google-deepmind / google-deepmind/alphafold

Issues running alphafold with my script on local HPC

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Description

Hi there,

I have been experiencing issues running alphafold jobs on our HPC. I have used this script in the past and have been successfully been able to run jobs and output ranked models. However, as of recently, I keep getting this error file that says "/etc/profile.d/alphafold.sh: line 1: module: command not found"
[alphafold_test.pdf](https://github.com/deepmind/alphafold/files/11616635/alphafold_test.pdf)
[submit_alphafold_2022.pdf](https://github.com/deepmind/alphafold/files/11616636/submit_alphafold_2022.pdf)

In the output folder, it's able to give me the multiple sequence alignment and the .pkl file but no ranked models. Help?

The script I use is below:

```
#PBS -S /bin/bash
#PBS -q alphafold
#PBS -N alphafold_test
#PBS -l walltime=2:00:00:00
#PBS -l nodes=1:ppn=6

cd $PBS_O_WORKDIR
echo Host: $HOSTNAME
echo Date: `date`
echo Dir: $PBS_O_WORKDIR
echo $PBS_NODEFILE

module()
{
_module_raw "$@" 2>&1
}
module unload cuda10.0 cuda70 cuda80 cuda91

source /etc/profile.d/alphafold.sh

# flags need to be customized:
# -o output folder
# -f input fasta files
# -a GPU used; either 0,1 or 2,3
# then qsub the script.

#Modify the submit script by changing the fasta file (after '-f'), available GPUs (after '-a') and the mode ( either 'monomer' or 'multimer' after '-m').

#The submit script contains examples of both modes, you can choose the mode by removing the "#" and adding the "#" to the start of the other line.

#Submit the modified submit_alphafold.sh

# monomer mode
#/legacy/storage/projects/hli/xiangf/AlphaFold/run_alphafold_2022.sh -d /data/alphafold_data -o ./ -m monomer -f T1050.fasta -t 2022-2-13 -a 0,1
#/varidata/research/projects/jones/projects/Tinghai/AlphaFold/run_alphafold_2022.sh -d /data/alphafold_data -o ./ -m monomer -f TX3A2_3B3.fasta -t 2022-2-13 -a 2,3

# multimer mode
#/legacy/storage/projects/hli/xiangf/AlphaFold/run_alphafold_2022.sh -d /data/alphafold_data -o ./ -m multimer -f TX3A2_3B3.fasta -t 2022-2-13 -a 0,1
/varidata/research/projects/worden/Leena/AlphaFold/run_alphafold_2022.sh -d /data/alphafold_data -o ./ -m multimer -f Setdb1_FL_Atf7IP2_FL.fasta -t 2022-2-13 -a 2,3

# please remember to check whether the GPUs are taken.
# to run multmer mode, please use -m multimer. In this mode
# The fasta file needs to contain at least two fasta sequences arranged sequentially.
# e.g. Fasta file will looks like this:
# > XXXX
# XXXXXXXXX
# XXXXX...
# > YYYY
```

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