zhangyixing3
commented
1 week ago python -m jcvi.compara.catalog ortholog xihulu tiangua --no_strip_names
这步报latex was not able to process the following string，报错的原因可能是因为缺少 LaTeX。你可以在运行命令时添加 --notex 参数，或者在服务器上安装 LaTeX。
普通用户在服务器上安装 LaTeX，可以参考这篇文章：如何在不使用 root 权限下安装 LaTeX。
python -m jcvi.graphics.karyotype seqids layout 这步报错，是因为你的 layou文件错误
# y, xstart, xend, rotation, color, label, va, bed
.6, .1, .8, 0, , xihulu, top, xihulu.bed, center
.4, .1, .8, 0, , tiangua, top, tiangua.bed, center
# edges
e, 0, 1, xihulu.tiangua.anchors.simple改成
# y, xstart, xend, rotation, color, label, va, bed
.6, .1, .8, 0, , xihulu, top, xihulu.bed
.4, .1, .8, 0, , tiangua, top, tiangua.bed
# edges
e, 0, 1, grape.peach.anchors.simple
lindonghuia
作者您好，我在运行 python -m jcvi.graphics.karyotype seqids layout出现了这样的报错 [10/12/24 16:34:06] DEBUG Load file
main(sys.argv[1:])
File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/jcvi/graphics/karyotype.py", line 454, in main
Karyotype(
File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/jcvi/graphics/karyotype.py", line 365, in init
t = layout[i]
IndexError: list index out of range
layoutbase.py:36 DEBUG Load filexihulu.bedbase.py:36 DEBUG Load filetiangua.bedbase.py:36 Traceback (most recent call last): File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/runpy.py", line 196, in _run_module_as_main return _run_code(code, main_globals, None, File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/runpy.py", line 86, in _run_code exec(code, run_globals) File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/jcvi/graphics/karyotype.py", line 474, in以下是我的latout文件 (jcvi) lindonghui@swzx05:/data05/lindonghui/work/06_xihulu/04_mcscan$ more layout
y, xstart, xend, rotation, color, label, va, bed
.6, .1, .8, 0, , xihulu, top, xihulu.bed, center .4, .1, .8, 0, , tiangua, top, tiangua.bed, center
edges
e, 0, 1, xihulu.tiangua.anchors.simple (jcvi) lindonghui@swzx05:/data05/lindonghui/work/06_xihulu/04_mcscan$ more seqids Chr01,Chr02,Chr03,Chr04,Chr05 GWHDTVT00000001,GWHDTVT00000002,GWHDTVT00000003,GWHDTVT00000004
此外，我在运行前一步时出现了这样的错误
(jcvi) lindonghui@swzx05:/data05/lindonghui/work/06_xihulu/04_mcscan$ python -m jcvi.compara.catalog ortholog xihulu tiangua --no_strip_names [10/12/24 16:36:18] DEBUG File
main()
File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/jcvi/compara/catalog.py", line 88, in main
p.dispatch(globals())
File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/jcvi/apps/base.py", line 131, in dispatch
globalsaction
File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/jcvi/compara/catalog.py", line 768, in ortholog
dotplot_main(dargs)
File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/jcvi/graphics/dotplot.py", line 518, in dotplotmain
dotplot(
File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/jcvi/graphics/dotplot.py", line 352, in dotplot
xlim, = plot_breaks_and_labels(
File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/jcvi/graphics/dotplot.py", line 159, in plot_breaks_and_labels
th = TextHandler(fig, usetex=usetex)
File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/jcvi/graphics/base.py", line 94, in init
self.build_height_array(fig, usetex=usetex)
File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/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 "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/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 "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/matplotlib/textpath.py", line 355, in init
*text_to_path.get_text_path(prop, s, ismath=ismath),
File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/matplotlib/textpath.py", line 109, in get_text_path
glyph_info, glyph_map, rects = self.get_glyphs_tex(prop, s)
File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/matplotlib/textpath.py", line 219, in get_glyphs_tex
dvifile = TexManager().make_dvi(s, self.FONT_SCALE)
File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/matplotlib/texmanager.py", line 295, in make_dvi
cls._run_checked_subprocess(
File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/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'
xihulu.tiangua.lastfound. Computation skipped. base.py:1382 DEBUG Filexihulu.tiangua.last.filteredfound. Computation skipped. base.py:1382 DEBUG Filexihulu.tiangua.lifted.anchorsfound. Computation skipped. base.py:1382 DEBUG Assuming --qbed=xihulu.bed --sbed=tiangua.bed synteny.py:390 DEBUG Load filexihulu.bedbase.py:36 DEBUG Load filetiangua.bedbase.py:36 DEBUG Showing a random subset of 10000 data points (total 21553) for clarity. dotplot.py:233 [10/12/24 16:36:19] DEBUG xsize=27627 ysize=24499 dotplot.py:349 Traceback (most recent call last): File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/runpy.py", line 196, in _run_module_as_main return _run_code(code, main_globals, None, File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/runpy.py", line 86, in _run_code exec(code, run_globals) File "/data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/python3.10/site-packages/jcvi/compara/catalog.py", line 982, inHere is the full command invocation and its output:
latex -interaction=nonstopmode --halt-on-error --output-directory=tmpuc6_ory2 c86bca16e72db77513e4bcf36d49be7d.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023) (preloaded format=latex) restricted \write18 enabled.
kpathsea: Running mktexfmt latex.fmt Can't locate mktexlsr.pl in @INC (@INC contains: /data05/lindonghui/software/mamba/mambaforge/envs/jcvi/share/tlpkg /data05/lindonghui/software/mamba/mambaforge/envs/jcvi/share/texmf-dist/scripts/texlive /data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi /data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/perl5/site_perl/5.22.0 /data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/perl5/5.22.0/x86_64-linux-thread-multi /data05/lindonghui/software/mamba/mambaforge/envs/jcvi/lib/perl5/5.22.0 .) at /data05/lindonghui/software/mamba/mambaforge/envs/jcvi/bin/mktexfmt line 23. BEGIN failed--compilation aborted at /data05/lindonghui/software/mamba/mambaforge/envs/jcvi/bin/mktexfmt line 25. I can't find the format file `latex.fmt'! 但是除了pdf其他文件都输出了，请问这是否影响后续分析 感谢！！