SNAP_FAST_db_dir database error running in comprehensive mode

[bhykes1]

Hi, I am running surpi on a dataset using comprehensive mode. I do not have a SNAP_FAST_db_dir database, and i a getting an error message in the generated log file as a result. Do I need to have the SNAP_FAST_db_dir database even if I am not running in fast mode?

[sfederman]

Hi,

You do not need a SNAP_FAST database when running in comprehensive mode, though currently SURPI does require it. In order to change this, you can change the code in the following way:

In the SURPI.sh script, remove the following lines (Lines 563-576). That will remove the FAST check...

echo -e "SNAP FAST Mode database"
for f in $SNAP_FAST_db_dir/*
do
    if [ -f $f/Genome ]
    then
        echo -e "\t$f: ${green}OK${endColor}"
    else
        echo -e "\t$f: ${red}BAD${endColor}"
        if [ "$run_mode" = "Fast" ]
        then
            reference_check="FAIL"
        fi
    fi
done

[bhykes1]

Ahh thank you very much

On Jan 30, 2017, at 5:31 PM, Scot Federman notifications@github.com<mailto:notifications@github.com> wrote:

Hi,

You do not need a SNAP_FAST database when running in comprehensive mode, though currently SURPI does require it. In order to change this, you can change the code in the following way:

In the SURPI.sh script, remove the following lines (Lines 563-576). That will remove the FAST check...

echo -e "SNAP FAST Mode database" for f in $SNAP_FAST_db_dir/* do if [ -f $f/Genome ] then echo -e "\t$f: ${green}OK${endColor}" else echo -e "\t$f: ${red}BAD${endColor}" if [ "$run_mode" = "Fast" ] then reference_check="FAIL" fi fi done

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