steuernb/nlr-parser

Annotation Pipeline for NLR genes

nlr-parser's Issues

Exception in thread "main" java.lang.NullPointerException

hello
The following problems occurred during operation. The following is my shell picture. How can I solve them

NLR-Parser can't work because of "java.lang.NullPointerException"

shell command :

java  -jar NLR-Parser.jar -i mast.xml -o output.txt

java version : 1.8.0

Exception in thread "main" java.lang.NullPointerException
    at coreClasses.MastXMLReader.<init>(MastXMLReader.java:58)
    at coreClasses.MastFile.readEntries(MastFile.java:69)
    at coreClasses.MastFile.<init>(MastFile.java:65)
    at coreClasses.NLRParser.main(NLRParser.java:106)

thanks~

Exception in thread "main" java.lang.NullPointerException

My fasta file is too big to txt compressed file, you can try it
Uploading Zm-B73-REFERENCE-NAM-5.0.protein.zip…
从大

Exception in thread "main" java.lang.IllegalStateException: No match found

Hi,
I wanted to try the program NLR-parser however I get an error when I try running it:

Exception in thread "main" java.lang.IllegalStateException: No match found
at java.base/java.util.regex.Matcher.group(Matcher.java:645)
at coreClasses.MastEntry.(MastEntry.java:27)
at coreClasses.MastXMLReader.readEntry(MastXMLReader.java:95)
at coreClasses.MastFile.readEntries(MastFile.java:70)
at coreClasses.MastFile.(MastFile.java:65)
at coreClasses.NLRParser.main(NLRParser.java:106)

JRE version:
java version "1.8.0_221"
Java(TM) SE Runtime Environment (build 1.8.0_221-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.221-b11, mixed mode)

Meme-suite version:
meme 5.0.2 py36pl526h96dd833_5 bioconda

NLR-parser version:
latest release 1.0

I ran mast with the meme.xml from your GitHub page:
mast -o /path/to/my/output meme.xml /path/to/my/fasta/fasta.fa

Results are present and mast.html can be viewed.

I ran NLR-parser with the mast.xml output from mast:
java -jar /path/to/NLR-parser.jar -i /path/to/mast_out/mast.xml -o /path/to/output/out.nlrparser.txt -a /path/to/my/fasta/fasta.fa

This throws the error from above.
What do I need to change to get the program running?

Cheers,
Daniel

GFF3 vs tsv

Hi,
I am using your nice software to find the NLR candidate genes in my transcriptome data. When I am using the GFF3 output I get more genes, with exactly the same other options, compared to tsv version. Would you please let me know what could be the source of problem?
The bests,
Pezhman Safdari

Question about differences between passing anotated amino acid sequences and nucleotide sequences to NLR-parser

Dear developers:

Since NLR-parser is capable to translate DNA sequcnes to amino acid sequnces in a 6-frame fashion, how can I just convert the whole-genome assembly (several mega-base level chorosomes) to NLR-parser-recognized protein sequences? I don't suppose that translating one whole choromsome using the "translate6frame" java program is making sense.

If I just use the protein sequcnes from annotated gene models but NOT the genomic DNA-translated protein sequcnes, will the performance of NLR-parser drop?

Many thanks
Hongbo