Error "Detected join operation duplicate emission on left channel" when using "--save_output_as_bam" on WGS data

[ahwanpandey]

Hello,

I am using SAREK v3.8.0 on WGS data. The nextflow version is v25.10.3.

When I use --save_output_as_bam, I am getting this error at the "GATK4_APPLYBQSR" step. Some of the "GATK4_APPLYBQSR" jobs get ABORTED and the whole pipeline fails.

nextflow.exception.AbortOperationException: Detected join operation duplicate emission on left channel -- offending element: key=[patient:AOCS-095-5-9, sample:AOCS-095-5-9, sex:XX, status:0, n_fastq:36, data_typ
e:cram, id:AOCS-095-5-9, num_intervals:19]; value=/researchers/ahwan.pandey/Projects/WholeGenome/Project_NB/Goel_CDK2/test_sarek/preprocess/Sample_AOCS-095-5-9/work/83/ab518a72d3cb2ab7d5d62d4741f36f/AOCS-095-5-9
_chrY_1-57227415.recal.bam

But if I dont use --save_output_as_bam and just use the default cram output, there are no issues.

Thanks!
Ahwan

[famosab]

Hey, i am not entirely sure if that issue occurs because of the same reason but I added a fix for multi-lane support which might have also fixed this? Can you test

nextflow run nf-core/sarek -r fix/syntax-preprocessing --save_output_as_bam ....

and report back?

If that does not fix the issue please provide us with the nextflow.log file of your run!

[famosab]

Seems to be similar to #2064

[ahwanpandey]

Hello,

Thanks for the help! I ran it with the fix but the error still persists. Attached nextflow logs for output to bam which doesn't work (bam_out.nextflow.log) and output to cram which works fine (cram_out.nextflow.log). Both run with the "fix/syntax-preprocessing" repo.

bam_out.nextflow.log
cram_out.nextflow.log

And this is the step where the errors are happening:
NFCORE_SAREK:SAREK:FASTQ_PREPROCESS_GATK:BAM_APPLYBQSR:GATK4_APPLYBQSR

Thanks!
Ahwan

[famosab]

Ok we are currently discussing how we can change the APPLYBQSR implementation anyways, so we will have another look at that part of the code and probably restructure it a lot.

In the meantime you can either try with --skip_tools baserecalibrator or not create the bam output at all.