Error reading region [..] from pybigwig object. Exception is: Invalid interval bounds! #64
Description
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!