Level sample compare not accessing index file

[lthomp06]

Hello,

I am trying to compare methylation between two samples using the Tombo level_sample_compare command. When I run this command I get the following output:

tombo resquiggle ~/Desktop/Tombo/Ont-Fast5-Api_tombo/single_reads_EK09-1/ CP009273.fasta --processes 8 --num-most-common-errors 5 --overwrite tombo resquiggle ~/Desktop/Tombo/Ont-Fast5-Api_tombo/single_reads_EK09R5-1/ CP009273.fasta --processes 8 --num-most-common-errors 5 --overwrite tombo detect_modifications level_sample_compare --fast5-basedirs ~/Dropbox/Tombo/Ont-Fast5-Api_tombo/single_reads_EK09-1
--alternate-fast5-basedirs ~/Dropbox/Tombo/Ont-Fast5-Api_tombo/single_reads_EK09R5-1
--statistics-file-basename EK09-1.level_compare_EK09R5-1_2 [07:56:13] Loading minimap2 reference. [07:56:13] Getting file list. [07:56:15] Loading default canonical ***** DNA ***** model. [07:56:15] Re-squiggling reads (raw signal to genomic sequence alignment). 5 most common unsuccessful read types (approx. %): 2.8% ( 5065 reads) : Alignment not produced
2.3% ( 4174 reads) : Poor raw to expected signal matching (revert with tombo filter clear_filters) 2.3% ( 4119 reads) : Read event to sequence alignment extends beyond bandwidth
0.0% ( 1 reads) : Too much raw signal for mapped sequence
----- 100%|██████████████████████████| 178282/178282 [1:41:57<00:00, 29.14it/s] [09:38:13] Final unsuccessful reads summary (7.5% reads unsuccessfully processed; 13359 total reads): 2.8% ( 5065 reads) : Alignment not produced
2.3% ( 4174 reads) : Poor raw to expected signal matching (revert with tombo filter clear_filters) 2.3% ( 4119 reads) : Read event to sequence alignment extends beyond bandwidth
0.0% ( 1 reads) : Too much raw signal for mapped sequence
[09:38:13] Saving Tombo reads index to file. [09:38:16] Loading minimap2 reference. [09:38:16] Getting file list. [09:38:17] Loading default canonical ***** DNA ***** model. [09:38:17] Re-squiggling reads (raw signal to genomic sequence alignment). 5 most common unsuccessful read types (approx. %): 3.0% ( 4536 reads) : Read event to sequence alignment extends beyond bandwidth
2.7% ( 4214 reads) : Alignment not produced
2.1% ( 3244 reads) : Poor raw to expected signal matching (revert with tombo filter clear_filters) ----- ----- 100%|██████████████████████████| 153704/153704 [1:35:22<00:00, 26.86it/s] [11:13:40] Final unsuccessful reads summary (7.8% reads unsuccessfully processed; 11994 total reads): 3.0% ( 4536 reads) : Read event to sequence alignment extends beyond bandwidth
2.7% ( 4214 reads) : Alignment not produced
2.1% ( 3244 reads) : Poor raw to expected signal matching (revert with tombo filter clear_filters) [11:13:40] Saving Tombo reads index to file. [11:13:43] Parsing Tombo index file(s). ******************** WARNING ******************** Tombo index file does not exist for one or more directories. If --skip-index was not set for re-squiggle command, ensure that the specified directory is the same as for the re-squiggle command. [11:13:43] Performing two-sample group comparison significance testing. [11:13:43] Parsing Tombo index file(s). ******************** WARNING ******************** Tombo index file does not exist for one or more directories. If --skip-index was not set for re-squiggle command, ensure that the specified directory is the same as for the re-squiggle command. [11:13:43] Calculating read coverage regions. [11:13:43] Calculating read coverage. [11:13:43] Calculating read coverage. [11:13:43] Performing modified base detection across genomic regions. 0it [00:00, ?it/s]

The resulting text file has no data in it and contains the text: âHDF ˇˇˇˇˇˇˇˇ! ˇˇˇˇˇˇˇˇ

[SycamoreLeaf]

Hi lthomp. Looks like you opened a binary HDF5 file in a text editor. You may want to try the tombo text_output browser_files commands to produce files you can open in a genome browser. Be warned the documentation is a tad sparse.

Good luck ~Chris