EM04-Larvae_R1_001.fastp-trim.20220827.report.html --json EF08-EM04-Larvae_R1_001.fastp-trim.20220827.report.json --out1 EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz --out2 EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz