`FUSIONCATCHER` fails with out of memory error

[bounlu]

Description of the bug

It seems FUSIONCATCHER process runs out of memory due to bbduk.sh:

Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'RNAFUSION:FUSIONCATCHER_WORKFLOW:FUSIONCATCHER_FUSIONCATCHER (XYZ_TCA_E7_sub_10M)'

Caused by:
  Process `RNAFUSION:FUSIONCATCHER_WORKFLOW:FUSIONCATCHER_FUSIONCATCHER (XYZ_TCA_E7_sub_10M)` terminated with an error exit status (1)


Command executed:

  fusioncatcher \
      --input=XYZ_TCA_E7_sub_10M_1.fastp.fastq.gz,XYZ_TCA_E7_sub_10M_2.fastp.fastq.gz \
      --output=. \
      --data=fusioncatcher \
      --threads=6 \
      --Xmx=29491M \
      --limitSjdbInsertNsj 2000000 --skip-blat 
  
  mv final-list_candidate-fusion-genes.txt XYZ_TCA_E7_sub_10M.fusion-genes.txt
  mv summary_candidate_fusions.txt XYZ_TCA_E7_sub_10M.summary.txt
  mv fusioncatcher.log XYZ_TCA_E7_sub_10M.log
  
  cat <<-END_VERSIONS > versions.yml
  "RNAFUSION:FUSIONCATCHER_WORKFLOW:FUSIONCATCHER_FUSIONCATCHER":
      fusioncatcher: "$(fusioncatcher --version 2>&1 | awk '{print $2}')"
  END_VERSIONS

Command exit status:
  1

Command output:
  --------------------------------------------------------------------------------
  +-->EXECUTING...
  --------------------------------------------------------------------------------
  ==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)
  ////////////////////////////////////////////////////////////////////////////////
    Running: step = 107   Time: 08:25   Date: 2025-09-24 (elapsed time: 0d:0h:5m)
  \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\
  ==> Current working directory: '/data/nextflow/rnafusion/test/work/6e/4d4c2f4a9032f01ce2c366136f9c81'
  Moving from:
  'init-phred-head-shuffle-sra-clear-noadapt-0_blox-0.fq'
  to:
  'orig__.fq'
  --------------------------------------------------------------------------------
  ==> Execution time: 0 day(s), 0 hour(s), 0 minute(s), and 0 second(s)
  ////////////////////////////////////////////////////////////////////////////////
    Running: step = 108   Time: 08:25   Date: 2025-09-24 (elapsed time: 0d:0h:5m)
  \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\
  ==> Current working directory: '/data/nextflow/rnafusion/test/work/6e/4d4c2f4a9032f01ce2c366136f9c81'
  bbduk.sh \
  forcetrimmod=5 \
  qin=33 \
  in=orig__.fq \
  out=orig__x.fq
  --------------------------------------------------------------------------------
  +-->EXECUTING...
  
  
  ERROR: Workflow execution failed at step 108 while executing:
  ----------------
     bbduk.sh \
     forcetrimmod=5 \
     qin=33 \
     in=orig__.fq \
     out=orig__x.fq
  ----------------
    * Size 'orig__.fq' = 4719958464 bytes
    * Size 'orig__x.fq' = 25672080 bytes
  
  
  Executing second time the same step/command in order to capture error messages (i.e. STDERR)...
  
  -------------------------------------------
  
  
  WARNING: First execution ended with error but second execution did not! Therefore cannot capture the STDERR!
  ################################################################################
  ################################################################################
  TOTAL RUNNING TIME: 0 day(s), 0 hour(s), 6 minute(s), and 27 second(s) 
  ################################################################################
  ################################################################################

Command error:
  Version 38.44
  
  0.036 seconds.
  Initial:
  Memory: max=69m, total=69m, free=40m, used=29m
  
  Input is being processed as paired
  Started output streams:	0.009 seconds.
  Exception in thread "Thread-95" Exception in thread "Thread-50" java.lang.OutOfMemoryError: Java heap space
  java.lang.OutOfMemoryError: Java heap space
  	at stream.FASTQ.quadToRead_slow(FASTQ.java:809)
  	at stream.FASTQ.toReadList(FASTQ.java:625)
  	at stream.FastqReadInputStream.fillBuffer(FastqReadInputStream.java:107)
  	at stream.FastqReadInputStream.nextList(FastqReadInputStream.java:93)
  	at stream.ConcurrentGenericReadInputStream$ReadThread.readLists(ConcurrentGenericReadInputStream.java:680)
  	at stream.ConcurrentGenericReadInputStream$ReadThread.run(ConcurrentGenericReadInputStream.java:656)
  java.lang.OutOfMemoryError: Java heap space
  	at stream.ConcurrentGenericReadOutputStream.addDisordered(ConcurrentGenericReadOutputStream.java:197)
  	at stream.ConcurrentGenericReadOutputStream.add(ConcurrentGenericReadOutputStream.java:97)
  	at jgi.BBDuk$ProcessThread.run(BBDuk.java:3045)
  
  This program ran out of memory.
  Try increasing the -Xmx flag and using tool-specific memory-related parameters.
  -----------------------------------------------------
  +-->EXECUTING...
  
  
  ERROR: Workflow execution failed at step 108 while executing:
  ----------------
     bbduk.sh \
     forcetrimmod=5 \
     qin=33 \
     in=orig__.fq \
     out=orig__x.fq
  ----------------
    * Size 'orig__.fq' = 4719958464 bytes
    * Size 'orig__x.fq' = 25672080 bytes
  
  
  Executing second time the same step/command in order to capture error messages (i.e. STDERR)...
  
  -------------------------------------------
  
  
  WARNING: First execution ended with error but second execution did not! Therefore cannot capture the STDERR!
  ################################################################################
  ################################################################################
  TOTAL RUNNING TIME: 0 day(s), 0 hour(s), 6 minute(s), and 27 second(s) 
  ################################################################################
  ################################################################################

Work dir:
  /data/nextflow/rnafusion/test/work/6e/4d4c2f4a9032f01ce2c366136f9c81

Container:
  quay.io/biocontainers/fusioncatcher:1.33b--hdfd78af_0

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details

-[nf-core/rnafusion] Pipeline completed with errors-
WARN: Killing running tasks (11)

Command used and terminal output

nextflow run nf-core/rnafusion \
-revision dev \
-latest \
-resume \
-profile docker \
--tools all \
--genomes_base '/data/rnafusion_reference' \
--input 'samplesheet_rnafusion_test.csv' \
--outdir '/data/nextflow/rnafusion/test/results/' \
-work-dir '/data/nextflow/rnafusion/test/work/' \
-c 'custom_local.config'

Relevant files

No response

System information

Version: 25.04.7 build 5955
Created: 08-09-2025 13:29 UTC (21:29 SGST)
System: Linux 5.15.0-144-generic
Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src
Encoding: UTF-8 (UTF-8)