SID generated by this script aren't always unique:

[sporkmonger]

e.g.

alert http any any -> $HOME_NET any (msg:"OTX - FILE MD5 from pulse Inside the spyware campaign against Argentine troublemakers";  filemd5:55d79cc967db8c7bb8cb5a72.txt; reference: url, otx.alienvault.com/pulse/55d79cc967db8c7bb8cb5a72; sid:414932; rev:1;)
alert http any any -> $HOME_NET any (msg:"OTX - FILE MD5 from pulse Macro Downloaders (Aga Dell)";  filemd5:58c69a109c4484412c9d2a3b.txt; reference: url, otx.alienvault.com/pulse/58c69a109c4484412c9d2a3b; sid:414932; rev:1;)

[Kolano]

Doesn't seem like this tool is ever going to be updated to account for this.

Here's a script I'm using to revise duplicate SIDs...

#Loop over duplicate SIDs
for sid in $(grep -P -o "(?<=sid:)\d*" /etc/suricata/rules/otx_file_rules.rules | sort | uniq -d); do
	increment=0
	#Loop over lines with duplicate SIDs, stripping out first match
	grep "$sid" /etc/suricata/rules/otx_file_rules.rules | sed 1d | while read -r line ; do
		#Increment the incrementor
		increment=$((increment+1))
		#Get unique non-sid match
		filemd5=$(echo $line | sed 's/.*filemd5:\([^;]*\).*/\1/')
		#Postfix each sid with incrementor to hopefully generate unique IDs
		sed -i "s/\($filemd5.*sid:[^;]*\)/\1$increment/" /etc/suricata/rules/otx_file_rules.rules
	done
done

It might be better to insert a GID on each duplicate to make them unique, rather than revising the SIDs.