Jdbeck66
commented
2 days ago 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
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