job failed due to global variable assignment

[akhileshmishra0908]

Hi, I am getting this error while I am running the example file, may you please help me in this,

(clinker) akhileshmishra@x86_64-apple-darwin13 Clinker-1.32 % bpipe -p out=/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/run -p caller=$CLINKERDIR/test/caller/bcr_abl1.csv -p col=1,2,3,4 -p genome=19 -p print=true -p competitive=true -p header=true -p align_mem=31025992405 -p genome_mem=31025992405 -p fusions=BCR:ABL1 $CLINKERDIR/workflow/clinker.pipe $CLINKERDIR/test/fastq/*.fastq.gz ╒══════════════════════════════════════════════════════════════════════════════════════════════════╕ | Starting Pipeline at 2022-04-04 19:23 | ╘══════════════════════════════════════════════════════════════════════════════════════════════════╛

======================================== Stage generate_fst ========================================

====================================== Stage star_genome_gen =======================================

===================================== Stage star_align (test) ====================================== ERROR: stage star_align failed:

An attempt was made to assign to global variable files after your pipeline already started running. To ensure thread safety, global variables may only be assigned before the pipeline starts. Solutions include:

• add 'def', 'var', or 'requires' before this assignment to define a local variable, eg: def files = "/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R1.fastq.gz /Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R2.fastq.gz" or: var files : "/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R1.fastq.gz /Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R2.fastq.gz"
• define a branch variable using: branch.files = "/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R1.fastq.gz /Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R2.fastq.gz"

You can disable this behavior at your own risk by setting allowGlobalWrites=true in your bpipe.config file. ========================================= Pipeline Failed ==========================================

In stage Unknown: One or more parallel stages aborted. The following messages were reported:

-------------------------------------- star_align ( test ) ---------------------------------------

An attempt was made to assign to global variable files after your pipeline already started running. To ensure thread safety, global variables may only be assigned before the pipeline starts. Solutions include:

• add 'def', 'var', or 'requires' before this assignment to define a local variable, eg: def files = "/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R1.fastq.gz /Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R2.fastq.gz" or: var files : "/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R1.fastq.gz /Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R2.fastq.gz"
• define a branch variable using: branch.files = "/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R1.fastq.gz /Users/akhileshmishra/Documents/Clinker/Clinker-1.32/test/fastq/test_R2.fastq.gz"

You can disable this behavior at your own risk by setting allowGlobalWrites=true in your bpipe.config file. Use 'bpipe errors' to see output from failed commands.

Looking forward for your support.

AKhilesh Mishra [email protected]

[ssadedin]

hi @akhileshmishra0908 .... just checking the pipeline code, it looks to me like the problem you're hitting may have been addressed in this commit. I'm thinking it may be a good start if you can update to the latest version of Clinker and see if it helps.

[ssadedin]

Closing due to inactivity