Error in demultiplexing of GBS data using GBSX_v1.3.jar

Question

[harshraje19]

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

[harshraje19]

Finally below written scrip is working

java -jar /home/harshraj/Downloads/GBSX_v1.3.jar --Demultiplexer -f1 NISAR1_CKDL200148447-1a_H7JMMBBXX_L5_1.fq.gz -f2 NISAR1_CKDL200148447-1a_H7JMMBBXX_L5_2.fq.gz -i B1.txt -gzip true -o L5_demultiplex/

[Pierre Lindenbaum]

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

[harshraje19]

Thank you Pierre Lindenbaum for your response. I am new to bioinformatics, can you please elaborate your response?

[Pierre Lindenbaum]

there must be a file named "gbsDemultiplex.log" in your home directory.

[harshraje19]

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

[Pierre Lindenbaum]

ahahah what a wrong error message; I think the best you can do is to ask at : https://github.com/GenomicsCoreLeuven/GBSX/issues