ONT Guppy GPU Submit Script Reference
Introduction
This reference contains information on about which variables to change in the ONT Guppy submit script provided by the UFS HPC.
Please note that the line numbers for the variables may be subject to change (as the script might change). They are only provided as a relative guide to locate the relevant variables in the script.
The Guppy base caller has many options. To obtain information on the options available, load the ONT Guppy GPU module and execute:
$ guppy_basecaller --help
Required Variables
| Line Number(s) | Script Variable | Guppy Parameter | Description |
|---|---|---|---|
| 3, 9, 10 | {job_name} | - | An appropriate title for the submission |
| 28 | INPUT_FILES | -i | Path to directory that contains fast5 files. Note that the -r option is implemented, meaning the directory will be recursively searched for fast5 files |
| 35 | OUTPUT_DIR | -s | Directory where output should be created. Path is relative to the directory created in step 2. |
| 53 | USE_CONFIG_FILE | - | Set value equal to yes to use a configure file as input.These files are in the Guppy data directory and can be displayed using guppy_basecaller --print_workflows. Note that USE_COMBO variable should be set to no if the value for this variable is equal to yes |
| 54 | CONFIG_FILE | -c | Configuration file name as listed in: guppy_basecaller --print_workflows |
| 73 | USE_COMBO | - | Set value equal to yes to use a combination of flowcell and kit as input.These files are in the Guppy data directory and can be displayed using guppy_basecaller --print_workflows. Note that USE_CONFIG_FILE variable should be set to no if the value for this variable is equal to yes |
| 74 | FLOWCELL | --flowcell | Flowcell name as listed in: guppy_basecaller --print_workflows |
| 75 | KIT | --kit | Kit name as listed in: guppy_basecaller --print_workflows |
Optional variables
| Line Number(s) | Script Variable | Guppy Parameter | Description |
|---|---|---|---|
| 84 | COMPRESS_FASTQ | –compress_fastq | Set value to yes to add the flag to the run command |
Notes:
-
To add additional flags to guppy_basecaller, uncomment (remove the #) line 111 and replace everything in <> (including the brackets themselves) with the parameters to add.
-
To use the submission script as template for other programs in the Guppy suite do the following:
- Delete lines 88 - 107
- Set the desired command to run equal to the RUN_CMD variable in line 87.