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wodanaz / Assembling_viruses

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run-dds-escape-variants.sh deprecation? #45

Open wodanaz opened 3 years ago

wodanaz commented 3 years ago

Hi John, I hope you are well. Noted that there are some flags in run-dds-escape -variants.sh that doesn't work.

in particular the -l and -o

Best,

Alejo

echo "Running escape variants pipeline - logs at $OUTPUT_RESULTS_DIR/logs"
# run pipeline
SBATCH_FLAGS="--wait" ./run-escape-variants.sh \
  $REV_ARGS \
  -p $DDS_INPUT_PROJECT \
  -g $GENOME \
  -i $INPUT_PROJECT_DIR \
  -o $OUTPUT_RESULTS_DIR \
  -l $OUTPUT_RESULTS_DIR/logs
echo ""
johnbradley commented 3 years ago

@wodanaz What do you mean by doesn't work? Are you seeing the output directory and logs being created in the wrong location when running run-dds-escape-variants.sh? What does your run-dds-escape-variants.sh command line look like when you see this problem?

FYI: You can see the command line help for run-dds-escape-variants.sh by running it without arguments. For example:

./run-dds-escape-variants.sh
wodanaz commented 3 years ago

I mean, they don't appear to be legal variables.

I tried to used them as in the example but they show an error message:

/var/spool/slurmd/job25346606/slurm_script: illegal option -- l
DDS Escape Variants Starting

Downloading  to /gpfs/fs1/data/covid19lab/CoV_data/waste/input/

No project named /gpfs/fs1/data/covid19lab/CoV_data/waste/input/ found.

and was the same for -o option. I think we can just remove those lines from the run-dds-escape-variants.sh file

johnbradley commented 3 years ago

The -l and -o options are for run-escape-variants.sh. The run-dds-escape-variants.sh script uses a -d datadir option instead. This specifies one directory where input and output/log files are stored. The input files are staged into a directory at <datadir>/input/<projectname>, the output files are written into datadir/output/<projectname>. The logs are written to <datadir>/output/<projectname>/logs.

johnbradley commented 3 years ago

The script should have quit when it encountered an illegal option instead of continuing. To fix this I can change the scripts to check for the the unknown option value "?" from getops and quit.