WARNING 010

[WRran-Hydrogen]

Hi guys,

I'm runing trimAl for my aligned amino acid sequences, but when I run the common command there is always a WARING 010 :
This is my command:
trimal -in PF00905_test.afa -out alig.msa -automated1

and the results in terminal:
[WARNING 010] [fasta] -> To prevent overriding file alig.msa a suffix has been added. Final filename: alig.msa.0

When I use multiple specifie formats to output, I will have the same problem. I don't want to have the suffix automatically added.
Does anyone have this problem?

trimAl version: 2.0

[nicodr97]

Hi @WRran-Hydrogen ,

Currently that is the automatic behaviour of the program when the output file already exists. We will add a parameter to allow overwriting.

[WRran-Hydrogen]

Thanks for your reply. Some problem were found in trimAl align algorithm between normal align and automated1.
The first command for heuristic selection: trimal -in Integrase.afa -out Integrase.msa -automated1
The next command for normal align: trimal -in Integrase.afa -out Integrase.msa -gt 0.7
After that, they show diffenent alignment results as follows:

(-automated1)
>IMGVR_UViG_2974792740_000001
------G------------------
>IMGVR_UViG_3300029768_000208
------G------------------
>IMGVR_UViG_3300031555_010270
------G------------------
(-gt 0.7)
>IMGVR_UViG_2974792740_000001
MEYTYYVVD---QPEAIDL--YTEI*
>IMGVR_UViG_3300029768_000208
MGLLILKTT---QRQYLDY--NRPF*
>IMGVR_UViG_3300031555_010270
-----LKTA---QRQYIDY--NRPF*

so they get completely different results will affect the later building ML tree process by IQ-TREE.

Another question about amino acid fuzzy translations:

IMGVR_UViG_7000000289_000277
-----------X------------ (X is the result of fuzzy translation and does not represent any amino acid )
IQ-TREE program was terminated due to trimAl result problem

[nicodr97]

First of all, let me correct myself because I was not right about the current functioning of the -out parameter. It's adding the suffix in all case but that's solved in #80. As for your second comment, I don't really understand what your question is. Using -automated1 will trim the MSA using a similarity or a gap method with a particular threshold depending on certain characteristics of the alignment. The parameter -gt, on the other hand, will trim based on the value you establish manually. It's completely normal that they don't generate the same MSA.

[WRran-Hydrogen]

I apologize for my unclear formulation of the second question, and I have carefully consulted the trimAl documentation:"Automated trimming heuristic: automated1. (Optimized for Maximum Likelihood phylogenetic tree reconstruction)."

So I just don't know how to choose better parameters (-automated1 or -gt custom Vakyes)for the next work (This is my fault😢), because I found that the ML phylogenetic tree constructed using the results of automated1 is not completely plausible either, maybe using Bayesian tree building of the prior model will give better results, but keeping relatively more amino acid/nucleotide sites could get better mutation model features.