Sample command DMSO_1 fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/DMSO_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/DMSO_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/DMSO_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/DMSO_1.fastp.json DMSO_2 fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/DMSO_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/DMSO_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/DMSO_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/DMSO_2.fastp.json DMSO_3 fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/DMSO_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/DMSO_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/DMSO_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/DMSO_3.fastp.json HSC_D12_DMSO_1_bio fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_DMSO_1_bio_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_DMSO_1_bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_DMSO_1_bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_DMSO_1_bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_DMSO_1_bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_DMSO_1_bio.fastp.json HSC_D12_DMSO_1_tech fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_DMSO_1_tech_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_DMSO_1_tech_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_DMSO_1_tech_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_DMSO_1_tech_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_DMSO_1_tech.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_DMSO_1_tech.fastp.json HSC_D12_DMSO_2_bio fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_DMSO_2_bio_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_DMSO_2_bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_DMSO_2_bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_DMSO_2_bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_DMSO_2_bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_DMSO_2_bio.fastp.json HSC_D12_DMSO_2_tech fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_DMSO_2_tech_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_DMSO_2_tech_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_DMSO_2_tech_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_DMSO_2_tech_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_DMSO_2_tech.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_DMSO_2_tech.fastp.json HSC_D12_DMSO_3_bio fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_DMSO_3_bio_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_DMSO_3_bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_DMSO_3_bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_DMSO_3_bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_DMSO_3_bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_DMSO_3_bio.fastp.json HSC_D12_DMSO_3_tech fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_DMSO_3_tech_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_DMSO_3_tech_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_DMSO_3_tech_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_DMSO_3_tech_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_DMSO_3_tech.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_DMSO_3_tech.fastp.json HSC_D12_RU_1uM_1_bio fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_1_bio_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_1_bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_1_bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_1_bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_1_bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_1_bio.fastp.json HSC_D12_RU_1uM_1_tech fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_1_tech_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_1_tech_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_1_tech_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_1_tech_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_1_tech.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_1_tech.fastp.json HSC_D12_RU_1uM_2_bio fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_2_bio_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_2_bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_2_bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_2_bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_2_bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_2_bio.fastp.json HSC_D12_RU_1uM_2_tech fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_2_tech_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_2_tech_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_2_tech_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_2_tech_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_2_tech.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_2_tech.fastp.json HSC_D12_RU_1uM_3_bio fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_3_bio_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_3_bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_3_bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_3_bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_3_bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_3_bio.fastp.json HSC_D12_RU_1uM_3_tech fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_3_tech_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_3_tech_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_3_tech_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_3_tech_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_3_tech.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_3_tech.fastp.json HSC_D12_RU_1uM_plus_TA_100nM_1_bio fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_plus_TA_100nM_1_bio_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_plus_TA_100nM_1_bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_plus_TA_100nM_1_bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_plus_TA_100nM_1_bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_plus_TA_100nM_1_bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_plus_TA_100nM_1_bio.fastp.json HSC_D12_RU_1uM_plus_TA_100nM_1_tech fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_plus_TA_100nM_1_tech_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_plus_TA_100nM_1_tech_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_plus_TA_100nM_1_tech_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_plus_TA_100nM_1_tech_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_plus_TA_100nM_1_tech.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_plus_TA_100nM_1_tech.fastp.json HSC_D12_RU_1uM_plus_TA_100nM_2_bio fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_plus_TA_100nM_2_bio_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_plus_TA_100nM_2_bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_plus_TA_100nM_2_bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_plus_TA_100nM_2_bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_plus_TA_100nM_2_bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_plus_TA_100nM_2_bio.fastp.json HSC_D12_RU_1uM_plus_TA_100nM_2_tech fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_plus_TA_100nM_2_tech_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_plus_TA_100nM_2_tech_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_plus_TA_100nM_2_tech_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/fastq_trimmed/HSC_D12_RU_1uM_plus_TA_100nM_2_tech_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_plus_TA_100nM_2_tech.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/trimming/HSC_D12_RU_1uM_plus_TA_100nM_2_tech.fastp.json HSC_D12_RU_1uM_plus_TA_100nM_3_bio fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/fastqs/HSC_D12_RU_1uM_plus_TA_100nM_3_bio_R1.fastq.gz --in2 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