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PapenfussLab / gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite
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Unrecognized option: -r #668

Closed gamzemdn closed 3 months ago

gamzemdn commented 3 months ago

Hi,

I want to use GRIDSS for my structural variant calling thesis topic but I couldn't get it run even though I setup everything. When I say gridss -r ... it throws error like : Unrecognized option: -r Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit. Error: Could not find or load main class gridss Caused by: java.lang.ClassNotFoundException: gridss I tried every gridss file in the source tar folder and I also tried bioconda setup but I can not use gridss command. When I only type gridss, it shows me outputs below but there is no -r option for reference genome since I am following the gridss.sh code :

Usage: java [options] [args...] (to execute a class) or java [options] -jar [args...] (to execute a jar file) or java [options] -m [/] [args...] java [options] --module [/] [args...] (to execute the main class in a module) or java [options] [args] (to execute a single source-file program)

Arguments following the main class, source file, -jar , -m or --module / are passed as the arguments to main class. .......

I need to run this analyses so I really appreciate every help

Thank you

gamzemdn commented 3 months ago

Hello again, since I am not very familiar with java cmd syntax I open up this issue. Somehow I wrote this code below and it works. My question is if this is right way to call germline structural variant ?

java -cp '/gridss-2.13.2-gridss-jar-with-dependencies.jar' gridss.CallVariants OUTPUT=/output.vcf ASSEMBLY=/data/file_output3/assembly.bam BLACKLIST='/ENCFF356LFX.bed' THREADS=4 INPUT='/hg00514.bam' REFERENCE_SEQUENCE='/GRCh38_full_analysis_set_plus_decoy_hla.fa'

gamzemdn commented 3 months ago

I got this error:

ERROR 2024-08-10 20:36:06 CallVariants Fatal exception thrown by worker thread. java.lang.RuntimeException: Subprocess terminated with with exit status 1. Failed executing "bwa mem -K 10000000 -L 0,0 -t 12 /GRCh38_full_analysis_set_plus_decoy_hla.fa ./hg00514.bam.gridss.working/hg00514.bam.realign.0.fq". Can you run the alignment command from the command line? Is the aligner on PATH? Did you build an index with prefix GRCh38_full_analysis_set_plus_decoy_hla.fa?

I don't need alignment I already provide aligned file bam. I only need structural variants. Can I get some help to figure this out please?

gamzemdn commented 3 months ago

Anyways I removed GRIDSS since I couldn't manage to get it work, my last issue was Error parsing SAM header. @SQ line missing LN tag. I never understood why this tool creates bam file again, it didn't make sense since I was already providing bam file. Long story short, I couldn't get any feedback and couldn't solve it myself, so I deleted the tool and closing the issue...