8000 Error reading region [..] from pybigwig object. Exception is: Invalid interval bounds! · Issue #64 · loosolab/TOBIAS · GitHub
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Error reading region [..] from pybigwig object. Exception is: Invalid interval bounds! #64

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KalinNonchev opened this issue Mar 7, 2021 · 2 comments
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Error reading region [..] from pybigwig object. Exception is: Invalid interval bounds! #64

KalinNonchev opened this issue Mar 7, 2021 · 2 comments
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@KalinNonchev
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Hi,

I am running TOBIAS through the snakemake pipeline on all motifs from JASPAR vertebrates on a given ATAC-seq dataset.

However, in the final rule "plot_heatmaps_across" I am getting Error reading region [..] from pybigwig object. Exception is: Invalid interval bounds! for some of the motifs and I can not figure out why this happens.

Do you have an idea what could the problem be?

Thanks in advance!

Best,

P.S. Here is the log file from the job.

less -S TFBS/KLF2_MA1515.1/plots/logs/KLF2_MA1515.1_heatmap_comparison.log

# TOBIAS 0.12.9 PlotHeatmap (run started 2021-03-07 21:53:45.608037)
# Working directory: /TOBIAS_snakemake
# Command line call: TOBIAS PlotHeatmap --signals .../bias_correction/monocyte_corrected.bw >

# ----- Input parameters -----
# TFBS: [['.../TFBS/KLF2_MA1515.1/beds/KLF2_MA1515.1_monocyte_bound.bed', '...>
# signals:      [.../bias_correction/monocyte_corrected.bw', '...>
# output:       .../TFBS/KLF2_MA1515.1/plots/KLF2_MA1515.1_heatmap_comparison.pdf
# plot_boundaries:      False
# share_colorbar:       True
# flank:        75
# title:        KLF2_MA1515.1 heatmap across conditions
# TFBS_labels:  None
# signal_labels:        ['monocyte', 'progenitor_monocyte']
# show_columns: []
# sort_by:      -1
# verbosity:    3


# ----- Output files -----
# .../TFBS/KLF2_MA1515.1/plots/KLF2_MA1515.1_heatmap_comparison.pdf


2021-03-07 21:53:45 (1061202) [INFO]    Using ['.../TFBS/KLF2_MA1515.1/beds/KLF2_MA1515.1_monocyte_bound.bed', ...>
2021-03-07 21:53:45 (1061202) [INFO]    Using ['.../TFBS/KLF2_MA1515.1/beds/KLF2_MA1515.1_progenitor_monocyte_bound.bed', ....>

2021-03-07 21:53:45 (1061202) [INFO]    Reading bedfiles
2021-03-07 21:53:45 (1061202) [INFO]    - Read 13897 sites from ...TFBS/KLF2_MA1515.1/beds/KLF2_MA1515.1_monocyte_bound.bed of wid>
2021-03-07 21:53:46 (1061202) [INFO]    - Read 33309 sites from .../TFBS/KLF2_MA1515.1/beds/KLF2_MA1515.1_monocyte_unbound.bed of w>
2021-03-07 21:53:46 (1061202) [INFO]    - Read 16239 sites from .../TFBS/KLF2_MA1515.1/beds/KLF2_MA1515.1_progenitor_monocyte_bound>
2021-03-07 21:53:47 (1061202) [INFO]    - Read 30967 sites from.../TFBS/KLF2_MA1515.1/beds/KLF2_MA1515.1_progenitor_monocyte_unbou>

2021-03-07 21:53:47 (1061202) [INFO]    Reading signals from bigwigs
2021-03-07 21:53:47 (1061202) [INFO]    - Reading .../TFBS/KLF2_MA1515.1/beds/KLF2_MA1515.1_monocyte_bound.bed from ...
2021-03-07 21:53:50 (1061202) [INFO]    - Reading .../TFBS/KLF2_MA1515.1/beds/KLF2_MA1515.1_monocyte_unbound.bed from ...
2021-03-07 21:53:55 (1061202) [ERROR]   Error reading region: ('JH584295.1', -25, 125, 'KLF2_MA1515.1', '-') from pybigwig object. Exception is: Invalid interval bounds!
msbentsen added a commit that referenced this issue Mar 8, 2021
@msbentsen
Fix for #64 out-of-bounds error in PlotHeatmap
6d43c16
@msbentsen
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Hi,

Thank you for the logfile - that was really helpful! As you see in the last line of the log, pybigwig is trying to read a region with coordinates "-25->125" from the bigwig file, which is not a valid region, since it has negative coordinates. Such scenarios should be excluded, so this was a bug in PlotHeatmap. Please fetch TOBIAS 0.12.10 for the fix!

However, I would urge you to have a look at whether you want to include such regions in general. The chromosome name suggests that it is an alternative chromosome or scaffold, which can be hard to make biological interpretations on (because you don't actually know where they are located). But it of course depends on the project.

Are you by any chance in the same group as @Hypercruse?

@msbentsen msbentsen added the bug Something isn't working label Mar 8, 2021
@KalinNonchev
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Hello,

Thank you for your fast reaction! I updated TOBIAS and it worked like a charm!!

Overall, we are more or less interested in the standard chromosomes. We will definitely consider your suggestion.

Yes, he is from our team.

Best,

@Knetsy Knetsy mentioned this issue Jun 9, 2021
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