Fusioncatcher: JVM Initialization Fails: Too small maximum heap due to missing unit in -Xmx parameter #680
Description
Description of the bug
I am using the dev version of RNAfusion
As visible, the JVM option -Xmx29491 was passed without any unit. As per JVM specifications, the value is interpreted as 29491 bytes, which leads to JVM failing to initialize due to insufficient heap size.
Expected behavior:
The -Xmx parameter should include a unit (m for megabytes, g for gigabytes).
For example: -Xmx29491m or -Xmx29g.
Suggested fix:
Ensure that the workflow or bbmerge wrapper appends the correct unit to the memory specification when constructing the command line.
Possibly include input validation to prevent passing unitless values to -Xmx.
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Running: step = 483 Time: 14:54 Date: 2025-06-18 (elapsed time: 0d:0h:20m)
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==> Current working directory: '/scratch/firenze/Nextflow/work/93/3a5227efba98d864f71f90ce96d30e'
bbmerge-auto.sh \
in=candidate_focus_reads.txt.0.fq \
out=candidate_focus_reads.txt.0_m.fq \
threads=6 \
extend2=20 \
iterations=3 \
k=17 \
mindepthseed=1 \
mindepthextend=1 \
minoverlap=11 \
-Xmx29491
--------------------------------------------------------------------------------
+-->EXECUTING...
ERROR: Workflow execution failed at step 483 while executing:
----------------
bbmerge-auto.sh \
in=candidate_focus_readsError occurred during initialization of VM
Too small maximum heap
.txt.0.fq \
out=candidate_focus_reads.txt.0_m.fq \
threads=6 \
extend2=20 \
iterations=3 \
k=17 \
mindepthseed=1 \
mindepthextend=1 \
minoverlap=11 \
-Xmx29491
----------------
* Size 'candidate_focus_reads.txt.0.fq' = 424 bytes
* Size 'candidate_focus_reads.txt.0_m.fq' = 0 bytes
Executing second time the same step/command in order to capture error messages (i.e. STDERR)...
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java -Djava.library.path=/usr/local/opt/bbmap-38.44-0/jni/ -ea -Xmx29491 -Xms29491 -cp /usr/local/opt/bbmap-38.44-0/current/ jgi.BBMerge in=candidate_focus_reads.txt.0.fq out=candidate_focus_reads.txt.0_m.fq threads=6 extend2=20 iterations=3 k=17 mindepthseed=1 mindepthextend=1 minoverlap=11 -Xmx29491Command used and terminal output
export NXF_SINGULARITY_CACHEDIR=/scratch/singularity/RNAfusion/
export NXF_ANSI_LOG=false
nextflow run nf-core/rnafusion -r dev -profile singularity -params-file rnafusion_params.yamlRelevant files
No response
System information
No response