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Added missing '\' to slurm scripts
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DimaMolod committed Nov 15, 2023
1 parent 759964e commit 54dd2bd
Showing 1 changed file with 5 additions and 5 deletions.
10 changes: 5 additions & 5 deletions example_3.md
Original file line number Diff line number Diff line change
Expand Up @@ -61,8 +61,8 @@ run_multimer_jobs.py \
--multimeric_mode=True \
--msa_depth=<any number you want> \
--gradient_msa_depth=<True or False, overwrites msa_depth if provided> \
--model_names=<coma separated names of the models>
--job_index=<any number you want>
--model_names=<coma separated names of the models> \
--job_index=<corresponds to the string number from custom_mode.txt, don't provide for sequential execution>
```


Expand Down Expand Up @@ -102,10 +102,10 @@ source activate AlphaPulldown
--path_to_mmt=templates/ \
--data_dir=/scratch/AlphaFold_DBs/2.3.2/ \
--save_msa_files=True \
--output_dir=features\
--output_dir=features \
--use_precomputed_msas=True \
--max_template_date=2050-01-01 \
--skip_existing=True
--skip_existing=True \
--job_index=$SLURM_ARRAY_TASK_ID
```

Expand Down Expand Up @@ -167,7 +167,7 @@ and then run using:
mkdir -p logs
count=`grep -c "" description.csv` #count lines even if the last one has no end of line
sbatch --array=1-$count create_feature_jobs_SLURM.sh
count=`grep -c "" custom_mode.txt`
count=`grep -c "" custom_mode.txt` #likewise for predictions
sbatch --array=1-$count run_multimer_jobs_SLURM.sh
```
After the successful run one can evaluate and visualise the results in a usual manner (see e.g. [Example 2](https://github.com/KosinskiLab/AlphaPulldown/blob/main/example_2.md#3rd-step-evalutaion-and-visualisation))

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