No chromosome_density_plots.pdf

[bijendrabio]

Hello @oushujun @FayeFang17 , Although the EDTA run completed successfully, I received the following error message and couldn’t find chromosome_density_plots.pdf. Is it possible to generate chromosome_density_plots.pdf from the output?

Errror Fri Oct 4 18:50:43 EDT 2024 Execution of EDTA_raw.pl is finished! Sun Oct 6 02:04:23 EDT 2024 Homology-based annotation of TEs using testgenome.EDTA.fasta.mod.EDTA.TElib.fa from scratch.

mv: cannot stat 'chromosome_density_plots.pdf': No such file or directory Use of uninitialized value $mod_time in localtime at /tools/EDTA/EDTA.pl line 847. cp: cannot stat ' testgenome.fasta.mod.EDTA.TEanno.density_plots.pdf': No such file or directory

Regards, B

[Jdbeck66]

Similar.

Error encountered: [Errno 2] No such file or directory: 'samtools' mv: cannot stat 'chromosome_density_plots.pdf': No such file or directory Sat Nov 2 09:20:53 MDT 2024 TE annotation using the EDTA library has finished! Check out: Whole-genome TE annotation (total TE: 64.47%): BEA_div10.purged.fa.mod.EDTA.TEanno.gff3 Whole-genome TE annotation summary: BEA_div10.purged.fa.mod.EDTA.TEanno.sum Whole-genome TE divergence plot: BEA_div10.purged.fa.mod_divergence_plot.pdf Whole-genome TE density plot: BEA_div10.purged.fa.mod.EDTA.TEanno.density_plots.pdf Low-threshold TE masking for MAKER gene annotation (masked: 39.69%): BEA_div10.purged.fa.mod.MAKER.masked

Use of uninitialized value $mod_time in localtime at /lfs/jimbeck.bsu/EDTA/EDTA.pl line 847. cp: cannot stat 'BEA_div10.purged.fa.mod.EDTA.TEanno.density_plots.pdf': No such file or directory

Used the build suggested in issue #483 - I'm thinking samtools should be included in:

mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter

[WWilen]

Hello @oushujun @FayeFang17 ，I have installed all the software as prompted #483 ，but the sam problem still exists.

2024年 11月 16日 星期六 00:03:47 CST Execution of EDTA_raw.pl is finished!

Warning: No sequences were masked 2024年 11月 16日 星期六 00:04:07 CST Homology-based annotation of TEs using genome.fa.mod.EDTA.TElib.fa from scratch.

mv: 对 'chromosome_density_plots.pdf' 调用 stat 失败: 没有那个文件或目录 Use of uninitialized value $mod_time in localtime at ../EDTA.pl line 847. cp: 对 'genome.fa.mod.EDTA.TEanno.density_plots.pdf' 调用 stat 失败: 没有那个文件或目录

[WWilen]

In addition,I installed it by downloading zip

[WWilen]

I also tried different servers and different EDTA2 versions，the problem still exists