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phylogenetic tree build fails #931
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I am having hard time reproducing this :/ Can you please send the FASTA file you used to get this error? :) |
I just sent it. |
Still unable to reproduce: $ anvi-gen-phylogenomic-tree -f seqs-for-phylogenomics-Viehwege.fa -o phylogenomic-tree.txt
Input aligment file path .....................: /Users/meren/workshop-jena/INFANT-GUT-TUTORIAL/seqs-for-phylogenomics-Viehwege.fa
Output file path .............................: /Users/meren/workshop-jena/INFANT-GUT-TUTORIAL/phylogenomic-tree.txt
Alignment names ..............................: Streptococcus, P_rhinitidis, L_citreum, C_albicans, S_epidermidis, F_magna, P_avidum, E_facealis, S_hominis, Aneorococcus_sp, S_aureus
Alignment sequence length ....................: 8,816
Version ......................................: FastTree Version 2.1.10 No SSE3
Alignment ....................................: standard input
Info .........................................: Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000
Search .......................................: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits ......................................: 1.00*sqrtN close=default refresh=0.80
ML Model .....................................: Jones-Taylor-Thorton, CAT approximation with 20 rate categories
FastTree output newick file ..................: /Users/meren/workshop-jena/INFANT-GUT-TUTORIAL/phylogenomic-tree.txt
$ cat phylogenomic-tree.txt
((Streptococcus:0.27715,E_facealis:0.10530)0.791:0.03751,(P_avidum:0.60808,L_citreum:0.16850)1.000:0.08870,((S_aureus:0.03558,(S_epidermidis:0.04069,S_hominis:0.04839)0.808:0.01802)1.000:0.08470,(C_albicans:0.43611,(Aneorococcus_sp:0.41781,(F_magna:0.18320,P_rhinitidis:0.17801)0.993:0.04472)0.999:0.05406)1.000:0.08265)1.000:0.06239); |
Odd. When I run anvi-interactive --tree phylogenomic-tree.txt \
-p temp-profile.db \
--title "Pylogenomics of IGD Bins" \
--manual then all's well. I reinstalled One observation is that the error about |
Can you please run the same command with the flag |
Sure: anvi-gen-phylogenomic-tree -f seqs-for-phylogenomics.fa -o phylogenomic-tree.txt --debug
Input aligment file path .....................: .../gone-fishing/INFANT-GUT-TUTORIAL/seqs-for-phylogenomics.fa
Output file path .............................: .../gone-fishing/INFANT-GUT-TUTORIAL/phylogenomic-tree.txt
Alignment names ..............................: P_avidum, F_magna, L_citreum, S_aureus, Aneorococcus_sp, Streptococcus, S_epidermidis, C_albicans, P_rhinitidis, S_hominis, E_facealis
Alignment sequence length ....................: 8,816
Version ......................................: FastTree Version 2.1.10 SSE3
Alignment ....................................: standard input
Info .........................................: Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000
Search .......................................: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits ......................................: 1.00*sqrtN close=default refresh=0.80
ML Model .....................................: Jones-Taylor-Thorton, CAT approximation with 20 rate categories
Traceback for debugging
================================================================================
File "/usr/local/bin/anvi-gen-phylogenomic-tree", line 70, in <module>
main(args)
File "/usr/local/bin/anvi-gen-phylogenomic-tree", line 52, in main
program().run_command(input_file_path, output_file_path)
File "/usr/local/Cellar/anvio/5.1/libexec/lib/python3.7/site-packages/anvio/drivers/fasttree.py", line 63, in run_command
if filesnpaths.is_proper_newick(output_stdout):
File "/usr/local/Cellar/anvio/5.1/libexec/lib/python3.7/site-packages/anvio/filesnpaths.py", line 57, in is_proper_newick
to say about this: '%s'. Pity :/" % e)
================================================================================
File/Path Error: Your tree doesn't seem to be properly formatted. Here is what ETE had to say
about this: 'Unexisting tree file or Malformed newick tree structure. You may
want to check other newick loading flags like 'format' or 'quoted_node_names'.'.
Pity :/ |
I was just going through old issues that were not fully addressed and saw this one. I hope it sorted itself out :( thanks for your time to report this and for your followup to help identify the problem. and apologies for not getting back to this earlier. |
Hi @meren, I am getting the same error as described in this issue. os: MacOS Catalina 10.15.4 anvio version
This was my original command and the
I then went back into the interactive interface and made a new, significantly smaller selection of SCGs (n = 5) and
Here are the differences in alignment lengths between the input files: I also attempted to use MUSCLE and FastTree individually with my original
Thank you for taking a look and please let me know if you want me to send you any of my files for reproducibility. |
This is simply too many residues to consider. That's why Mahmoud has implemented functional homogeneity estimates per gene cluster, so you can choose only those gene clusters with meaningful variation (most of them will have functional homogeneity of 1.0, meaning that there is no variation across genes within them) and no alignment issues (i.e., geometric homogeneity > 0.95). |
Thanks for the suggestions @meren. I went back and filtered for a group of 70 SCGs using the combined homogeneity index and was successfully able to use |
Hi guys,
But when I run:
File/Path Error: Your tree doesn't seem to be properly formatted. Here is what ETE had to say Of course what's saying about Xac_301 (expected 526407 but have 526397 instead) is not really true. Any suggestions? |
Hey @Sirbius, would you please consider using the Docker container for Plus,
0.5 million nucleotides is a little too much for any meaningful analysis I think :) I think you should consider using these flags instead:
Yours seem to be the opposite of the best practice. |
Hello @meren, Andrea |
Hi @MrCorylus, would you mind sharing with me a private download link for the PAN.db and genomes storage (GENOMES.db) via email so I can take look at the data before making a suggestion? |
Hi again Andrea, Thanks for the email.
I'm sorry, I can see that I've made a mistake in my suggestion. It should've been I was able to get 30 gene clusters, and was able to generate a tree: I used the interactive interface for convenience, but you should be able to translate my parameters to the command line easily. I hope this helps. Best wishes, |
Hi,
I am having problems similar to issue #690 related to building a phylogenetic tree.
Housekeeping first:
I installed anvio via
brew
on a Mac HighSierra 10.13.5brew tap merenlab/anvio brew install merenlab/anvio/anvio anvi-self-test --suite mini # all fine
I am following Murat's tutorial on the infant gut dataset:
Thank you for looking into this.
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