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I am having issues running tests and I don't know ...
# modules
e
I am having issues running tests and I don't know what can be going on: If I run the parabricks/fq2bammeth it works well on my instance with GPUs, but running the same command for the parabricks/fq2bam (which should be the same implementation) it crashes. This is with a fresh branch of nf-core/modules. Any thoughts on what is going on? How I run it:
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nf-test test --profile docker,gpu modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test # Passes tests

 nf-test test --profile docker,gpu modules/nf-core/parabricks/fq2bam/tests/main.nf.test # Crashes tests
Test [45474132] 'sarscov2 - fastq - se - cram' Assertion failed: assert process.success | | | false PARABRICKS_FQ2BAM java.lang.NullPointerException: Cannot invoke method getAt() on null object FAILED (10.171s) Assertion failed: 2 of 2 assertions failed Nextflow stdout: ERROR ~ Error executing process > 'PARABRICKS_FQ2BAM (test)' Caused by: Process 
PARABRICKS_FQ2BAM (test)
terminated with an error exit status (255) Command executed: INDEX=
find -L ./ -name "*.amb" | sed 's/\.amb$//'
cp genome.fasta $INDEX pbrun \ fq2bam \ --ref $INDEX \ --in-se-fq test_1.fastq.gz \ --out-bam test.cram \ \ \ \ \ --low-memory cat <<-END_VERSIONS > versions.yml "PARABRICKS_FQ2BAM": pbrun: $(echo $(pbrun version 2>&1) | sed 's/^Please.* //' ) END_VERSIONS Command exit status: 255 Command output: [Parabricks Options Mesg]: Checking argument compatibility [Parabricks Options Mesg]: Automatically generating ID prefix [Parabricks Options Mesg]: Read group created for /root/modules/.nf- test/tests/4547413281303caab75cc14d939554f3/work/14/efe15c78f7182cc84b6afbc3062949/test_1.fastq.gz [Parabricks Options Mesg]: @RG\tIDERR5069949.2151832.1\tLBlib1\tPLbar\tSMsample\tPU:ERR5069949.2151832.1 [Parabricks Options Mesg]: Using --low-memory sets the number of streams in bwa mem to 1. Process terminated with signal [SIGKILL: 9]. SIGKILL cannot be caught. A common reason for SIGKILL is running out of host memory. If the user has root access, they may be able to check by running
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sudo journalctl -k --since "<#> minutes
    ago" | grep "Killed process"
to see the reason why processes were recently killed. For technical support visit https://docs.nvidia.com/clara/index.html#parabricks Exiting... Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation Could not run fq2bam Exiting pbrun ... Command error: [Parabricks Options Mesg]: Checking argument compatibility [Parabricks Options Mesg]: Automatically generating ID prefix [Parabricks Options Mesg]: Read group created for /root/modules/.nf- test/tests/4547413281303caab75cc14d939554f3/work/14/efe15c78f7182cc84b6afbc3062949/test_1.fastq.gz [Parabricks Options Mesg]: @RG\tIDERR5069949.2151832.1\tLBlib1\tPLbar\tSMsample\tPU:ERR5069949.2151832.1 [Parabricks Options Mesg]: Using --low-memory sets the number of streams in bwa mem to 1. [PB Info 2025-Oct-21 152831] ------------------------------------------------------------------------------ [PB Info 2025-Oct-21 152831] || Parabricks accelerated Genomics Pipeline || [PB Info 2025-Oct-21 152831] || Version 4.6.0-1 || [PB Info 2025-Oct-21 152831] || GPU-PBBWA mem, Sorting Phase-I || [PB Info 2025-Oct-21 152831] ------------------------------------------------------------------------------ [PB Info 2025-Oct-21 152831] Mode = single-ended-gpu [PB Info 2025-Oct-21 152831] Running with 4 GPU(s), using 1 stream(s) per device with 4 group(s) of 16 CPU worker thread(s) [PB Info 2025-Oct-21 152831] Time spent reading: 0.000053 seconds Process terminated with signal [SIGKILL: 9]. SIGKILL cannot be caught. A common reason for SIGKILL is running out of host memory. If the user has root access, they may be able to check by running
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sudo journalctl -k --since "<#> minutes
    ago" | grep "Killed process"
to see the reason why processes were recently killed. For technical support visit https://docs.nvidia.com/clara/index.html#parabricks Exiting... Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation Could not run fq2bam Exiting pbrun ... Work dir: /root/modules/.nf-test/tests/4547413281303caab75cc14d939554f3/work/14/efe15c78f7182cc84b6afbc3062949 Container: nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1 Tip: when you have fixed the problem you can continue the execution adding the option 
-resume
to the run command line -- Check '/root/modules/.nf-test/tests/4547413281303caab75cc14d939554f3/meta/nextflow.log' file for details Nextflow stderr: Nextflow 25.04.8 is available - Please consider updating your version to it
m
panic
@Famke Bäuerle any pointers?
f
Can you get the latest version? I think this still uses the filecopy mode but we swapped to symlinks
e
This is already on the latest version of parabricks/fq2bam just pulled from nf-core/modules. I also have the latest (4.6.0-1) parabricks version installed.
f
I am a little confused because I changed up a lot of things with this module and the command.sh that you showed does not equal the latest version of the module.
But that being said I am a little confused why it fails.
Also I will be swapping back to copying the files for now as the symlinking did not work on the cluster
g
@Eduard Casas I just ran fq2bammeth and fq2bam tests on the main branch on a 
g4dn.xlarge
instance with no issues. Is this a problem you're still facing?
nftests_log.txt
e
I haven't tried in a few days but the instance definitely had enought memory. It must be some configuration of the nf-test on my instance since I can run fq2bam with big fastq/bam files but couldnt run the tests.
g
Hmm.. yeah I would check the nextflow configs to see if there are any memory limits being imposed. I would also make sure no other big GPU jobs are running on the node that could be taking up more memory.
e
Conversation on another thread but: I ended up fixing this by adding the flags '--memory=64g --memory-swap=64g' to the file: tests\config\nf-test.config line 83 (gpu {docker.runOptions))
g
I'm glad to hear that you fixed the issue! Although i'm not entire sure how this error arose, or how I can reproduce it, so I'm still a little bit confused about what's causing it.
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