Hi,
Whe trying to test sashimi_plot I am getting a errors and a plot without
MISO estimates? Any help is appreciated.
Thanks,
JJ
part of the terminal output (full output is attached)
miso_prefix:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data
Searching for MISO files in:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT1
- Looking for chromosome chr17 directories
Error:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT1
not a directory.
Error: Could not find MISO output files for sample heartWT1 (after
searching in
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT1
and its subdirectories). Are you sure MISO output files are present in that
directory?
Searching for MISO files in:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT2
- Looking for chromosome chr17 directories
Error:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT2
not a directory.
Error: Could not find MISO output files for sample heartWT2 (after
searching in
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT2
and its subdirectories). Are you sure MISO output files are present in that
directory?
Searching for MISO files in:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOa
- Looking for chromosome chr17 directories
Error:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOa
not a directory.
Error: Could not find MISO output files for sample heartKOa (after
searching in
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOa
and its subdirectories). Are you sure MISO output files are present in that
directory?
Searching for MISO files in:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOb
- Looking for chromosome chr17 directories
Error:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOb
not a directory.
Error: Could not find MISO output files for sample heartKOb (after
searching in
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOb
and its subdirectories). Are you sure MISO output files are present in that
directory?
Reading dimensions from settings...
- Height: 5.00
- Width: 7.00
Plotting read densities and MISO estimates along event...
- Event: chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17
:45814875:45814965:-
Setting up plot using dimensions: [7.0, 5.0]
Using intron scale 30.0
Using exon scale 4.0
Reading sample label: heartWT1.sorted.bam
Processing BAM: ./test-data/bam-data/heartWT1.sorted.bam
Warning: MISO file not found
Loading MISO file:
Posterior plot failed.
Reading sample label: heartWT2.sorted.bam
Processing BAM: ./test-data/bam-data/heartWT2.sorted.bam
Warning: MISO file not found
Loading MISO file:
Posterior plot failed.
Reading sample label: heartKOa.sorted.bam
Processing BAM: ./test-data/bam-data/heartKOa.sorted.bam
Warning: MISO file not found
Loading MISO file:
Posterior plot failed.
Reading sample label: heartKOb.sorted.bam
Processing BAM: ./test-data/bam-data/heartKOb.sorted.bam
Warning: MISO file not found
Loading MISO file:
Posterior plot failed.
Saving plot to:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-plot/chr17:45816186:45816265:-@chr17
:45815912:45815950:-@chr17:45814875:45814965:-.pdf
sudo sashimi_plot --plot-event
"chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-"
test-data/event-data/ ../settings/sashimi_plot_settings.txt --output-dir
test-plot
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/cbook/deprecation.py:106:
MatplotlibDeprecationWarning: The mpl_toolkits.axes_grid module was deprecated
in version 2.1. Use mpl_toolkits.axes_grid1 and mpl_toolkits.axisartist provies
the same functionality instead.
warnings.warn(message, mplDeprecation, stacklevel=1)
Reading settings from:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/settings/sashimi_plot_settings.txt
Parsing data:bam_prefix
Parsing data:miso_prefix
Parsing data:bam_files
Parsing data:miso_files
Parsing plotting:fig_width
Parsing plotting:fig_height
Parsing plotting:intron_scale
Parsing plotting:exon_scale
Parsing plotting:logged
Parsing plotting:font_size
Parsing plotting:bar_posteriors
Parsing plotting:ymax
Parsing plotting:nyticks
Parsing plotting:nxticks
Parsing plotting:show_ylabel
Parsing plotting:show_xlabel
Parsing plotting:show_posteriors
Parsing plotting:number_junctions
Parsing plotting:resolution
Parsing plotting:posterior_bins
Parsing plotting:gene_posterior_ratio
Parsing plotting:colors
Parsing plotting:coverages
Parsing plotting:bar_color
Parsing plotting:bf_thresholds
miso_prefix:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data
Searching for MISO files in:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT1
- Looking for chromosome chr17 directories
Error:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT1
not a directory.
Error: Could not find MISO output files for sample heartWT1 (after searching in
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT1
and its subdirectories). Are you sure MISO output files are present in that
directory?
Searching for MISO files in:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT2
- Looking for chromosome chr17 directories
Error:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT2
not a directory.
Error: Could not find MISO output files for sample heartWT2 (after searching in
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT2
and its subdirectories). Are you sure MISO output files are present in that
directory?
Searching for MISO files in:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOa
- Looking for chromosome chr17 directories
Error:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOa
not a directory.
Error: Could not find MISO output files for sample heartKOa (after searching in
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOa
and its subdirectories). Are you sure MISO output files are present in that
directory?
Searching for MISO files in:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOb
- Looking for chromosome chr17 directories
Error:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOb
not a directory.
Error: Could not find MISO output files for sample heartKOb (after searching in
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOb
and its subdirectories). Are you sure MISO output files are present in that
directory?
Reading dimensions from settings...
- Height: 5.00
- Width: 7.00
Plotting read densities and MISO estimates along event...
- Event:
chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-
Setting up plot using dimensions: [7.0, 5.0]
Using intron scale 30.0
Using exon scale 4.0
Reading sample label: heartWT1.sorted.bam
Processing BAM: ./test-data/bam-data/heartWT1.sorted.bam
Warning: MISO file not found
Loading MISO file:
Posterior plot failed.
Reading sample label: heartWT2.sorted.bam
Processing BAM: ./test-data/bam-data/heartWT2.sorted.bam
Warning: MISO file not found
Loading MISO file:
Posterior plot failed.
Reading sample label: heartKOa.sorted.bam
Processing BAM: ./test-data/bam-data/heartKOa.sorted.bam
Warning: MISO file not found
Loading MISO file:
Posterior plot failed.
Reading sample label: heartKOb.sorted.bam
Processing BAM: ./test-data/bam-data/heartKOb.sorted.bam
Warning: MISO file not found
Loading MISO file:
Posterior plot failed.
Saving plot to:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-plot/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.pdf
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