[BUG] Config Error: Drivers::Muscle: anvio-8

[Alesita0381]

Hi!

Im working with anvio-8 and im following the instructions to create a phylogenetic tree, but when i run this command to concatenate ribosomal proteins, show a config error. What can i do?

command:

anvi-get-sequences-for-hmm-hits --external-genomes external-genomes.txt  \
                                -o concatenated-proteins.fa  \
                                --hmm-source Bacteria_71  \
                                --gene-names Ribosomal_L1,Ribosomal_L13,Ribosomal_L14,Ribosomal_L16,Ribosomal_L17,Ribosomal_L18p  \
                                --return-best-hit  \
                                --get-aa-sequences  \
                                --concatenate 

Screen result:

WARNING
===============================================
You (or the programmer) requested genome descriptions for your internal and/or
external genomes to be loaded _without_ a 'full init'. There is nothing for you
to be concerned. This is just a friendly reminder to make sure you know that if
something goes terribly wrong later (like your computer sets itself on fire),
this may be the reason.

Sources ......................................: Bacteria_71                                                                
Hits .........................................: 593 HMM hits for 1 source(s)
Genes of interest ............................: Ribosomal_L1, Ribosomal_L13, Ribosomal_L14, Ribosomal_L16, Ribosomal_L17,
                                                Ribosomal_L18p
Filtered hits ................................: 43 hits remain after filtering for 6 gene(s)

WARNING
===============================================
You requested only the best hits to be reported, which means, if, say, there are
more than one RecA hits in a bin for a given HMM source, only the one with the
lowest e-value will be kept, and others will be removed from your final results.

WARNING
===============================================
You requested to get only the best hits, but you did not provide a profile
database. At this point anvi'o just hopes you know what you are doing. Since
this is like the zone of 'potentially a terrible idea but it may be quite
relevant when done right'.

Filtered hits ................................: 28 hits remain after removing weak hits for multiple genes

CITATION
===============================================
The workflow you are using will likely use 'muscle' by Edgar,
doi:10.1093/nar/gkh340 (http://www.drive5.com/muscle) to align your sequences.
If you publish your findings, please do not forget to properly credit this tool.

[16 Mar 24 10:01:09 Aligning homolog gene sequences pre-concatenation] working on Ribosomal_L13 (1 of 6) ...               

**Config Error: Drivers::Muscle: Something went wrong with this alignment that was working on 6
              sequences :/ You can find the output in this log file:                         
              /tmp/tmp1jslp7u3/00_log.txt**       

[meren]

Config Error: Drivers::Muscle: Something went wrong with this alignment that was working on 6
              sequences :/ You can find the output in this log file:                         
              /tmp/tmp1jslp7u3/00_log.txt

What does the log file say, @Alesita0381?

[Alesita0381]

@meren This is what the log file says:

DATE: 17 Mar 24 11:03:28

CMD LINE: muscle -quiet

THIS IS THE OUTPUT YOU ARE LOOKING FOR:

[meren]

This is weird and makes no sense :(

Would you consider switching to the master branch and testing your run there, @Alesita0381?

[Alesita0381]

Can you be a little more specific?

El dom., 17 mar. 2024 12:22, A. Murat Eren (Meren) @.***> escribió:

This is weird and makes no sense :(

Would you consider switching to the master branch and testing your run there, @Alesita0381 https://github.com/Alesita0381?

— Reply to this email directly, view it on GitHub https://github.com/merenlab/anvio/issues/2243#issuecomment-2002545591, or unsubscribe https://github.com/notifications/unsubscribe-auth/BGM7MBKUFKCAT7SXWQOWBNLYYXGOPAVCNFSM6AAAAABEZMRBMCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBSGU2DKNJZGE . You are receiving this because you were mentioned.Message ID: @.***>

[ivagljiva]

@Alesita0381 , please install the development version of anvi'o and test the same command using that version :) we cannot tell from the log file what is wrong with the muscle run, but before we can do any debugging (which would happen in the development version anyway), we want to make sure that this remains a problem when you upgrade.

[Alesita0381]

HI @meren I already installed what the instructions indicated and it worked, thank you!!!!! I only have one question left. Why when I run anvi-interactive does it not show me the names of the bacteria in the phylogenetic tree? only appears the project name no the estimated taxonomy

i run like this: anvi-interactive -p phylogenomic-profile.db -t phylogenomic-tree.txt --title "Pseudomonas_tree" --taxonomic-level t_species --manual

[Ge0rges]

Hey @Alesita0381 you might get more prompt help/or perhaps find the answer on the Discord.