JAFFA errow

[Keisuke Kato]

I will ask you a question.

I set the environment and installed JAFFA 2.2-0 via bioconda. 

I prepared the commands, references, tools.groovy, and JAFFA_stages.groovy appropriately. However, when I execute the analysis, the program spits out the following alert.

     

     WARNING: An illegal reflective access operation has occurred

WARNING: Illegal reflective access by org.codehaus.groovy.reflection.CachedClass$3$1 (file:/home/GENE1/miniconda3/envs/JAFFA/share/jaffa-2.2-0/tools/bpipe-0.9.9.2/bin/../lib/bpipe.jar) to method java.lang.Object.finalize()
WARNING: Please consider reporting this to the maintainers of org.codehaus.groovy.reflection.CachedClass$3$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
====================================================================================================
|                              Starting Pipeline at 2022-05-01 08:41                               |
====================================================================================================
Error: output meta data property file .bpipe/outputs/align_transcripts_to_genome.ドキュメント_55555_Dx_jaffa_55555_Dx_fastP.fastq_55555_Dx_fastP.fastq_genome.psl.properties is missing essential outputFile property
Properties are: [:]
=========================================== Bpipe Error ============================================

An error occurred executing your pipeline:

                            Cannot invoke method exists() on null object                            

When I checked the groovy version, the following alert appeared.

    WARNING: An illegal reflective access operation has occurred
    WARNING: Illegal reflective access by org.codehaus.groovy.reflection.CachedClass     

    (file:/usr/share/groovy/lib/groovy-2.4.17.jar) to method java.lang.Object.finalize()
    WARNING: Please consider reporting this to the maintainers of 

       org.codehaus.groovy.reflection.CachedClass
     WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective 

        access operations
      WARNING: All illegal access operations will be denied in a future release
      Groovy Version: 2.4.17 JVM: 11.0.13 Vendor: JetBrains s.r.o. OS: Linux

I would like to know how to set up the JAFFA pipeline.
I appreciate your kindness in advance.

Sincerely yours, 

Keisuke Kato

[Nadia Davidson]

Hi Keisuke Kato,

JAFFA has not been updated in bioconda for version 2 yet. Until we fix this, you can install JAFFA outside conda using the instructions at: https://github.com/Oshlack/JAFFA/wiki/HowToSetUpJAFFA

Regards,

Nadia.