Exit code 9 when using hs37d5

Hi,

I'm getting an exit code of 9 but when I check the log file there is no error mesage. I'm using hs37d5 as my reference.


^[^[[A^[[A"$timecmd java -Xmx$jvmheap $jvm_args -Dgridss.output_to_temp_file=true -cp $gridss_jar gridss.AssembleBreakends JOB_INDEX=$jobindex JOB_NODES=$jobnodes TMP_DIR=$workingdir WORKING_DIR=$workingdir REFERENCE_SEQUENCE=$reference WORKER_THREADS=$threads $in│························································································································
put_args $blacklist_arg $config_args $picardoptions $readpairing_args O=$assembly" command completed with exit code 9.  ```

This is the content of the log file

```INFO    2023-10-03 17:07:21     GridssConfiguration     variantcalling.includeSupportingReadNames=false                                                                                                                                                                 │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     variantcalling.breakpointLowQuality=500.0                                                                                                                                                                       │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     variantcalling.breakendLowQuality=1500.0                                                                                                                                                                        │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     variantcalling.breakendMaxAssemblySupportBias=0.5                                                                                                                                                               │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     variantcalling.ignoreMissingAssemblyFile=false                                                                                                                                                                  │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     terminateOnFirstError=true                                                                                                                                                                                      │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     visualisation.directory=visualisation                                                                                                                                                                           │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     visualisation.buffers=false                                                                                                                                                                                     │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     visualisation.bufferTrackingItervalInSeconds=60                                                                                                                                                                 │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     visualisation.timeouts=false                                                                                                                                                                                    │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     visualisation.evidenceAllocation=false                                                                                                                                                                          │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     visualisation.assemblyProgress=false                                                                                                                                                                            │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     visualisation.assemblyTelemetry=false                                                                                                                                                                           │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     visualisation.maxCliqueTelemetry=false                                                                                                                                                                          │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     visualisation.assemblyGraph=false                                                                                                                                                                               │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     visualisation.assemblyGraphFullSize=false                                                                                                                                                                       │························································································································
INFO    2023-10-03 17:07:21     GridssConfiguration     visualisation.assemblyContigMemoization=false                                                                                                                                                                   │························································································································
INFO    2023-10-03 17:07:21     TwoBitBufferedReferenceSequenceFile     Loading reference genome from cache hs37d5.fa.gridsscache                                                                                                    │························································································································
INFO    2023-10-03 17:07:21     MultipleSamFileCommandLineProgram       Loading aligner                                                                                                                                                                                 │························································································································
INFO    2023-10-03 17:07:21     AlignerFactory  sswjni library loading successful.                                                                                                                                                                                      │························································································································
WARNING: BAM index file sample.bam.bai is older than BAM sample.bam                                                                                                   │························································································································
INFO    2023-10-03 17:07:21     MultipleSamFileCommandLineProgram       Using 8 worker threads                                                                                                                                                                          │························································································································
WARNING: BAM index file sample.bam.bai is older than BAM sample.bam                                                                                                   │························································································································
INFO    2023-10-03 17:07:22     AssemblyEvidenceSource  Starting assembly on chunk 0 (1:1-1:10000000)                                                                                                                                                                   │························································································································
INFO    2023-10-03 17:07:22     AssemblyEvidenceSource  Starting assembly on chunk 9 (1:90000001-1:100000000)                                                                                                                                                           │························································································································
