python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa BD-L600-bdellovibrio_bacteriovorus-ICPB_3264_gDNA.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L600-bdellovibrio_bacteriovorus-ICPB_3264_gDNA.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L600-bdellovibrio_bacteriovorus-ICPB_3264_gDNA.bwameth.pUC19
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa BD-L601-fixed_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L601-fixed_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L601-fixed_SMF_200.bwameth.pUC19
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa BD-L602-fixed_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L602-fixed_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L602-fixed_SMF_200.bwameth.pUC19
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa BD-L603-fixed_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L603-fixed_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L603-fixed_SMF_20.bwameth.pUC19
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa BD-L604-fixed_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L604-fixed_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L604-fixed_SMF_20.bwameth.pUC19
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa BD-L605-native_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L605-native_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L605-native_SMF_200.bwameth.pUC19
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa BD-L606-native_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L606-native_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L606-native_SMF_200.bwameth.pUC19
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa BD-L607-native_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L607-native_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L607-native_SMF_20.bwameth.pUC19
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa BD-L608-native_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L608-native_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/pUC19/bwameth-indexes/pUC19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L608-native_SMF_20.bwameth.pUC19
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa BD-L600-bdellovibrio_bacteriovorus-ICPB_3264_gDNA.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L600-bdellovibrio_bacteriovorus-ICPB_3264_gDNA.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L600-bdellovibrio_bacteriovorus-ICPB_3264_gDNA.bwameth.lambda
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa BD-L601-fixed_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L601-fixed_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L601-fixed_SMF_200.bwameth.lambda
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa BD-L602-fixed_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L602-fixed_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L602-fixed_SMF_200.bwameth.lambda
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa BD-L603-fixed_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L603-fixed_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L603-fixed_SMF_20.bwameth.lambda
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa BD-L604-fixed_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L604-fixed_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L604-fixed_SMF_20.bwameth.lambda
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa BD-L605-native_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L605-native_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L605-native_SMF_200.bwameth.lambda
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa BD-L606-native_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L606-native_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L606-native_SMF_200.bwameth.lambda
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa BD-L607-native_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L607-native_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L607-native_SMF_20.bwameth.lambda
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa BD-L608-native_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L608-native_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Viruses/Lambda_phage/bwameth-indexes/lamda.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L608-native_SMF_20.bwameth.lambda
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta BD-L600-bdellovibrio_bacteriovorus-ICPB_3264_gDNA.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L600-bdellovibrio_bacteriovorus-ICPB_3264_gDNA.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - D-L600-bdellovibrio_bacteriovorus-ICPB_3264_gDNA.bwameth.SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta BD-L601-fixed_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L601-fixed_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L601-fixed_SMF_200.bwameth.SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta BD-L602-fixed_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L602-fixed_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L602-fixed_SMF_200.bwameth.SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta BD-L603-fixed_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L603-fixed_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L603-fixed_SMF_20.bwameth.SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta BD-L604-fixed_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L604-fixed_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L604-fixed_SMF_20.bwameth.SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta BD-L605-native_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L605-native_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L605-native_SMF_200.bwameth.SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta BD-L606-native_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L606-native_SMF_200.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L606-native_SMF_200.bwameth.SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta BD-L607-native_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L607-native_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L607-native_SMF_20.bwameth.SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2
python /oak/stanford/groups/akundaje/marinovg/programs/bwa-meth/bwameth.py --threads 20 --reference /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta BD-L608-native_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end1.fastq.gz BD-L608-native_SMF_20.CKDL230030534-1A_22CWN2LT3_L8.end2.fastq.gz | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F 1804 -q 30 -bT /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-gDNA/L2786-bdellovibrio_bacteriovorus-ICPB_3264_gDNA_cloudy/SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2/scaffolds.fasta - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - BD-L608-native_SMF_20.bwameth.SPAdes-3.15.4-2023-04-19-B_b_gDNA_check.pass-V2