Errorpaired_sample_wgs:remove_realigned_bams

[tgebo]

• Pipeline release version v7.2.0
• Cluster you are using (SGE/Slurm-Dev/Slurm-Test) Slurm-Dev
• Node type (F2s (lowmem) / F72s (midmem) / M64s (execute)) F72
• Submission method (interactive/submission script) python
• Actual submission script (python submission script, "nextflow run ...", etc.) .py script
• Sbatch or qsub command and logs if applicable
• Config files /hot/users/tgebo/WCDT/scripts/call-gSNP/DTB-059.config
• Path to the working directory /hot/users/tgebo/pipelines/pipeline-call-gSNP
• Any logs produced by the pipeline /hot/users/tgebo/pipelines/pipeline-call-gSNP/DTB-059.log

*** Changed parameter from default value 50 to: scatter_count = 70

Caused by:
  Process `paired_sample_wgs:remove_realigned_bams (27)` terminated with an error exit status (2)

Command executed:

  set -euo pipefail
  
  if [[ -L DTB-059_indelrealigned_13.bai ]]
  then
      rm `readlink -f DTB-059_indelrealigned_13.bai`
  fi
  
  rm DTB-059_indelrealigned_13.bai

Command exit status:
  2

Command output:
  (empty)

Command error:
  00007ffeeabfd678:  0000000000000000  000000000000000d 
  00007ffeeabfd688:  00002b85793a29d9  0000000000000000 
  00007ffeeabfd698:  00002b857932d213  000000000000000d 
  00007ffeeabfd6a8:  00002b857967b1c0  0000000000000001 
  00007ffeeabfd6b8:  00002b857967b243  00002b8579677380 
  00007ffeeabfd6c8:  00002b857932ea2e  00002b857967b1c0 
  00007ffeeabfd6d8:  000000000000000a  0000564210475c20 
  00007ffeeabfd6e8:  0000000000000000  000056420e9fa4a0 
  
  goroutine 1 [runnable, locked to thread]:
  github.com/docker/cli/vendor/k8s.io/apimachinery/pkg/runtime.(*Scheme).AddKnownTypeWithName(0xc000268700, 0x56420e7bf04c, 0x4, 0x56420e7c3a76, 0x7, 0x56420ec56612, 0xa, 0x56420f072780, 0xc000399680)
        /go/src/github.com/docker/cli/vendor/k8s.io/apimachinery/pkg/runtime/scheme.go:206 +0x345
  github.com/docker/cli/vendor/k8s.io/apimachinery/pkg/runtime.(*Scheme).AddKnownTypes(0xc000268700, 0x56420e7bf04c, 0x4, 0x56420e7c3a76, 0x7, 0xc0006d94b0, 0x8, 0x8)
        /go/src/github.com/docker/cli/vendor/k8s.io/apimachinery/pkg/runtime/scheme.go:180 +0x245
  github.com/docker/cli/vendor/k8s.io/api/apps/v1beta1.addKnownTypes(0xc000268700, 0x0, 0x0)
        /go/src/github.com/docker/cli/vendor/k8s.io/api/apps/v1beta1/register.go:46 +0x254
  github.com/docker/cli/vendor/k8s.io/apimachinery/pkg/runtime.(*SchemeBuilder).AddToScheme(0x56420fdff6e0, 0xc000268700, 0x0, 0x0)
        /go/src/github.com/docker/cli/vendor/k8s.io/apimachinery/pkg/runtime/scheme_builder.go:29 +0x6f
  github.com/docker/cli/vendor/k8s.io/apimachinery/pkg/runtime.(*SchemeBuilder).AddToScheme(0x56420fd66430, 0xc000268700, 0x56420f074558, 0xc0001af900)
        /go/src/github.com/docker/cli/vendor/k8s.io/apimachinery/pkg/runtime/scheme_builder.go:29 +0x6f
  github.com/docker/cli/vendor/k8s.io/client-go/kubernetes/scheme.init.0()
/go/src/github.com/docker/cli/vendor/k8s.io/client-go/kubernetes/scheme/register.go:129 +0x67
  
  goroutine 15 [chan receive]:
  github.com/docker/cli/vendor/k8s.io/klog.(*loggingT).flushDaemon(0x56420fe0a3c0)
        /go/src/github.com/docker/cli/vendor/k8s.io/klog/klog.go:1010 +0x8d
  created by github.com/docker/cli/vendor/k8s.io/klog.init.0
        /go/src/github.com/docker/cli/vendor/k8s.io/klog/klog.go:411 +0xd8
  
  rax    0x0
  rbx    0x2b857967b868
  rcx    0xffffffffffffffff
  rdx    0x6
  rdi    0x746f
  rsi    0x746f
  rbp    0x56420ea1ef69
  rsp    0x7ffeeabfd5f8
  r8     0xa
  r9     0x2b8578c9f780
  r10    0x8
  r11    0x206
  r12    0x564210475c20
  r13    0x0
  r14    0x56420e9fa4a0
  r15    0x0
  rip    0x2b85792e9337
  rflags 0x206
  cs     0x33
  fs     0x0
  gs     0x0