Segmentation fault (core dumped) for fusion_catcher

[ZheFrench]

Description of the bug

fusioncatcher error due to STAR mapping which creates a segmentation fault.

Command used and terminal output

nextflow run rnafusion -profile singularity  --arriba --fusioncatcher --pizzly --starfusion --stringtie --fusionreport --input /data2/villemin/Myelome/fusion/samples/sampleFusion-bug.csv --genomes_base  /data2/villemin/Myelome/fusion --outdir /data2/villemin/Myelome/fusion/results

fusioncatcher.py \
    -d human_v102 \
    -i E6026_R1.fastq.gz,E6026_R2.fastq.gz \
    -p 12 \
    -o . \
    --skip-blat \
     \
    --limitSjdbInsertNsj 2000000

.command.out

ERROR: Workflow execution failed at step 408 while executing:
----------------
   STAR \
   --runRNGseed 54321 \
   --twopass1readsN -1 \
   --twopassMode Basic \
   --genomeSAindexNbases 13 \
   --sjdbOverhang 74 \
   --alignIntronMax 1340259 \
   --sjdbOverhang 74 \
   --alignIntronMax 1340259 \
   --outFilterMatchNmin 16 \
   --outFilterMatchNminOverLread 0.2667 \
   --outFilterScoreMinOverLread 0.2667 \
   --alignSplicedMateMapLminOverLmate 0.2667 \
   --genomeDir /data2/USERS/villemin/Myelome/fusion/work/a1/20a6dbbccf2772dd77a777ff5a7e83/gene-gene-star/ \
   --runThreadN 12 \
   --seedSearchStartLmax 16 \
   --alignSJoverhangMin 16 \
   --alignSJstitchMismatchNmax 5 -1 5 5 \
   --outSJfilterOverhangMin 10 10 10 10 \
   --outSJfilterCountUniqueMin 1 1 1 1 \
   --outSJfilterCountTotalMin 1 1 1 1 \
   --outSJfilterDistToOtherSJmin 0 0 0 0 \
   --outSJfilterIntronMaxVsReadN 1340259 \
    1340259 \
    1340259 \
   --limitOutSAMoneReadBytes 100000000 \
   --scoreGapNoncan -4 \
   --scoreGapATAC -4 \
   --limitSjdbInsertNsj 2000000 \
   --readFilesIn Jan 18 17:33:06 ..... started STAR run
Jan 18 17:33:06 ..... loading genome
Jan 18 17:33:10 ..... started 1st pass mapping
Jan 18 17:39:54 ..... finished 1st pass mapping
Jan 18 17:39:55 ..... inserting junctions into the genome indices
Jan 18 17:42:40 ..... started mapping
/data2/USERS/villemin/Myelome/fusion/work/a1/20a6dbbccf2772dd77a777ff5a7e83/reads_gene-gene_no-str_fixed.fq \
   --outFileNamePrefix /data2/USERS/villemin/Myelome/fusion/work/a1/20a6dbbccf2772dd77a777ff5a7e83/gene-gene-star-results/
----------------
  * Size '/data2/USERS/villemin/Myelome/fusion/work/a1/20a6dbbccf2772dd77a777ff5a7e83/star_sdjboverhang.txt' = 2 bytes
  * Size '/data2/USERS/villemin/Myelome/fusion/work/a1/20a6dbbccf2772dd77a777ff5a7e83/gene-gene_longest.txt' = 7 bytes
  * Size '/data2/USERS/villemin/Myelome/fusion/work/a1/20a6dbbccf2772dd77a777ff5a7e83/gene-gene-star/' = 3922865482 bytes
  * Size '/data2/USERS/villemin/Myelome/fusion/work/a1/20a6dbbccf2772dd77a777ff5a7e83/gene-gene_longest.txt' = 7 bytes
  * Size '/data2/USERS/villemin/Myelome/fusion/work/a1/20a6dbbccf2772dd77a777ff5a7e83/gene-gene_longest.txt' = 7 bytes
  * Size '/data2/USERS/villemin/Myelome/fusion/work/a1/20a6dbbccf2772dd77a777ff5a7e83/gene-gene_longest.txt' = 7 bytes
  * Size '/data2/USERS/villemin/Myelome/fusion/work/a1/20a6dbbccf2772dd77a777ff5a7e83/reads_gene-gene_no-str_fixed.fq' = 466180000 bytes
  * Size '/data2/USERS/villemin/Myelome/fusion/work/a1/20a6dbbccf2772dd77a777ff5a7e83/gene-gene-star-results/' = 54847603 bytes


