Hello, I think there is a major issue with sashimi_plot version vs miso version.
TL;DR: sashimi_plot need ".miso" files, which are removed by "miso_pack" function since Miso 0.5.0. In fact miso_pack will pick up all the .miso files under each chr* folder and put them into a .miso_db file, and remove those .miso files. Temporary solution: Make a copy of ".miso" files right after miso --run. According to the manual miso_zip will also pack the files if that's not done already. Now to answer Jermaine Jenkins: You are probably using a different version of Miso, and the test files are partially missing and / or files structure is not correct. In my legace files of miso 0.4.9, the test-data/miso-data contains folders "heartWT1", "heartWT2", "heartKOa", "heartKOb" and under each of those folders there is a file named "chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso" When I run my current miso/sashimi package (miso 0.5.3) on those test data, everything is OK and I got my output as in the manual. >From the setting files, and from the flow of the analysis, I would assume that >you need 4 bam files (one for each sample) and 4 miso output folders. Thus you >need 4 .miso files for the test. Except in my 0.5.3 test files I have just one >.miso file under /miso-data . When I do the test on that set of test data, I >got the sashimi plot without BF intervals on the right of the output. Questions to developpers: When I tried to download from the git https://github.com/yarden/MISO/zipball/fastmiso it seems to point to miso0.4.9 (file name yarden-MISO-1ca049f). Can you confirm that pip / last commit on git / zip download all point to the same version? Is there a more recent version of sashimi plot that no longer relies on .miso files but on .miso_db files? On the current git the test files still contain .miso files, so I wonder if sashimi plot is ever updated since Miso 0.5.0. In fact, the miso_pack is released within Miso 0.5.0 during Feb 20, 2014, while the last sashimi_plot update was in Feb 11 2014. On the git, the last commit on sashimi_plot is Feb 23 2014 while the last commit on Miso is Aug 2017 in the same time of Miso 0.5.4. Delong ________________________________ From: [email protected] <[email protected]> on behalf of Jermaine Jenkins <[email protected]> Sent: April 9, 2018 7:58:08 PM To: [email protected] Subject: [miso-users] error in testing sashimi_plot 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
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