Pangenome analysis when dispaly result, can't see the Phylogenetic tree

[GZL217]

there is the code that uesd

ls *fasta

ls *fasta | awk 'BEGIN{FS="_"}{print $1}' > genomes.txt cat genomes.txt

for g in cat genomes.txt do echo echo "Working on $g ..." echo anvi-script-reformat-fasta ${g}_scaffolds.fasta \ --min-len 2500 \ --simplify-names \ -o ${g}_scaffolds_2.5K.fasta done

for g in cat genomes.txt do echo echo "Working on $g ..." echo anvi-gen-contigs-database -f ${g}_scaffolds2.5K.fasta \ -o M${g}.db \ --num-threads 4 \ -n M_${g}
done

for g in *.db do anvi-run-hmms -c $g --num-threads 8 anvi-run-ncbi-cogs -c $g --num-threads 8 anvi-scan-trnas -c $g --num-threads 8 anvi-run-scg-taxonomy -c $g --num-threads 8 done

anvi-display-contigs-stats *db -I localhost

anvi-script-gen-genomes-file --input-dir . \ -o external-genomes.txt

anvi-estimate-genome-completeness -e external-genomes.txt

anvi-profile -c M_marinusZ4.db \ --sample-name M_marinusZ4 \ --output-dir M_marinusZ4 \ --blank

anvi-interactive -c M_marinusZ4.db \ -p M_marinusZ4/PROFILE.db -I localhost

anvi-split -p M_marinusZ4/PROFILE.db \ -c M_marinusZ4.db \ -C default \ -o M_marinusZ4_SPLIT

sed 's/M_marinusZ4.db/M_marinusZ4_SPLIT\/M_marinusZ4_CLEAN\/CONTIGS.db/g' external-genomes.txt > external-genomes-final.txt

anvi-estimate-genome-completeness -e external-genomes.txt anvi-estimate-genome-completeness -e external-genomes-final.txt

anvi-gen-genomes-storage -e external-genomes-final.txt \ -o M_-GENOMES.db

anvi-pan-genome -g M-GENOMES.db \
--project-name M \ --num-threads 16

anvi-display-pan -p M/M-PAN.db \ -g M_-GENOMES.db -I localhost

![Uploading QQ截图20240531220617.png…]()

[meren]

Is this prematurely sent? :) I don't see a question here. Neither I see the screenshot.

[GZL217]

how about now? I already uplode the picture

[meren]

It didn't work again.

[metehaansever]

I can't see either. Can you wait until you see the preview after uploading the image?

[GZL217]

no

[metehaansever]

Maybe you can share in our discord channel: https://discord.com/invite/C6He6mSNY4

[GZL217]

thanks I am try

[GZL217]

[GZL217]

finally！！

[GZL217]

[meren]

Ah. If there are more than 25,000 gene clusters, a dendrogram is not computed automatically (which is not a phylogenetic tree, but a clustering dendrogram).

That said, if you look at the help menu of the anvi-pan-genome, you will see that there is a parameter to 'enforce' it. If you re-run it with that flag, it should work.

[GZL217]

the picture have already uplod so you can see there is no Phylogenetic tree in the middle of the diagram

[meren]

I understand that. Please read my message again, @GZL217.