Deepvariant v0.10 uses python3 by default

Version info

bcbio version (bcbio_nextgen.py --version): 1.2.1
OS name and version: Ubuntu 19.10

To Reproduce
bcbio_nextgen.py ../config/config.yaml -n 18

---
upload:
  dir: ../final
details:
  - files: [../input/THOMAS_1.fastq.gz, ../input/THOMAS_2.fastq.gz]
    description: THOMAS
    analysis: variant2
    genome_build: hg38
    algorithm:
      aligner: bwa
      mark_duplicates: true
      recalibrate: false
      realign: false
      variantcaller: [gatk-haplotype, deepvariant]
      remove_lcr: true

Observed behavior

[2020-03-27T18:48Z] multiprocessing: calculate_sv_bins
[2020-03-27T18:48Z] multiprocessing: calculate_sv_coverage
[2020-03-27T18:48Z] multiprocessing: normalize_sv_coverage
[2020-03-27T18:48Z] Timing: hla typing
[2020-03-27T18:48Z] Resource requests: deepvariant, gatk, gatk-haplotype, picard; memory: 6.00, 6.00, 6.00, 6.00; cores: 18, 18, 18, 18
[2020-03-27T18:48Z] Configuring 18 jobs to run, using 1 cores each with 6.00g of memory reserved for each job
[2020-03-27T18:48Z] Timing: alignment post-processing
[2020-03-27T18:48Z] multiprocessing: piped_bamprep
[2020-03-27T18:48Z] Timing: variant calling
[2020-03-27T18:48Z] multiprocessing: variantcall_sample
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] Remove problematic regions: nolcr
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] DeepVariant make_examples THOMAS
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-27T18:48Z] Computers / CPU cores / Max jobs to run
[2020-03-27T18:48Z] 1:local / 20 / 1
[2020-03-27T18:48Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 193, in _run_module_as_main
[2020-03-27T18:48Z]     "__main__", mod_spec)
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 85, in _run_code
[2020-03-27T18:48Z]     exec(code, run_globals)
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 252, in <module>
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 233, in Main
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 287, in call
[2020-03-27T18:48Z]     with Popen(*popenargs, **kwargs) as p:
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 729, in __init__
[2020-03-27T18:48Z]     restore_signals, start_new_session)
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 1364, in _execute_child
[2020-03-27T18:48Z]     raise child_exception_type(errno_num, err_msg, err_filename)
[2020-03-27T18:48Z] FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/python3.6': '/usr/bin/python3.6'
[2020-03-27T18:48Z] parallel: This job failed:
[2020-03-27T18:48Z] /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/align/THOMAS/THOMAS-sort.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr2/THOMAS-chr2_32868268_54338356-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
[2020-03-27T18:48Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/align/THOMAS/THOMAS-sort.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr2/THOMAS-chr2_32868268_54338356-regions-nolcr.bed --logdir /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr2/THOMAS-chr2_32868268_54338356-work/log --examples /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/bcbiotx/tmpz7_3t3sc --sample THOMAS
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 252, in <module>
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 233, in Main
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 287, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 729, in __init__
    restore_signals, start_new_session)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 1364, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/python3.6': '/usr/bin/python3.6'
parallel: This job failed:
/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/align/THOMAS/THOMAS-sort.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr2/THOMAS-chr2_32868268_54338356-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 1.
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 193, in _run_module_as_main
[2020-03-27T18:48Z]     "__main__", mod_spec)
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 85, in _run_code
[2020-03-27T18:48Z]     exec(code, run_globals)
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 252, in <module>
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 233, in Main
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 287, in call
[2020-03-27T18:48Z]     with Popen(*popenargs, **kwargs) as p:
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 729, in __init__
[2020-03-27T18:48Z]     restore_signals, start_new_session)
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 1364, in _execute_child
[2020-03-27T18:48Z]     raise child_exception_type(errno_num, err_msg, err_filename)
[2020-03-27T18:48Z] FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/python3.6': '/usr/bin/python3.6'
[2020-03-27T18:48Z] parallel: This job failed:
[2020-03-27T18:48Z] /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/align/THOMAS/THOMAS-sort.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr8/THOMAS-chr8_17408415_40434823-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
[2020-03-27T18:48Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/align/THOMAS/THOMAS-sort.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr8/THOMAS-chr8_17408415_40434823-regions-nolcr.bed --logdir /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr8/THOMAS-chr8_17408415_40434823-work/log --examples /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/bcbiotx/tmpz08prroj --sample THOMAS
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 252, in <module>
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 233, in Main
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 287, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 729, in __init__
    restore_signals, start_new_session)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 1364, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/python3.6': '/usr/bin/python3.6'
parallel: This job failed:
/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/align/THOMAS/THOMAS-sort.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr8/THOMAS-chr8_17408415_40434823-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 1.
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 193, in _run_module_as_main
[2020-03-27T18:48Z]     "__main__", mod_spec)
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 85, in _run_code
[2020-03-27T18:48Z]     exec(code, run_globals)
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 252, in <module>
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 233, in Main
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 287, in call
