Error in demultiplexing of GBS data using GBSX_v1.3.jar
Dear friends,
I got error in demultiplexing of GBS data. can you please help me in that?
We have used following command line in linux for demultiplexing.
java -jar /home/harshraj/Downloads/GBSX_v1.3.jar --Demultiplexer -f1 NISAR1_CKDL200148447-1a_H7JMMBBXX_L5_1.fq.gz -f2 NISAR2_CKDL200148448-1a_H7JMMBBXX_L6_1.fq.gz -i barcode.txt -m 0 -al no -gzip true -o 01_Nisar_Demultiplexing
then we got following error
GBS demultiplexing ended with Major Errors
Can anyone help me to solve this error.
Thanks
Raj
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The java code clearly shows that there must be an associated an error report in your HOME. https://github.com/GenomicsCoreLeuven/GBSX/blob/c881f605c5aa80b85439545db6cda815a970405b/src/be/uzleuven/gc/logistics/GBSX/demultiplexer/GBSdemultiplex.java#L88
Thank you Pierre Lindenbaum for your response. I am new to bioinformatics, can you please elaborate your response?
there must be a file named "gbsDemultiplex.log" in your home directory.
Oh thank you. I have gbsDemultiplex.log" file in home directory. It has following message.
Arguments where: [Ljava.lang.String;@6d311334
Contains invalid argumentsEnded on Tue Mar 10 17:13:11 EDT 2020
ahahah what a wrong error message; I think the best you can do is to ask at : https://github.com/GenomicsCoreLeuven/GBSX/issues
Finally below written scrip is working