INFO    2023-10-03 17:07:22     AssemblyEvidenceSource  Starting assembly on chunk 10 (1:100000001-1:110000000)                                                                                                                                                         │························································································································
INFO    2023-10-03 17:07:22     AssemblyEvidenceSource  Starting assembly on chunk 11 (1:110000001-1:120000000)                                                                                                                                                         │························································································································
INFO    2023-10-03 17:07:22     AssemblyEvidenceSource  Starting assembly on chunk 14 (1:140000001-1:150000000)                                                                                                                                                         │························································································································
INFO    2023-10-03 17:07:22     AssemblyEvidenceSource  Starting assembly on chunk 15 (1:150000001-1:160000000)                                                                                                                                                         │························································································································
INFO    2023-10-03 17:07:22     AssemblyEvidenceSource  Starting assembly on chunk 16 (1:160000001-1:170000000)                                                                                                                                                         │························································································································
INFO    2023-10-03 17:07:22     AssemblyEvidenceSource  Starting assembly on chunk 17 (1:170000001-1:180000000)                                                                                                                                                         │························································································································
INFO    2023-10-03 17:07:28     TwoBitBufferedReferenceSequenceFile     Loading reference genome complete      ```

Exit code 9 indicates the process was killed. Either another user or another system killed your gridss job. Did you run out of time/memory on a HPC job?

On Tue, 3 Oct 2023, 5:26 pm Jennifer Ureta, @.***> wrote:

Hi,

I'm getting an exit code of 9 but when I check the log file there is no error mesage. I'm using hs37d5 as my reference.

Tue Oct 3 17:22:35 AEDT 2023: Running AssembleBreakends sample.bam job 0 total jobs 1 │························································································································ ^[^[[A^[[A"$timecmd java -Xmx$jvmheap $jvm_args -Dgridss.output_to_temp_file=true -cp $gridss_jar gridss.AssembleBreakends JOB_INDEX=$jobindex JOB_NODES=$jobnodes TMP_DIR=$workingdir WORKING_DIR=$workingdir REFERENCE_SEQUENCE=$reference WORKER_THREADS=$threads $in│························································································································ put_args $blacklist_arg $config_args $picardoptions $readpairing_args O=$assembly" command completed with exit code 9.

This is the content of the log file INFO 2023-10-03 17:07:21 GridssConfiguration variantcalling.includeSupportingReadNames=false │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration variantcalling.breakpointLowQuality=500.0 │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration variantcalling.breakendLowQuality=1500.0 │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration variantcalling.breakendMaxAssemblySupportBias=0.5 │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration variantcalling.ignoreMissingAssemblyFile=false │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration terminateOnFirstError=true │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration visualisation.directory=visualisation │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration visualisation.buffers=false │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration visualisation.bufferTrackingItervalInSeconds=60 │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration visualisation.timeouts=false │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration visualisation.evidenceAllocation=false │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration visualisation.assemblyProgress=false │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration visualisation.assemblyTelemetry=false │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration visualisation.maxCliqueTelemetry=false │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration visualisation.assemblyGraph=false │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration visualisation.assemblyGraphFullSize=false │························································································································ INFO 2023-10-03 17:07:21 GridssConfiguration visualisation.assemblyContigMemoization=false │························································································································ INFO 2023-10-03 17:07:21 TwoBitBufferedReferenceSequenceFile Loading reference genome from cache hs37d5.fa.gridsscache │························································································································ INFO 2023-10-03 17:07:21 MultipleSamFileCommandLineProgram Loading aligner │························································································································ INFO 2023-10-03 17:07:21 AlignerFactory sswjni library loading successful. │························································································································ WARNING: BAM index file sample.bam.bai is older than BAM sample.bam │························································································································ INFO 2023-10-03 17:07:21 MultipleSamFileCommandLineProgram Using 8 worker threads │························································································································ WARNING: BAM index file sample.bam.bai is older than BAM sample.bam │························································································································ INFO 2023-10-03 17:07:22 AssemblyEvidenceSource Starting assembly on chunk 0 (1:1-1:10000000) │························································································································ INFO 2023-10-03 17:07:22 AssemblyEvidenceSource Starting assembly on chunk 9 (1:90000001-1:100000000) │························································································································ INFO 2023-10-03 17:07:22 AssemblyEvidenceSource Starting assembly on chunk 10 (1:100000001-1:110000000) │························································································································ INFO 2023-10-03 17:07:22 AssemblyEvidenceSource Starting assembly on chunk 11 (1:110000001-1:120000000) │························································································································ INFO 2023-10-03 17:07:22 AssemblyEvidenceSource Starting assembly on chunk 14 (1:140000001-1:150000000) │························································································································ INFO 2023-10-03 17:07:22 AssemblyEvidenceSource Starting assembly on chunk 15 (1:150000001-1:160000000) │························································································································ INFO 2023-10-03 17:07:22 AssemblyEvidenceSource Starting assembly on chunk 16 (1:160000001-1:170000000) │························································································································ INFO 2023-10-03 17:07:22 AssemblyEvidenceSource Starting assembly on chunk 17 (1:170000001-1:180000000) │························································································································ INFO 2023-10-03 17:07:28 TwoBitBufferedReferenceSequenceFile Loading reference genome complete

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PapenfussLab / gridss

Exit code 9 when using hs37d5 #641