! LaTeX Error: File `type1ec.sty' not found.

[liuqz-bot]

[07/07/24 16:08:25] DEBUG File Cmelo.Mcharantia.last found. Computation skipped. base.py:1382
DEBUG File Cmelo.Mcharantia.last.filtered found. Computation skipped. base.py:1382
DEBUG File Cmelo.Mcharantia.lifted.anchors found. Computation skipped. base.py:1382
DEBUG Assuming --qbed=Cmelo.bed --sbed=Mcharantia.bed synteny.py:390
DEBUG Load file Cmelo.bed base.py:36
DEBUG Load file Mcharantia.bed base.py:36
[07/07/24 16:08:26] DEBUG Showing a random subset of 10000 data points (total 14795) for clarity. dotplot.py:233
DEBUG xsize=28299 ysize=39449 dotplot.py:349
Traceback (most recent call last):
File "", line 198, in _run_module_as_main
File "", line 88, in _run_code
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/jcvi/compara/catalog.py", line 982, in
main()
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/jcvi/compara/catalog.py", line 88, in main
p.dispatch(globals())
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/jcvi/apps/base.py", line 131, in dispatch
globalsaction
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/jcvi/compara/catalog.py", line 768, in ortholog
dotplot_main(dargs)
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/jcvi/graphics/dotplot.py", line 518, in dotplot_main
dotplot(
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/jcvi/graphics/dotplot.py", line 352, in dotplot
xlim, _ = plot_breaks_and_labels(
^^^^^^^^^^^^^^^^^^^^^^^
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/jcvi/graphics/dotplot.py", line 159, in plot_breaks_and_labels
th = TextHandler(fig, usetex=usetex)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/jcvi/graphics/base.py", line 94, in init
self.build_height_array(fig, usetex=usetex)
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/jcvi/graphics/base.py", line 110, in build_height_array
w, h = TextHandler.get_text_width_height(fig, size=i, usetex=usetex)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/jcvi/graphics/base.py", line 102, in get_text_width_height
tp = mpl.textpath.TextPath((0, 0), txt, size=size, usetex=usetex)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/matplotlib/textpath.py", line 355, in init
*text_to_path.get_text_path(prop, s, ismath=ismath),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/matplotlib/textpath.py", line 109, in get_text_path
glyph_info, glyph_map, rects = self.get_glyphs_tex(prop, s)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/matplotlib/textpath.py", line 219, in get_glyphs_tex
dvifile = TexManager().make_dvi(s, self.FONT_SCALE)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/matplotlib/texmanager.py", line 295, in make_dvi
cls._run_checked_subprocess(
File "/hdd/data/lqzdata/miniconda3/envs/orthofinder/lib/python3.11/site-packages/matplotlib/texmanager.py", line 258, in _run_checked_subprocess
raise RuntimeError(
RuntimeError: latex was not able to process the following string:
b'chr01'

Here is the full command invocation and its output:

latex -interaction=nonstopmode --halt-on-error --output-directory=tmpa9uedhv0 c86bca16e72db77513e4bcf36d49be7d.tex

This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2024) (preloaded format=latex)
restricted \write18 enabled.
entering extended mode
(./c86bca16e72db77513e4bcf36d49be7d.tex
LaTeX2e <2024-06-01> patch level 2
L3 programming layer <2024-05-27>
(/home/liuqz/.TinyTeX/texmf-dist/tex/latex/base/article.cls
Document Class: article 2024/02/08 v1.4n Standard LaTeX document class
(/home/liuqz/.TinyTeX/texmf-dist/tex/latex/base/size10.clo)) (/home/liuqz/.TinyTeX/texmf-dist/tex/latex/psnfss/helvet.sty (/home/liuqz/.TinyTeX/texmf-dist/tex/latex/graphics/keyval.sty)) (/home/liuqz/.TinyTeX/texmf-dist/tex/latex/type1cm/type1cm.sty)

! LaTeX Error: File `type1ec.sty' not found.

Type X to quit or to proceed,
or enter new name. (Default extension: sty)

Enter file name:
! Emergency stop.
<read *>

l.9 \usepackage
[utf8]{inputenc}^^M
No pages of output.
Transcript written on tmpa9uedhv0/c86bca16e72db77513e4bcf36d49be7d.log.

[tanghaibao]

@liuqz-bot

There is a missing Latex package. See here to install it:
https://stackoverflow.com/questions/11354149/python-unable-to-render-tex-in-matplotlib