[2020-03-27T18:48Z]     with Popen(*popenargs, **kwargs) as p:
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 729, in __init__
[2020-03-27T18:48Z]     restore_signals, start_new_session)
[2020-03-27T18:48Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 1364, in _execute_child
[2020-03-27T18:48Z]     raise child_exception_type(errno_num, err_msg, err_filename)
[2020-03-27T18:48Z] FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/python3.6': '/usr/bin/python3.6'
[2020-03-27T18:48Z] parallel: This job failed:
[2020-03-27T18:48Z] /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/align/THOMAS/THOMAS-sort.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
[2020-03-27T18:48Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/align/THOMAS/THOMAS-sort.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-regions-nolcr.bed --logdir /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-work/log --examples /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/bcbiotx/tmpea3y42bm --sample THOMAS
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 252, in <module>
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 233, in Main
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 287, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 729, in __init__
    restore_signals, start_new_session)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 1364, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/python3.6': '/usr/bin/python3.6'
parallel: This job failed:
/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/align/THOMAS/THOMAS-sort.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 1.
[2020-03-27T18:48Z] Remove problematic regions: nolcr
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 600, in __call__
    return self.func(*args, **kwargs)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 256, in __call__
    for func, args, kwargs in self.items]
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 256, in <listcomp>
    for func, args, kwargs in self.items]
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/utils.py", line 55, in wrapper
    return f(*args, **kwargs)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/multitasks.py", line 315, in variantcall_sample
    return genotype.variantcall_sample(*args)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/genotype.py", line 377, in variantcall_sample
    out_file = caller_fn(align_bams, items, ref_file, assoc_files, region, out_file)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/deepvariant.py", line 24, in run
    region, out_file)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/deepvariant.py", line 32, in _run_germline
    example_dir = _make_examples(bam_file, data, ref_file, region_bed, out_file, work_dir)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/deepvariant.py", line 52, in _make_examples
    do.run(cmd, "DeepVariant make_examples %s" % dd.get_sample_name(data))
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/align/THOMAS/THOMAS-sort.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-regions-nolcr.bed --logdir /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-work/log --examples /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/bcbiotx/tmpea3y42bm --sample THOMAS
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 252, in <module>
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 233, in Main
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 287, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 729, in __init__
    restore_signals, start_new_session)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 1364, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/python3.6': '/usr/bin/python3.6'
parallel: This job failed:
/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/align/THOMAS/THOMAS-sort.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 1.
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/bcbio_nextgen.py", line 245, in <module>
    main(**kwargs)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/bcbio_nextgen.py", line 46, in main
    run_main(**kwargs)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 50, in run_main
    fc_dir, run_info_yaml)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 91, in _run_toplevel
    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 154, in variant2pipeline
    samples = genotype.parallel_variantcall_region(samples, run_parallel)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/genotype.py", line 208, in parallel_variantcall_region
    "vrn_file", ["region", "sam_ref", "config"]))
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/split.py", line 35, in grouped_parallel_split_combine
    final_output = parallel_fn(parallel_name, split_args)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
    return run_multicore(fn, items, config, parallel=parallel)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
    for data in joblib.Parallel(parallel["num_jobs"], batch_size=1, backend="multiprocessing")(joblib.delayed(fn)(*x) for x in items):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 1016, in __call__
    self.retrieve()
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 908, in retrieve
    self._output.extend(job.get(timeout=self.timeout))
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/multiprocessing/pool.py", line 644, in get
    raise self._value
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/align/THOMAS/THOMAS-sort.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-regions-nolcr.bed --logdir /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-work/log --examples /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/bcbiotx/tmpea3y42bm --sample THOMAS
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 252, in <module>
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip/__main__.py", line 233, in Main
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 287, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 729, in __init__
    restore_signals, start_new_session)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 1364, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/python3.6': '/usr/bin/python3.6'
parallel: This job failed:
/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-0/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/align/THOMAS/THOMAS-sort.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 1.
kokyriakidis@Konstantinos:/media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work$

Expected behavior
Deepvariant v0.10 uses python3 by default but it is installed in a python2 env. Can you provide an env fix so I can check if deepvariant finally works fine in bcbio.

