--methy_extract docs

[antonkulaga]

I am having troubles with --methy-extract command. I succeeded in generating *bmm files but I am having problems with understanding how to pass them properly as the option is not documented. Judging from the wechat instructions you gave me I tried something like:

/opt/BitMapperBS/bitmapperBS --methy_extract /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-240390738/human_bs_index --seq "/cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_0.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_1.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_10.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_11.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_12.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_13.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_14.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_15.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_16.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_17.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_18.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_19.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_2.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_20.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_21.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_22.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_23.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_24.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_25.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_26.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_27.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_28.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_29.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_3.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_30.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_31.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_32.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_33.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_34.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_35.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_36.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_37.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_38.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_39.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_4.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_40.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_41.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_42.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_43.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_44.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_45.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_46.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_47.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_48.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_49.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_5.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_50.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_51.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_52.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_53.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_54.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_55.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_56.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_57.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_58.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_59.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_6.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_60.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_61.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_62.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_63.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_7.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_8.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_9.bmm" --output SRR948855.bedGraph

but it complained about:

Unavailable parameter: seq

I think I did not get your example in wechat propertly. Maybe you wanted to pass the folder where to search for the bmm-s? Because passing all the bmm-s makes the bash command too long.

[chhylp123]

I am having troubles with --methy-extract command. I succeeded in generating *bmm files but I am having problems with understanding how to pass them properly as the option is not documented. Judging from the wechat instructions you gave me I tried something like:

/opt/BitMapperBS/bitmapperBS --methy_extract /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-240390738/human_bs_index --seq "/cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_0.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_1.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_10.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_11.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_12.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_13.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_14.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_15.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_16.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_17.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_18.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_19.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_2.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_20.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_21.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_22.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_23.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_24.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_25.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_26.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_27.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_28.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_29.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_3.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_30.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_31.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_32.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_33.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_34.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_35.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_36.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_37.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_38.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_39.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_4.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_40.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_41.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_42.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_43.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_44.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_45.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_46.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_47.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_48.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_49.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_5.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_50.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_51.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_52.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_53.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_54.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_55.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_56.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_57.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_58.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_59.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_6.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_60.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_61.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_62.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_63.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_7.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_8.bmm /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output_9.bmm" --output SRR948855.bedGraph

but it complained about:

Unavailable parameter: seq

I think I did not get your example in wechat propertly. Maybe you wanted to pass the folder where to search for the bmm-s? Because passing all the bmm-s makes the bash command too long.

Hi antonkulaga,

You should try as this:

/opt/BitMapperBS/bitmapperBS --methy_extract /cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-240390738/human_bs_index --seq "/cromwell-executions/bs_map/22997b41-fffa-432e-a8ac-cabd1ac51313/call-bitmapper_extract/inputs/-707515999/output

The results will be written into:

output_CpG.bedGraph

Thank you very much. : )

[antonkulaga]

I get a problem, when I run:

/opt/BitMapperBS/bitmapperBS --methy_extract /cromwell-executions/bs_map_fast/743a92c3-eaf7-45f9-a804-cf92307e933a/call-methylation_extraction/inputs/-240390716/human_bs_index --bmm_folder /cromwell-executions/bs_map_fast/743a92c3-eaf7-45f9-a804-cf92307e933a/call-methylation_extraction/inputs/15000707/output

I get:

fileName[0]: /cromwell-executions/bs_map_fast/743a92c3-eaf7-45f9-a804-cf92307e933a/call-methylation_extraction/inputs/-240390716/human_bs_index
fileName[1]: /cromwell-executions/bs_map_fast/743a92c3-eaf7-45f9-a804-cf92307e933a/call-methylation_extraction/inputs/-240390716/human_bs_index.index
Load hash table index failed!

The content of human_bs_index is:

genome.index               genome.index.bs.index.occ  genome.index.methy
genome.index.bs.index      genome.index.bs.index.sa
genome.index.bs.index.bwt  genome.index.bs.pac

Why should it search for index.index?

[chhylp123]

Sorry for the delay. I will update it this weekend. I am moving to a new lab, so I haven't a stable environment to write code in the last a few days. Thanks very much for your patience. : )

I get a problem, when I run:

/opt/BitMapperBS/bitmapperBS --methy_extract /cromwell-executions/bs_map_fast/743a92c3-eaf7-45f9-a804-cf92307e933a/call-methylation_extraction/inputs/-240390716/human_bs_index --bmm_folder /cromwell-executions/bs_map_fast/743a92c3-eaf7-45f9-a804-cf92307e933a/call-methylation_extraction/inputs/15000707/output

I get:

fileName[0]: /cromwell-executions/bs_map_fast/743a92c3-eaf7-45f9-a804-cf92307e933a/call-methylation_extraction/inputs/-240390716/human_bs_index
fileName[1]: /cromwell-executions/bs_map_fast/743a92c3-eaf7-45f9-a804-cf92307e933a/call-methylation_extraction/inputs/-240390716/human_bs_index.index
Load hash table index failed!

The content of human_bs_index is:

genome.index               genome.index.bs.index.occ  genome.index.methy
genome.index.bs.index      genome.index.bs.index.sa
genome.index.bs.index.bwt  genome.index.bs.pac

Why should it search for index.index?

[chhylp123]

This problem has been fixed. Please try version 1.0.1.4.

I get a problem, when I run:

/opt/BitMapperBS/bitmapperBS --methy_extract /cromwell-executions/bs_map_fast/743a92c3-eaf7-45f9-a804-cf92307e933a/call-methylation_extraction/inputs/-240390716/human_bs_index --bmm_folder /cromwell-executions/bs_map_fast/743a92c3-eaf7-45f9-a804-cf92307e933a/call-methylation_extraction/inputs/15000707/output

I get:

fileName[0]: /cromwell-executions/bs_map_fast/743a92c3-eaf7-45f9-a804-cf92307e933a/call-methylation_extraction/inputs/-240390716/human_bs_index
fileName[1]: /cromwell-executions/bs_map_fast/743a92c3-eaf7-45f9-a804-cf92307e933a/call-methylation_extraction/inputs/-240390716/human_bs_index.index
Load hash table index failed!

The content of human_bs_index is:

genome.index               genome.index.bs.index.occ  genome.index.methy
genome.index.bs.index      genome.index.bs.index.sa
genome.index.bs.index.bwt  genome.index.bs.pac

Why should it search for index.index?