Issue with DiscoverySNPCallerPluginV2 on SCINet

[Zachary Winn]

Hi everyone,

I am trying to run a GBS pipeline on Atlas and I am using their module load of tassel version 5.0. I have most things running alright, but the process hangs up at this point in the pipeline. Attached is the log for this entire process up to DiscoverySNPCallerPluginV2.log. If you see something that looks amiss, I would greatly appreciate guidance!

Thanks,

Zach

[Zachary Winn]

To anyone looking at this and asking for a work around: 

There is an issue on Atlas's tassel installation. You can use an installation that you pull from bitbucket yourself, and make sure that you module load sqlite. If you don't call sqlite from their system, you the tassel installation won't be able to run properly.  See code below:

```bash

### Logic for your SLURM submission

# Load necessary modules
module load beagle
module load bwa
module load samtools
module load bcftools
module load vcftools
module load sqlite # This is the really important module to load
module load bowtie2
module load bzip2

# Directory and file names
directory="tassel-5-standalone"
run_script="tassel-5-standalone/run_pipeline.pl"
repo_url="https://bitbucket.org/tasseladmin/tassel-5-standalone.git"

# Check if the directory exists in the current working directory
if [ ! -d "$directory" ]; then
    echo "$directory not found. Cloning repository..."
    git clone "$repo_url"
else
    echo "$directory already exists."
fi

# Define tassel in the user's path
export TASSEL_PL=$(realpath "$run_script")

### Continue logic here

```

Thanks,

Zach