Question: igv_plotter error, I cannot run igv_plotter on my BAM file, RuntimeError: Xvfb did not start
0
gravatar for cristian
9 weeks ago by
cristian80
cristian80 wrote:

Hi there,

I have installed igv_plotter with

sudo pip install igv_plotter

and

checked it with

igv_plotter 

igv_plotter
usage: igv_plotter [-h] [-o OUTPUT] [-L LOCUS_FILE] [-v] [--width WIDTH]
                   [--height HEIGHT] [--max-panel-height MAX_PANEL_HEIGHT]
                   [-c CONFIG_FILE] [-m MAX_MEMORY] [-g GENOME] [-p KEY=VALUE]
                   [--view-as-pairs] [--igv-jar-path IGV_JAR_PATH]
                   [--expand | --squish | --collapse]
                   files or loci [files or loci ...]
igv_plotter: error: too few arguments

but when I run it with my bam file, it does not work and gives me an error:

igv_plotter -g output/genome/celegans/ref/seq/celegans.fa output/alignment/celegans/ref/illumina/star/raw/saltlakecity1a/saltlakecity1aAligned.sortedByCoord.out.bam I:12345

Traceback (most recent call last):
  File "/Users/cr517/anaconda/envs/python2env/bin/igv_plotter", line 140, in <module>
    igv_robot.execute()
  File "/Users/cr517/anaconda/envs/python2env/lib/python2.7/site-packages/igv_api.py", line 256, in execute
    self._execute_impl(self.__command_queue)
  File "/Users/cr517/anaconda/envs/python2env/lib/python2.7/site-packages/igv_api.py", line 387, in _execute_impl
    fake_display.start()
  File "/Users/cr517/anaconda/envs/python2env/lib/python2.7/site-packages/xvfbwrapper.py", line 79, in start
    raise RuntimeError('Xvfb did not start')
RuntimeError: Xvfb did not start

Can anybody explain why this is happening, please?

Thanks, Best, C.

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by cristian80

Which operating system are you using? Did you log in using ssh -X (Unix)?

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by WouterDeCoster21k

Hi, I am using MacOS X. 10.12.5 Sierra. I am running it locally, so no ssh. What is the -X for?

ADD REPLYlink written 9 weeks ago by cristian80
1

That would be to enable X11 forwarding for graphical applications.

ADD REPLYlink written 9 weeks ago by WouterDeCoster21k

Thanks. Otherwise, any ideas about this RuntimeError? Do you know what Xvfb is?

ADD REPLYlink written 9 weeks ago by cristian80

We'll just have to wait for someone who knows more about MacOS X :-)

ADD REPLYlink written 9 weeks ago by WouterDeCoster21k
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