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 - You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#28 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AYKMN4pLCQ9r8ARIXfeHfFlPqpXPtJ7Jks5rXnLlgaJpZM4Lx9FA>.

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