Entering edit mode
4.8 years ago
harshraje19
▴
40
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
Finally below written scrip is working
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