python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_0/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_0.per_read_modified_base_calls.tsv 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_10/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_10.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_11/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_11.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_12/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_12.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_13/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_13.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_14/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_14.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_15/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_15.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_16/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_16.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_17/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_17.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_18/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_18.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_19/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_19.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_1/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_1.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_20/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_20.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_21/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_21.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_22/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_22.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_23/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_23.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_24/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_24.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_25/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_25.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_26/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_26.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_27/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_27.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_28/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_28.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_2/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_2.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_3/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_3.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_4/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_4.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_5/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_5.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_6/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_6.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_7/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_7.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_8/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_8.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_9/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_9.per_read_modified_base_calls.tsv
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_0/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_0.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_10/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_10.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_11/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_11.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_12/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_12.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_13/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_13.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_14/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_14.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_15/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_15.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_16/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_16.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_17/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_17.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_18/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_18.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_19/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_19.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_1/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_1.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_20/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_20.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_21/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_21.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_22/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_22.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_23/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_23.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_24/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_24.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_25/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_25.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_26/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_26.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_27/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_27.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_28/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_28.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_2/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_2.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_3/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_3.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_4/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_4.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_5/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_5.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_6/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_6.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_7/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_7.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_8/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_8.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa 
python ~/code/bisulfite/megalodon-to-single_line.py megalodon-FAK93201_74cd2ea4_9/per_read_modified_base_calls.txt /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa A megalodon-FAK93201_74cd2ea4_9.per_read_modified_base_calls.flippted.tsv -flipSign -excludeContext CG 1 /oak/stanford/groups/akundaje/marinovg/genomes/hg38/sequence/hg38-no-haps.fa