09. February 2021
NLR-annotator
https://github.com/steuernb/NLR-Annotator
Requirements
MEME suite and JRE are already on GACRC sapelo2, just module load them.
Usage and scripts
download the 3 jar and 1 meme.xml from the github page.
if using newer MEME, switch to NLR-Parse3 branch instead
1ml Java
2ml MEME
3# Chopping Sequences
4
5java -jar ChopSequence.jar -i <inputsequence.fasta> -o
6<outputsequence.fasta> -l <sub-sequence length> -p <length of overlap>
7
8# NLR-Parser
9java -jar NLR-Parser.jar -t <number of threads> -y <path/to/meme/bin/mast> -x <path/to/meme.xml> -i <sub-seqeunces.fasta> -c <output.nlr.xml>
10
11
12# NLR-annotator
13java -jar NLR-Annotator.jar -i <nlr.xml> -o <output.nlr.txt>
Resource / SEFF
1
2Nodes: 1
3Cores per node: 32
4CPU Utilized: 02:07:55
5CPU Efficiency: 66.44% of 03:12:32 core-walltime
6Job Wall-clock time: 00:06:01
7Memory Utilized: 3.20 GB
8
9Cores per node: 32
10CPU Utilized: 00:56:32
11CPU Efficiency: 55.50% of 01:41:52 core-walltime
12Job Wall-clock time: 00:03:11
13Memory Utilized: 3.37 GB
14
15