--aligner_extra_option in OMM_MACSE

[schwong]

Hi,

I’ve been trying to pass custom MAFFT options using the --aligner_extra_option parameter, but when I check the pipeline log it still reports that MAFFT was run with the default --localpair --maxiterate 1000 options, rather than my custom settings.

While looking into this, I noticed the following block in S_OMM_MACSE_V12.01.sh:

# handle aligner default options
if [ -z ${aligner_extra_option+x}  ];    then
  case $ALIGN_SOFT in
    "MAFFT" ) ALIGNER_EXTRA_OPTION="--localpair --maxiterate 1000";;
  *) ALIGNER_EXTRA_OPTION=""
  esac
fi

It looks like the script checks whether aligner_extra_option (lowercase) is set, whereas the user-provided options are assigned to ALIGNER_EXTRA_OPTION (uppercase). This may cause the condition to always evaluate as true and the default MAFFT options to be applied, even when custom options are provided.

I just wanted to flag this in case I’m missing something, or if it might be an unintended behavior in the script. Thanks very much for maintaining the pipeline!

Best regards,
Helen

[ranwez]

Hi,

Thanks for taking the time to make a detailed report of this issue. This took longer than expected to fix, partly because I identified a few other minor related issues, but mainly due to recent changes in GitHub policies, the transition from Singularity to Apptainer, and limited resources during the holiday period. I apologize for the inconvenience.

I have pushed a v12.02 release that resolves the issue. I tested it with:

./OMM_MACSE_V12.02.sif --in_seq_file examples/LOC_48720.fasta --out_dir RES_LOC_48720_TEST --aligner_extra_option "--maxiterate 100 --globalpair" --out_file_prefix LOC_48720

and obtained the expected output:

....
============== ALIGN AMINO SEQUENCES
+ case $ALIGN_SOFT in
+ mafft --quiet --maxiterate 100 --globalpair __LOC_48720_homol_AA.fasta
...

Unfortunately, I am currently unable to push the .sif from the VM used to build this container. For the moment, I am therefore sharing it via this temporary link. I will push it to Sylabs and Apptainer Cloud as soon as I have access to a full Linux machine.

During this update, I also realized that it would probably be worth updating the container with MUSCLE v5 and more recent versions of MAFFT and PRANK. I will try to work on this in the coming weeks.

I hope this helps resolve your issue, and please feel free to reach out again if you encounter any other problems or discover additional issues with these pipelines.

Best regards,

Vincent

[schwong]

Hi Vincent,

Thanks for your reply! I can now specify custom aligner options with the v12.02 release and look forward to the upcoming update with more recent aligner versions.