Konstantinos;
Thanks much for the heads up on the new DeepVariant release. The conda package is now adjusted to use py36 with the new dependencies and the conda install environment in bcbio is swapped over to use python 3 as well. If you run a bcbio update or just fix the deepvariant package:
bcbio_conda install -n dv -c conda-forge -c bioconda python=3.6 deepvariant

hopefully it'll run cleanly now.

Also:
kokyriakidis@Konstantinos:/media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work$ which python
/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python
kokyriakidis@Konstantinos:/media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work$ python
Python 3.6.10 | packaged by conda-forge | (default, Mar  5 2020, 10:05:08)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

@chapmanb
Is it similar to this?
https://github.com/bcbio/bcbio-nextgen/issues/3019

Konstantinos;
Sorry about the continued problems. It looks like my previous fix didn't totally re-wire everything to point at the anaconda python. There is now a new subversion of deepvariant (0.10.0_2) that I hope will do the right thing now. Thanks again for all the testing and hope this works for you.

Hi @chapmanb !
Now it gives me another error:
[2020-03-30T13:21Z] multiprocessing: calculate_sv_bins
[2020-03-30T13:21Z] multiprocessing: calculate_sv_coverage
[2020-03-30T13:21Z] multiprocessing: normalize_sv_coverage
[2020-03-30T13:21Z] Timing: hla typing
[2020-03-30T13:21Z] Resource requests: deepvariant, gatk, picard; memory: 6.00, 6.00, 6.00; cores: 18, 18, 18
[2020-03-30T13:21Z] Configuring 18 jobs to run, using 1 cores each with 6.00g of memory reserved for each job
[2020-03-30T13:21Z] Timing: alignment post-processing
[2020-03-30T13:21Z] multiprocessing: piped_bamprep
[2020-03-30T13:21Z] Timing: variant calling
[2020-03-30T13:21Z] multiprocessing: variantcall_sample
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] Remove problematic regions: nolcr
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] DeepVariant make_examples THOMAS
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
[2020-03-30T13:21Z] Computers / CPU cores / Max jobs to run
[2020-03-30T13:21Z] 1:local / 20 / 1
[2020-03-30T13:21Z] Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
[2020-03-30T13:21Z]   File "/tmp/Bazel.runfiles_87qyhtha/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 44, in <module>
[2020-03-30T13:21Z]     import tensorflow as tf
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
[2020-03-30T13:21Z]     from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 52, in <module>
[2020-03-30T13:21Z]     from tensorflow.core.framework.graph_pb2 import *
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/core/framework/graph_pb2.py", line 6, in <module>
[2020-03-30T13:21Z]     from google.protobuf import descriptor as _descriptor
[2020-03-30T13:21Z]   File "/tmp/Bazel.runfiles_87qyhtha/runfiles/com_google_protobuf/python/google/protobuf/descriptor.py", line 47, in <module>
[2020-03-30T13:21Z]     from google.protobuf.pyext import _message
[2020-03-30T13:21Z] ImportError: /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/Bazel.runfiles_87qyhtha/runfiles/com_google_protobuf/python/google/protobuf/pyext/_message.so)
[2020-03-30T13:21Z] parallel: This job failed:
[2020-03-30T13:21Z] /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-2/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr12/THOMAS-chr12_0_20709600-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
[2020-03-30T13:21Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr12/THOMAS-chr12_0_20709600-regions-nolcr.bed --logdir /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr12/THOMAS-chr12_0_20709600-work/log --examples /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/bcbiotx/tmp1q5xj556 --sample THOMAS
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
  File "/tmp/Bazel.runfiles_87qyhtha/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 44, in <module>
    import tensorflow as tf
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
    from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 52, in <module>
    from tensorflow.core.framework.graph_pb2 import *
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/core/framework/graph_pb2.py", line 6, in <module>
    from google.protobuf import descriptor as _descriptor
  File "/tmp/Bazel.runfiles_87qyhtha/runfiles/com_google_protobuf/python/google/protobuf/descriptor.py", line 47, in <module>
    from google.protobuf.pyext import _message
ImportError: /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/Bazel.runfiles_87qyhtha/runfiles/com_google_protobuf/python/google/protobuf/pyext/_message.so)
parallel: This job failed:
/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-2/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr12/THOMAS-chr12_0_20709600-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 1.
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
[2020-03-30T13:21Z]   File "/tmp/Bazel.runfiles_5g9djgac/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 44, in <module>
[2020-03-30T13:21Z]     import tensorflow as tf
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
[2020-03-30T13:21Z]     from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 52, in <module>
[2020-03-30T13:21Z]     from tensorflow.core.framework.graph_pb2 import *
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/core/framework/graph_pb2.py", line 6, in <module>
[2020-03-30T13:21Z]     from google.protobuf import descriptor as _descriptor
[2020-03-30T13:21Z]   File "/tmp/Bazel.runfiles_5g9djgac/runfiles/com_google_protobuf/python/google/protobuf/descriptor.py", line 47, in <module>
