rmats2sashimiplot issue: ValueError: max() arg is an empty sequence

[Patrick]

Hello,
I am testing out rmats2sashimiplot's grouping function on my Mac with OSX 10.11.6. I used the rMATS2sashimiplot February 14 release to make plots on this same data successfully. I am now interested in using the grouping function (from the newest release) to produce the "merged" plots, but keep on running into an error that states "ValueError: max() arg is an empty sequence".  Could you please assist me in understanding and resolving this error. Thank you.

My command, as well as the output of the command are below. The contents of my grouping file are in red below.

group1: 1-3 # group N2_rep1.bam,N2_rep2.bam,N2_rep3.bam
group2: 4-6 # group HPL2_rep1.bam,HPL2_rep2.bam,HPL2_rep3.bam

rmats2sashimiplot --b1 N2_rep1.bam,N2_rep2.bam,N2_rep3.bam --b2 HPL2_rep1.bam,HPL2_rep2.bam,HPL2_rep3.bam -c /Users/desktop/MATSoutHPL2Paper/MATS/rMATS/c_elegans.PRJNA13758.WS258.canonical_geneset.gtf --l1 N2 --l2 HPL-2 -t SE -e /Users/desktop/MATSoutHPL2Paper/MATS/rMATS/N2vHPL2long/MATS_output/SE_test.txt -o /Users/desktop/MATSoutHPL2Paper/MATS/rMATS/N2vHPL2long/plots/SEtest --group-info /Users/desktop/MATSoutHPL2Paper/MATS/rMATS/N2vHPL2long/MATS_output/hpl2grouping.gf

'N2_rep1.bam' seems to be indexed already. Please Check out this index file 'N2_rep1.bam.bai'
'N2_rep2.bam' seems to be indexed already. Please Check out this index file 'N2_rep2.bam.bai'
'N2_rep3.bam' seems to be indexed already. Please Check out this index file 'N2_rep3.bam.bai'
'HPL2_rep1.bam' seems to be indexed already. Please Check out this index file 'HPL2_rep1.bam.bai'
'HPL2_rep2.bam' seems to be indexed already. Please Check out this index file 'HPL2_rep2.bam.bai'
'HPL2_rep3.bam' seems to be indexed already. Please Check out this index file 'HPL2_rep3.bam.bai'

<module 'misopy' from '/Users/anaconda2/lib/python2.7/site-packages/rmats2sashimiplot-2.0.0-py2.7.egg/MISO/misopy/__init__.pyc'>
Indexing GFF...
  - GFF: /Users/desktop/MATSoutHPL2Paper/MATS/rMATS/N2vHPL2long/plots/SEtest/Sashimi_index_NA_1/tmp.gff3
  - Outputting to: /Users/desktop/MATSoutHPL2Paper/MATS/rMATS/N2vHPL2long/plots/SEtest/Sashimi_index_NA_1
Through 0 genes...
Loaded 1 genes
  - Loading of genes from GFF took 0.00 seconds
Making directory: /Users/desktop/MATSoutHPL2Paper/MATS/rMATS/N2vHPL2long/plots/SEtest/Sashimi_index_NA_1/chrIV
  - Chromosome serialization took 0.00 seconds
Outputting gene records in GFF format...
  - Output file: /Users/desktop/MATSoutHPL2Paper/MATS/rMATS/N2vHPL2long/plots/SEtest/Sashimi_index_NA_1/genes.gff
  - Serialization of genes from GFF took 0.01 seconds
Indexing of GFF took 0.01 seconds.
Reading settings from: /Users/desktop/MATSoutHPL2Paper/MATS/rMATS/N2vHPL2long/plots/SEtest/Sashimi_index_NA_1/sashimi_plot_settings.txt
Parsing data:bam_prefix
Parsing data:miso_prefix
Parsing data:bam_files
Parsing data:miso_files
Parsing plotting:font_size
Parsing plotting:reverse_minus
Parsing plotting:show_xlabel
Parsing plotting:nyticks
Parsing plotting:min_counts
Parsing plotting:text_background
Parsing plotting:logged
Parsing plotting:plot_label
Parsing plotting:show_ylabel
Parsing plotting:fig_height
Parsing plotting:nxticks
Parsing plotting:plot_title
Parsing plotting:exon_scale
Parsing plotting:fig_width
Parsing plotting:intron_scale
Parsing plotting:resolution
Parsing plotting:bar_posteriors
Parsing plotting:number_junctions
Parsing plotting:show_posteriors
Parsing plotting:colors
Parsing plotting:sample_labels
Reading dimensions from settings...
 - Height: 7.00
 - Width: 8.00
Plotting read densities and MISO estimates along event...
  - Event: IV:6024450:6024787:-@IV:6023722:6023851:-@IV:6022940:6023053:-
Setting up plot using dimensions:  [8.0, 7.0]
Using intron scale  1.0
Using exon scale  1.0
Traceback (most recent call last):
  File "/Users/anaconda2/lib/python2.7/site-packages/rmats2sashimiplot-2.0.0-py2.7.egg/MISO/misopy/sashimi_plot/sashimi_plot.py", line 293, in <module>
    main()
  File "/Users/anaconda2/lib/python2.7/site-packages/rmats2sashimiplot-2.0.0-py2.7.egg/MISO/misopy/sashimi_plot/sashimi_plot.py", line 289, in main
    plot_label=plot_label)
  File "/Users/anaconda2/lib/python2.7/site-packages/rmats2sashimiplot-2.0.0-py2.7.egg/MISO/misopy/sashimi_plot/sashimi_plot.py", line 160, in plot_event
    plot_label=plot_label)
  File "/Users/anaconda2/lib/python2.7/site-packages/rmats2sashimiplot-2.0.0-py2.7.egg/MISO/misopy/sashimi_plot/plot_utils/plot_gene.py", line 799, in plot_density_from_file
    plot_title=plot_title)
  File "/Users/anaconda2/lib/python2.7/site-packages/rmats2sashimiplot-2.0.0-py2.7.egg/MISO/misopy/sashimi_plot/plot_utils/plot_gene.py", line 389, in plot_density
    max_used_yval = math.ceil(max(used_yvals))
ValueError: max() arg is an empty sequence
mv: rename /Users/desktop/MATSoutHPL2Paper/MATS/rMATS/N2vHPL2long/plots/SEtest/Sashimi_plot/IV:6024450:6024787:-@IV:6023722:6023851:-@IV:6022940:6023053:-.pdf to /Users/desktop/MATSoutHPL2Paper/MATS/rMATS/N2vHPL2long/plots/SEtest/Sashimi_plot/1_NA_IV_6024450_6024787_-@IV_6023722_6023851_-@IV_6022940_6023053_-.pdf: No such file or directory

[Zhijie Xie (Jay)]

Hi Patrick,

Thanks for your email. It seems that the comments in grouing.gf caused this issue.

Could you please remove the comments in your grouping.gf and rerun the program?

Best,

Zhijie

在 2017年4月7日星期五 UTC+8下午11:58:51，Patrick写道：