[miso-users] error in testing sashimi_plot

[Jermaine Jenkins]

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:- at chr17:45815912:45815950:- at 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:- at chr17
:45815912:45815950:- at chr17:45814875:45814965:-.pdf
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sudo sashimi_plot --plot-event "chr17:45816186:45816265:- at chr17:45815912:45815950:- at 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:- at chr17:45815912:45815950:- at 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:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-.pdf