module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_0 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_0
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_100 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_100
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_101 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_101
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_102 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_102
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_103 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_103
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_104 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_104
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_105 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_105
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_106 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_106
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_107 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_107
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_108 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_108
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_109 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_109
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_10 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_10
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_110 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_110
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_111 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_111
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_112 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_112
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_113 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_113
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_114 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_114
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_115 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_115
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_116 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_116
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_117 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_117
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_118 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_118
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_119 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_119
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_11 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_11
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_120 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_120
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_121 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_121
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_122 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_122
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_123 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_123
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_124 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_124
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_125 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_125
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_126 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_126
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_127 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_127
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_128 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_128
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_129 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_129
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_12 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_12
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_130 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_130
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_131 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_131
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_132 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_132
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_133 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_133
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_134 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_134
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_135 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_135
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_136 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_136
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_137 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_137
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_138 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_138
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_139 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_139
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_13 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_13
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_140 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_140
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_141 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_141
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_142 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_142
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_143 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_143
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_144 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_144
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_145 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_145
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_146 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_146
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_147 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_147
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_148 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_148
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_149 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_149
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_14 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_14
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_150 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_150
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_151 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_151
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_152 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_152
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_153 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_153
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_154 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_154
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_155 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_155
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_156 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_156
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_157 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_157
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_158 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_158
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_159 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_159
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_15 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_15
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_160 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_160
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_161 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_161
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_162 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_162
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_163 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_163
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_164 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_164
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_165 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_165
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_166 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_166
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_167 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_167
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_168 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_168
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_169 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_169
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_16 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_16
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_170 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_170
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_171 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_171
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_172 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_172
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_173 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_173
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_174 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_174
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_175 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_175
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_176 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_176
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_177 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_177
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_178 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_178
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_179 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_179
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_17 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_17
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_180 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_180
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_181 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_181
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_182 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_182
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_183 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_183
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_184 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_184
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_185 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_185
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_186 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_186
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_187 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_187
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_188 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_188
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_189 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_189
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_18 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_18
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_190 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_190
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_191 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_191
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_192 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_192
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_193 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_193
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_194 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_194
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_195 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_195
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_196 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_196
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_197 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_197
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_198 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_198
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_199 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_199
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_19 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_19
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_1 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_1
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_200 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_200
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_201 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_201
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_202 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_202
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_203 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_203
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_204 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_204
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_205 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_205
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_206 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_206
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_207 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_207
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_208 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_208
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_209 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_209
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_20 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_20
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_210 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_210
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_211 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_211
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_212 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_212
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_213 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_213
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_214 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_214
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_215 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_215
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_216 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_216
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_217 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_217
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_218 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_218
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_219 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_219
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_21 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_21
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_220 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_220
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_221 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_221
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_222 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_222
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_223 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_223
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_224 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_224
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_225 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_225
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_226 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_226
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_227 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_227
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_228 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_228
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_229 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_229
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_22 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_22
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_230 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_230
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_231 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_231
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_232 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_232
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_233 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_233
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_234 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_234
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_235 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_235
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_236 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_236
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_237 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_237
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_238 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_238
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_239 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_239
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_23 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_23
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_240 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_240
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_241 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_241
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_242 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_242
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_243 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_243
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_244 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_244
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_245 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_245
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_246 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_246
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_247 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_247
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_248 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_248
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_249 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_249
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_24 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_24
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_250 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_250
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_251 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_251
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_252 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_252
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_253 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_253
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_254 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_254
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_255 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_255
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_256 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_256
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_257 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_257
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_258 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_258
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_259 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_259
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_25 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_25
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_260 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_260
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_261 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_261
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_262 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_262
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_263 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_263
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_264 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_264
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_265 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_265
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_266 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_266
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_267 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_267
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_268 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_268
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_269 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_269
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_26 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_26
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_270 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_270
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_271 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_271
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_272 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_272
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_273 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_273
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_274 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_274
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_275 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_275
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_276 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_276
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_277 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_277
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_278 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_278
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_279 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_279
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_27 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_27
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_280 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_280
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_281 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_281
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_282 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_282
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_283 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_283
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_284 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_284
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_285 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_285
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_286 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_286
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_287 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_287
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_288 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_288
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_289 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_289
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_28 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_28
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_290 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_290
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_291 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_291
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_292 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_292
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_293 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_293
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_294 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_294
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_295 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_295
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_296 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_296
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_297 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_297
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_298 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_298
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_299 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_299
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_29 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_29
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_2 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_2
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_300 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_300
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_301 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_301
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_302 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_302
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_303 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_303
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_304 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_304
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_305 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_305
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_306 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_306