Executing second time the same step/command in order to capture error messages (i.e. STDERR)...

-------------------------------------------
Segmentation fault (core dumped)


.command.err

Input is being processed as paired
Started output streams: 0.016 seconds.
Processing time:                85.048 seconds.

Input:                          57582010 reads          4376232760 bases.
FTrimmed:                       57582010 reads (100.00%)        57582010 bases (1.32%)
Total Removed:                  0 reads (0.00%)         57582010 bases (1.32%)
Result:                         57582010 reads (100.00%)        4318650750 bases (98.68%)

Time:                           85.069 seconds.
Reads Processed:      57582k    676.88k reads/sec
Bases Processed:       4376m    51.44m bases/sec
java -ea -Xmx38319m -Xms38319m -cp /opt/fusioncatcher/v1.33/tools/bbmap/current/ jgi.BBDuk entropy=0.1 entropymask=t entropyk=2 entropywindow=40 in=/data2/USERS/villemin/Myelome/fusion/work/a1/20a6dbbccf2
772dd77a777ff5a7e83/orig__x.fq out=/data2/USERS/villemin/Myelome/fusion/work/a1/20a6dbbccf2772dd77a777ff5a7e83/orig.fq
Executing jgi.BBDuk [entropy=0.1, entropymask=t, entropyk=2, entropywindow=40, in=/data2/USERS/villemin/Myelome/fusion/work/a1/20a6dbbccf2772dd77a777ff5a7e83/orig__x.fq, out=/data2/USERS/villemin/Myelome/
fusion/work/a1/20a6dbbccf2772dd77a777ff5a7e83/orig.fq]
Version 38.44

0.046 seconds.
Initial:
Memory: max=40181m, total=40181m, free=40131m, used=50m

Input is being processed as paired
Started output streams: 0.023 seconds.
Processing time:                79.601 seconds.

Input:                          57582010 reads          4318650750 bases.
Entropy-masked:                 137486 reads (0.24%)    8478188 bases (0.20%)
Total Removed:                  0 reads (0.00%)         0 bases (0.00%)
Result:                         57582010 reads (100.00%)        4318650750 bases (100.00%)

Time:                           79.628 seconds.
Reads Processed:      57582k    723.13k reads/sec
Bases Processed:       4318m    54.24m bases/sec
Using 12 process(es)...
Using 12 process(es)...
Found 1 reads with poly-A/C/G/T/N tails (equal or more 16 repeat nucleotides)
Total number of input reads = 4219147
Total number of reads written in the output = 4219146
Using 12 process(es)...
0.10571 % reads clipped due to low quality (less or equal than Q5) at 3' end (4460 out of 4219146)!
Found 249306 reads with poly-A/C/G/T/N tails (equal or more 16 repeat nucleotides)
Total number of input reads = 3346431
Total number of reads written in the output = 3346431
Using 12 process(es)...
0.00000 % reads clipped due to low quality (less or equal than Q5) at 3' end (0 out of 3346431)!
Segmentation fault (core dumped)
INFO:    Cleaning up image...

Relevant files

nextflow.log

System information

Nextflow version (eg. 23.04.0)
Hardware : HPC
Executor : local
Container engine: Singularity
OS : Linux Ubuntu
Version of nf-core/rnafusion 2.4

[rannick]

This is a fusioncatcher issue, rnafusion is a wrapper around the tools. You will hopefully find more help on the fusioncatcher side: https://github.com/ndaniel/fusioncatcher