tombo text_output browser_files outputs succinct error

[adalisan]

I am running this tombo command with detect_modifications

log = !tombo detect_modifications model_sample_compare --fast5-basedirs {sam_nanopores_seq_shape_mod_fast5_dir} --control-fast5-basedirs {sam_nanopores_fast5_dir} --rna --statistics-file-basename sam_nanopore_RNAshape_stats_rep_via_ipy --per-read-statistics-basename sam_nanopore_RNAshape_per_read_stats_rep_via_ipy --minimum-test-reads 100 --multiprocess-region-size 250

and then run

tombo text_output browser_files --fast5-basedirs {sam_nanopores_seq_shape_mod_fast5_dir} --control-fast5-basedirs {sam_nanopores_fast5_dir} --statistics-filename sam_nanopore_RNAshape_per_read_stats_rep_via_ipy.tombo.stats

The output looks like

[17:41:50] Parsing Tombo index file(s).
******************** WARNING ********************
	Failed to parse tombo index file for /hpc/projects/rvx/DSCV_US/PUBLIC_DATA/ONT_NanoSHAPE_FAST5/1623_native_ONT_data/1623_native-multi/tombo_data_rerun/ directory. Creating temporary index from FAST5 files.
******************** ERROR ********************
	No reads present in --fast5-basedirs.

and tombo produces a nearly empty tombo.stats files. The tombo.stats files exist and has non-zero size.

Does No reads present mean nothing that was found to be significant or the detect_modifications step failed? How large would you expect those files to be?

[kenneditodd]

@adalisan did you find an answer for this?

[adalisan]

@kenneditodd I did not get any replies and have ran into multiple issues with tombo, for which this is only one. If you can get it running Master of Pores2 https://github.com/biocorecrg/MOP2 seems to have a containerized pipeline, which include guppy and running tombo (in addition to alternatives for base modification detection )

[kenneditodd]

@adalisan ah thanks! a container is exactly what I have been looking for

[adalisan]

@kenneditodd If you are using tombo as part of a pipeline, I would recommend just using the containers which are in BiocoreCRG's Docker hub and running thing with shell scripts. Note there are multiple versions and some tombo functionalities like plotting with rpy2 and ggplot2 may not work.