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_307 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_307
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_308 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_308
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_309 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_309
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_30 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_30
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_310 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_310
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_311 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_311
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_312 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_312
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_313 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_313
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_314 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_314
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_315 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_315
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_316 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_316
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_317 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_317
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_318 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_318
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_319 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_319
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_31 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_31
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_320 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_320
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_321 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_321
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_322 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_322
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_323 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_323
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_324 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_324
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_325 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_325
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_326 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_326
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_327 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_327
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_328 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_328
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_329 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_329
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_32 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_32
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_330 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_330
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_331 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_331
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_332 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_332
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_333 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_333
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_334 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_334
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_335 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_335
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_336 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_336
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_337 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_337
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_338 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_338
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_339 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_339
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_33 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_33
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_340 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_340
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_341 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_341
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_342 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_342
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_343 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_343
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_344 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_344
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_345 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_345
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_346 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_346
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_347 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_347
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_348 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_348
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_349 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_349
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_34 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_34
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_350 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_350
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_351 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_351
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_352 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_352
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_353 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_353
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_354 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_354
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_355 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_355
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_356 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_356
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_357 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_357
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_358 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_358
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_359 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_359
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_35 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_35
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_360 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_360
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_361 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_361
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_362 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_362
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_363 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_363
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_364 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_364
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_365 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_365
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_366 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_366
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_367 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_367
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_368 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_368
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_369 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_369
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_36 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_36
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_370 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_370
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_371 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_371
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_372 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_372
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_373 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_373
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_374 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_374
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_375 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_375
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_376 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_376
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_377 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_377
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_378 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_378
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_379 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_379
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_37 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_37
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_380 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_380
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_381 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_381
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_382 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_382
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_383 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_383
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_384 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_384
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_385 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_385
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_386 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_386
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_387 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_387
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_388 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_388
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_389 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_389
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_38 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_38
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_390 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_390
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_391 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_391
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_392 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_392
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_393 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_393
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_394 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_394
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_395 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_395
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_396 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_396
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_397 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_397
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_398 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_398
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_399 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_399
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_39 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_39
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_3 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_3
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_400 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_400
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_401 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_401
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_402 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_402
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_403 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_403
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_404 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_404
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_405 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_405
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_406 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_406
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_407 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_407
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_408 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_408
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_409 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_409
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_40 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_40
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_410 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_410
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_411 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_411
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_412 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_412
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_413 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_413
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_414 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_414
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_415 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_415
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_416 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_416
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_417 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_417
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_418 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_418
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_419 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_419
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_41 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_41
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_420 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_420
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_421 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_421
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_422 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_422
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_423 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_423
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_424 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_424
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_425 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_425
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_426 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_426
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_427 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_427
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_428 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_428
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_429 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_429
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_42 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_42
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_430 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_430
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_431 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_431
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_432 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_432
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_433 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_433
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_434 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_434
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_435 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_435
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_436 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_436
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_437 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_437
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_438 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_438
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_439 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_439
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_43 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_43
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_440 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_440
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_441 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_441
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_442 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_442
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_443 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_443
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_444 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_444
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_445 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_445
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_446 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_446
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_447 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_447
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_448 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_448
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_449 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_449
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_44 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_44
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_450 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_450
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_451 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_451
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_452 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_452
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_453 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_453
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_454 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_454
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_455 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_455
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_45 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_45
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_46 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_46
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_47 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_47
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_48 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_48
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_49 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_49
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_4 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_4
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_50 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_50
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_51 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_51
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_52 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_52
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_53 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_53
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_54 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_54
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_55 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_55
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_56 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_56
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_57 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_57
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_58 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_58
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_59 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_59
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_5 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_5
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_60 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_60
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_61 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_61
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_62 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_62
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_63 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_63
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_64 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_64
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_65 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_65
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_66 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_66
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_67 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_67
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_68 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_68
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_69 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_69
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_6 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_6
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_70 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_70
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_71 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_71
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_72 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_72
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_73 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_73
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_74 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_74
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_75 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_75
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_76 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_76
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_77 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_77
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_78 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_78
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_79 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_79
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_7 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_7
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_80 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_80
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_81 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_81
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_82 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_82
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_83 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_83
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_84 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_84
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_85 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_85
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_86 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_86
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_87 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_87
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_88 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_88
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_89 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_89
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_8 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_8
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_90 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_90
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_91 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_91
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_92 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_92
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_93 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_93
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_94 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_94
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_95 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_95
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_96 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_96
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_97 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_97
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_98 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_98
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_99 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_99
module load py-numpy/1.20.3_py39; module load python/3.9.0; module load py-scipy/1.6.3_py39; module load libressl/2.5.3; export PATH=$PATH:/home/users/marinovg/.local/bin:/oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin; megalodon --guppy-params "--model_file /oak/stanford/groups/akundaje/marinovg/programs/rerio-2021-12-29/basecall_models/res_dna_r941_min_modbases-all-context_v001.jsn" --guppy-config res_dna_r941_min_modbases-all-context_v001.cfg --outputs basecalls mod_basecalls per_read_mods --reference /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa --write-mods-text --output-directory megalodon-FAW45643_05cfc757_be96c638_9 --overwrite --guppy-server-path /oak/stanford/groups/akundaje/marinovg/programs/ont-guppy-cpu_6.0.1_linux64/bin/guppy_basecall_server FAW45643_05cfc757_be96c638_9