Fail in runing votu task

[ShangLiii]

Hi,
I am trying to run votu and something is wrong.
Here is the commend I used:
phabox2 --task votu --dbdir /data2/lishang/phabox_db_v2/ \

    --outpth  $Prjdir/Phabox2 \
    --contigs $Prjdir/all_virus.fna \
    --threads 112 --proteins $Prjdir/all_virus.faa --len 1

PhaBOX2 is running with: 112 threads!
Running program: vOTU groupping
filtering the length of contigs...
[1/5] calling genes with prodigal...
Command 'makeblastdb -in /data2/lishang/Results/Phabox2/filtered_contigs.fa -dbtype nucl -parse_seqids -ou t /data2/lishang/Results/Phabox2/midfolder//selfdb > /dev/null 2>&1' failed with exit code 1

Can you please help me?
Thanks!

[KennthShang]

Hi there,

please make sure you have follow the commands below and install the packages correctly

conda create -n phabox2 phabox=2.1.5 -c conda-forge -c bioconda -y
conda activate phabox2

Then, please try conda list to check the packages blow are install correctly:

diamond=0.9.14 
blast=2.16.0 
mcl 
fasttree=2.1.11 
kcounter=0.1.1 
mafft=7.525

If not, you can reinstall them:

conda install diamond=0.9.14 blast=2.16.0 mcl fasttree=2.1.11 kcounter=0.1.1 mafft=7.525

If you cannot run all the above-mentioned commands successfully, I suggest installing phabox in a primitive ways:

# install dependencies
conda create --name phabox2 python=3.10
conda activate phabox2
conda config --add channels bioconda
conda install diamond=0.9.14 blast=2.16.0 mcl fasttree=2.1.11 kcounter=0.1.1 mafft=7.525
conda install numpy=1.26.4 pandas=2.2.3 networkx=3.4.2 seaborn-base=0.13.2 biopython=1.84 tqdm=4.66.5 scipy=1.14.1
conda install datasets transformers pytorch triton accelerate prodigal-gv

# install phabox binary 
git clone https://github.com/KennthShang/PhaBOX.git
cd PhaBOX
python  -m pip install . -vv
cd ..
# you can remove the PhaBOX folder once it is installed
rm -rf PhaBOX

# test
phabox2 --help

# Do not forget to download the database using wget (or go to the release page)
wget https://github.com/KennthShang/PhaBOX/releases/download/v2/phabox_db_v2.zip
unzip phabox_db_v2.zip > /dev/null

Best,
Jiayu

[ShangLiii]

I have fixed this issue.
For anyone who met the same problem, you may go to the "miniforge3/envs/phabox2/lib/python3.10/site-packages/phabox2/votu.py" file
and delete '-parse_seqids' from the command "makeblastdb -in {rootpth}/filtered_contigs.fa -dbtype nucl -parse_seqids -out {rootpth}/{midfolder}/selfdb > /dev/null 2>&1"
then it will run perfectly.

[KennthShang]

I see. But if it is not an issue caused by the version conflict, using the -parse_seqids option can sometimes lead to errors due to:

• Incorrect Format: The sequence IDs in the input file may not conform to the BLAST required format. Ensure they are unique and follow the FASTA format standards.
• Duplicate IDs: If sequence IDs aren't unique within the input file, this can cause errors. Make sure each sequence has a unique ID.
• Special Characters: Sequence IDs containing unsupported special characters can cause parsing errors. Stick to letters, numbers, underscores, or hyphens.

To avoid these issues, I suggest verifying the format and uniqueness of sequence IDs in your input file rather than revising the codes.

Best,
Jiayu