Hello,
I am trying to run a version of the joint-discovery-gatk4-local workflow slightly adjusted to run with a SLURM backend (I am running with gatk 4.0.12.0; the json and wdl files are both based on github.com/gatk-workflows/gatk4-germline-snps-indels 'local' version). When running with enough samples to trigger the scatter-gather of the metrics, the workflow stops at the "GatherMetrics" step. I get this error message:
htsjdk.samtools.SAMException: Cannot read non-existent file: file:///test_joint-call/cromwell-executions/JointGenotyping/0c5fec3d-ae6a-4740-b991-3c5832c36315/call-GatherMetrics/inputs/-343490749/test3000.0.variant_calling_detail_metrics.variant_calling_detail_metrics
This file (with the double suffix) is indeed non-existent, but the file test3000.0.variant_calling_detail_metrics does exist in the right location. And in the command line featured in the logs, the filename is correct, and points to an existing and readable file:
```
Using GATK jar /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/gatk/4.0.12.0/gatk-package-4.0.12.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx2g -Xms2g -jar /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/gatk/4.0.12.0/gatk-package-4.0.12.0-local.jar AccumulateVariantCallingMetrics --INPUT /test_joint-call/cromwell-executions/JointGenotyping/0c5fec3d-ae6a-4740-b991-3c5832c36315/call-GatherMetrics/inputs/-343490749/test3000.0.variant_calling_detail_metrics --INPUT [... follows a long list of input shards ...] --OUTPUT test3000
```
Have you seen such a problem before? Do you know how to solve it? Those file are generated and named automatically, it would be strange if there was really a problem reading one.
Many thanks,
Frederic
I am trying to run a version of the joint-discovery-gatk4-local workflow slightly adjusted to run with a SLURM backend (I am running with gatk 4.0.12.0; the json and wdl files are both based on github.com/gatk-workflows/gatk4-germline-snps-indels 'local' version). When running with enough samples to trigger the scatter-gather of the metrics, the workflow stops at the "GatherMetrics" step. I get this error message:
htsjdk.samtools.SAMException: Cannot read non-existent file: file:///test_joint-call/cromwell-executions/JointGenotyping/0c5fec3d-ae6a-4740-b991-3c5832c36315/call-GatherMetrics/inputs/-343490749/test3000.0.variant_calling_detail_metrics.variant_calling_detail_metrics
This file (with the double suffix) is indeed non-existent, but the file test3000.0.variant_calling_detail_metrics does exist in the right location. And in the command line featured in the logs, the filename is correct, and points to an existing and readable file:
```
Using GATK jar /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/gatk/4.0.12.0/gatk-package-4.0.12.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx2g -Xms2g -jar /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/gatk/4.0.12.0/gatk-package-4.0.12.0-local.jar AccumulateVariantCallingMetrics --INPUT /test_joint-call/cromwell-executions/JointGenotyping/0c5fec3d-ae6a-4740-b991-3c5832c36315/call-GatherMetrics/inputs/-343490749/test3000.0.variant_calling_detail_metrics --INPUT [... follows a long list of input shards ...] --OUTPUT test3000
```
Have you seen such a problem before? Do you know how to solve it? Those file are generated and named automatically, it would be strange if there was really a problem reading one.
Many thanks,
Frederic