Ghost Script For creating PDF file

[littlekoreanboy]

Hello!

I am having issues generating a PDF file for my weblogo. This is my command:

weblogo -f muscled_AaegyptiLVPWY_7tm_1_domain.fasta -D fasta -o Test -F pdf

And this is the issue:

Traceback (most recent call last):
File "/home/joelshin/miniconda3/envs/GPCR/bin/weblogo", line 10, in
sys.exit(main())
^^^^^^
File "/home/joelshin/miniconda3/envs/GPCR/lib/python3.11/site-packages/weblogo/_cli.py", line 94, in main
logo = formatter(data, format)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/joelshin/miniconda3/envs/GPCR/lib/python3.11/site-packages/weblogo/logo_formatter.py", line 50, in pdf_formatter
return gs.convert("pdf", eps, logoformat.logo_width, logoformat.logo_height)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/joelshin/miniconda3/envs/GPCR/lib/python3.11/site-packages/weblogo/logo_formatter.py", line 413, in convert
raise RuntimeError(error_msg)
RuntimeError: Unrecoverable error : Ghostscript conversion failed (Invalid postscript?). /usr/bin/gs -sDEVICE=pdfwrite -dPDFSETTINGS=/printer -sstdout=%stderr -dColorConversionStrategy=/LeaveColorUnchanged -sOutputFile=- -dDEVICEWIDTHPOINTS=470 -dDEVICEHEIGHTPOINTS=2110 -dSAFER -dNOPAUSE -r300 -
Return code: 1
b"GPL Ghostscript 9.55.0 (2021-09-27)\nCopyright (C) 2021 Artifex Software, Inc. All rights reserved.\nThis software is supplied under the GNU AGPLv3 and comes with NO WARRANTY:\nsee the file COPYING for details.\nQuerying operating system for font files...\nCan't find (or can't open) font file /usr/share/ghostscript/9.55.0/Resource/Font//usr/sh.\nCan't find (or can't open) font file ArialMT.\nDidn't find this font on the system!\nSubstituting font Helvetica for ArialMT.\nLoading NimbusSans-Regular font from /usr/share/ghostscript/9.55.0/Resource/Font/NimbusSans-Regular... 5143956 3625799 4050132 2693688 2 done.\nLoading NimbusMonoPS-Regular font from /usr/share/ghostscript/9.55.0/Resource/Font/NimbusMonoPS-Regular... 5230268 3860574 4110732 2734161 2 done.\nError: /unknownerror in --.FAPIBuildChar--\nOperand stack:\n --dict:17/19(ro)(G)-- 73\nExecution stack:\n %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 1990 1 3 %oparray_pop 1989 1 3 %oparray_pop 1988 1 3 %oparray_pop --nostringval-- 1977 1 3 %oparray_pop 1833 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- --nostringval-- --nostringval-- %finish_show --nostringval-- --nostringval-- 11 3 0 --nostringval-- (gs_show_enum) %op_show_continue\nDictionary stack:\n --dict:768/1123(ro)(G)-- --dict:0/20(G)-- --dict:194/200(L)--\nCurrent allocation mode is local\nGPL Ghostscript 9.55.0: Unrecoverable error, exit code 1\n"

Thank you in advance!

[SanityTree]

I know this was posted over a year ago but I just had the same issue and I just had to set the ghost script path to my computer's font files. In my case I typed this into my Anaconda prompt:

set GS_FONTPATH=C:\Windows\Fonts

I think this is the default Path for fonts on windows. This allowed me to generate pdf files, but you have to repeat it every time your open a new window.

For conda you can alter the environment so this is set whenever you use it:

conda env config vars set GS_FONTPATH=C:\Windows\Fonts

It will ask you to reset the environment afterwards but after that its fixed in place.

Obviously this solution is for windows.