probelm in plotting alleale depth using vcftools

[Zer0day-0]

Parsing bcftools stats output: AD68846579TE.hard-filtered.stats.stats
Plotting graphs: python plot.py
/data/sata_data/home/dl8/new-bcftools-test/plot.py:236: MatplotlibDeprecationWarning: The get_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use matplotlib.colormaps[name] or matplotlib.colormaps.get_cmap(obj) instead.
cm = mpl.cm.get_cmap('autumn')
Creating PDF: pdflatex summary.tex >plot-vcfstats.log 2>&1
The command exited with non-zero status, please consult the output of pdflatex: /data/sata_data/home/dl8/new-bcftools-test/plot-vcfstats.log

at /data/sata_data/home/dl8/anaconda3/envs/env-vcf/bin/plot-vcfstats line 99.
main::error("The command exited with non-zero status, please consult the o"...) called at /data/sata_data/home/dl8/anaconda3/envs/env-vcf/bin/plot-vcfstats line 2005
main::create_pdf(HASH(0x2881120)) called at /data/sata_data/home/dl8/anaconda3/envs/env-vcf/bin/plot-vcfstats line 71 plot-vcfstats.log summary.log

[pd3]

I pushed a change which should help with this.

In the attached log I noticed that there is another problem, the latex package multirow.sty is missing on your system.

[Zer0day-0]

Thank you, I will surely update it accordingly

[Zer0day-0]

Hello the @pd3, I updated it, Yet the final .pdf combining all the report is not being generated. The output I get is

`Plotting graphs: python plot.py /data/sata_data/home/dl8/a-folder/plot.py:236: MatplotlibDeprecationWarning: The get_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use matplotlib.colormaps[name] or matplotlib.colormaps.get_cmap(obj) instead. cm = mpl.cm.get_cmap('autumn') Note: The xcolor.sty package not available, black and white tables only...

Creating PDF: pdflatex summary.tex >plot-vcfstats.log 2>&1 The command exited with non-zero status, please consult the output of pdflatex: /data/sata_data/home/dl8/a-folder/plot-vcfstats.log

at /data/sata_data/home/dl8/anaconda3/envs/env-vcf/bin/plot-vcfstats line 99. main::error("The command exited with non-zero status, please consult the o"...) called at /data/sata_data/home/dl8/anaconda3/envs/env-vcf/bin/plot-vcfstats line 2005 main::create_pdf(HASH(0xc0d140)) called at /data/sata_data/home/dl8/anaconda3/envs/env-vcf/bin/plot-vcfstats line 71 `

and when I look into the log file, I see

`This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021) (preloaded format=pdflatex) restricted \write18 enabled.

kpathsea: Running mktexfmt pdflatex.fmt Can't locate mktexlsr.pl in @INC (@INC contains: /data/sata_data/home/dl8/anaconda3/envs/env-vcf/share/tlpkg /data/sata_data/home/dl8/anaconda3/envs/env-vcf/share/texmf-dist/scripts/texlive /data/sata_data /home/dl8/anaconda3/envs/env-vcf/lib/site_perl/5.34.0/x86_64-linux-thread-multi /data/sata_data/home/dl8/anaconda3/envs/env-vcf/lib/site_perl/5.34.0 /data/sata_data/home/dl8/anaconda3/envs/env-vcf/lib/5.34 .0/x86_64-linux-thread-multi /data/sata_data/home/dl8/anaconda3/envs/env-vcf/lib/5.34.0 .) at /data/sata_data/home/dl8/anaconda3/envs/env-vcf/bin/mktexfmt line 23. BEGIN failed--compilation aborted at /data/sata_data/home/dl8/anaconda3/envs/env-vcf/bin/mktexfmt line 25. I can't find the format file pdflatex.fmt'!

please have a look! I am using bcftools in a conda environment.

[pd3]

Are you sure you are working with the latest github version of plot-vcfstats?? If you look inside the script there is no occurrence of get_cmap anymore.