rgt-hint differential "GPL Ghostscript 8.70: Can't find initialization file gs_init.ps."

[mdurante1]

Hi,

After running rgt-hint differential I noticed that no output was produced even though the job looks as if it had completed successfully. When looking at the error output file I see the following error:

GPL Ghostscript 8.70: Can't find initialization file gs_init.ps.
GPL Ghostscript 8.70: Can't find initialization file gs_init.ps.
GPL Ghostscript 8.70: Can't find initialization file gs_init.ps.
GPL Ghostscript 8.70: Can't find initialization file gs_init.ps.

The error file contained multiple lines with this error. Any suggestions on how to resolve this?

Thanks,
Michael

[lzj1769]

Hi @mdurante1 ,

It seems that rgt-hint cannot find Ghostscript.

In rgt-hint differential, we use command 'epstopdf' to convert the plots from .eps to .pdf,
can you check if you can run this command successfully on you machine?

Thanks,

[mdurante1]

Yes, this command works

(atac_danpos) [mdurante@pegasus hint]$ epstopdf
EPSTOPDF 2.9.5gw, 2006/01/29 - Copyright 1998-2006 by Sebastian Rahtz et al.
Syntax:  epstopdf [options] <eps file>
Options:
  --help:           print usage
  --outfile=<file>: write result to <file>
  --(no)filter:     read standard input   (default: false)
  --(no)gs:         run ghostscript       (default: true)
  --(no)compress:   use compression       (default: true)
  --(no)hires:      scan HiResBoundingBox (default: false)
  --(no)exact:      scan ExactBoundingBox (default: false)
  --(no)debug:      debug informations    (default: false)
Examples for producing 'test.pdf':
  * epstopdf test.eps
  * produce postscript | epstopdf --filter >test.pdf
  * produce postscript | epstopdf -f -d -o=test.pdf
Example: look for HiResBoundingBox and produce corrected PostScript:
  * epstopdf -d --nogs -hires test.ps>testcorr.ps

!!! Error: Input filename missing!

[lzj1769]

Hi, @mdurante1

well, to make sure it works correctly, can you download the below example file and try to convert it to pdf using command:
epstopdf example.eps

https://www.dropbox.com/s/f6wul0ibbofiyiu/example.eps?dl

Thanks,

[mdurante1]

Yes, it's working correctly:

example.pdf

[lzj1769]

ok, thanks.

It would better if you can provide more information about your:

1. opertion system (Ubuntu? Centos? or MacOS)
2. python version
3. rgt version

In addtion, please check if the file gs_init.ps exists on you machine using command:
locate gs_init.ps

I find some people also reported this problem:
https://bugs.launchpad.net/ubuntu/+source/ghostscript/+bug/262000
https://bbs.archlinux.org/viewtopic.php?id=1331

[mdurante1]

(atac_danpos) [mdurante@pegasus ~]$ rgt-motifanalysis --version
Motif Analysis - Regulatory Analysis Toolbox (RGT) - v0.11.1
(atac_danpos) [mdurante@pegasus ~]$ python --version
Python 2.7.14
(atac_danpos) [mdurante@pegasus ~]$ cat /etc/centos-release
CentOS release 6.5 (Final)
(atac_danpos) [mdurante@pegasus ~]$ locate gs_init.ps
/usr/share/ghostscript/8.70/Resource/Init/gs_init.ps

I am also seeing this same issue separately on Ubuntu 16.04 with the same version of python and rgt

[lzj1769]

thanks for the information.

can you run our tutorial:
http://www.regulatory-genomics.org/hint/tutorial/
and see if it works?

Maybe setting environment variable GS_LIB will fix it:
GS_LIB=/usr/share/ghostscript/8.70/lib:/usr/share/ghostscript/8.70/Resource/Init/

Meanwhile, I will try to reproduce the error.

[lzj1769]

I can't reproduce the error on Ubtuntu 16.04 and CentOS Linux release 7.3.1611, so far.

Hi, @mdurante1
Can you download the below file and run test script on you machine.
test.tar.gz

it will create a .pdf and .eps file by merging the line plot and weblogo file, if everything is working.

Thanks,

[mdurante1]

Hi @lzj1769
I was able to fix this error by setting the environment variable GS_LIB.
Thanks for all of your help.

Best,
Michael