[2020-03-30T13:21Z]     from google.protobuf.pyext import _message
[2020-03-30T13:21Z] ImportError: /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/Bazel.runfiles_5g9djgac/runfiles/com_google_protobuf/python/google/protobuf/pyext/_message.so)
[2020-03-30T13:21Z] parallel: This job failed:
[2020-03-30T13:21Z] /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-2/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr6/THOMAS-chr6_128999541_149762654-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
[2020-03-30T13:21Z]   File "/tmp/Bazel.runfiles_2m37as5x/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 44, in <module>
[2020-03-30T13:21Z]     import tensorflow as tf
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
[2020-03-30T13:21Z]     from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 52, in <module>
[2020-03-30T13:21Z]     from tensorflow.core.framework.graph_pb2 import *
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/core/framework/graph_pb2.py", line 6, in <module>
[2020-03-30T13:21Z]     from google.protobuf import descriptor as _descriptor
[2020-03-30T13:21Z]   File "/tmp/Bazel.runfiles_2m37as5x/runfiles/com_google_protobuf/python/google/protobuf/descriptor.py", line 47, in <module>
[2020-03-30T13:21Z]     from google.protobuf.pyext import _message
[2020-03-30T13:21Z] ImportError: /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/Bazel.runfiles_2m37as5x/runfiles/com_google_protobuf/python/google/protobuf/pyext/_message.so)
[2020-03-30T13:21Z] parallel: This job failed:
[2020-03-30T13:21Z] /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-2/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr8/THOMAS-chr8_76425463_107108006-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
[2020-03-30T13:21Z]   File "/tmp/Bazel.runfiles_0ypk43co/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 44, in <module>
[2020-03-30T13:21Z]     import tensorflow as tf
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
[2020-03-30T13:21Z]     from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 52, in <module>
[2020-03-30T13:21Z]     from tensorflow.core.framework.graph_pb2 import *
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/core/framework/graph_pb2.py", line 6, in <module>
[2020-03-30T13:21Z]     from google.protobuf import descriptor as _descriptor
[2020-03-30T13:21Z]   File "/tmp/Bazel.runfiles_0ypk43co/runfiles/com_google_protobuf/python/google/protobuf/descriptor.py", line 47, in <module>
[2020-03-30T13:21Z]     from google.protobuf.pyext import _message
[2020-03-30T13:21Z] ImportError: /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/Bazel.runfiles_0ypk43co/runfiles/com_google_protobuf/python/google/protobuf/pyext/_message.so)
[2020-03-30T13:21Z] parallel: This job failed:
[2020-03-30T13:21Z] /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-2/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr9/THOMAS-chr9_33213907_60550632-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
[2020-03-30T13:21Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr6/THOMAS-chr6_128999541_149762654-regions-nolcr.bed --logdir /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr6/THOMAS-chr6_128999541_149762654-work/log --examples /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/bcbiotx/tmpe7q12e1r --sample THOMAS
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
  File "/tmp/Bazel.runfiles_5g9djgac/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 44, in <module>
    import tensorflow as tf
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
    from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 52, in <module>
    from tensorflow.core.framework.graph_pb2 import *
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/core/framework/graph_pb2.py", line 6, in <module>
    from google.protobuf import descriptor as _descriptor
  File "/tmp/Bazel.runfiles_5g9djgac/runfiles/com_google_protobuf/python/google/protobuf/descriptor.py", line 47, in <module>
    from google.protobuf.pyext import _message
ImportError: /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/Bazel.runfiles_5g9djgac/runfiles/com_google_protobuf/python/google/protobuf/pyext/_message.so)
parallel: This job failed:
/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-2/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr6/THOMAS-chr6_128999541_149762654-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 1.
[2020-03-30T13:21Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr8/THOMAS-chr8_76425463_107108006-regions-nolcr.bed --logdir /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr8/THOMAS-chr8_76425463_107108006-work/log --examples /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/bcbiotx/tmpvjro5uiw --sample THOMAS
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
  File "/tmp/Bazel.runfiles_2m37as5x/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 44, in <module>
    import tensorflow as tf
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
    from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 52, in <module>
    from tensorflow.core.framework.graph_pb2 import *
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/core/framework/graph_pb2.py", line 6, in <module>
    from google.protobuf import descriptor as _descriptor
  File "/tmp/Bazel.runfiles_2m37as5x/runfiles/com_google_protobuf/python/google/protobuf/descriptor.py", line 47, in <module>
    from google.protobuf.pyext import _message
ImportError: /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/Bazel.runfiles_2m37as5x/runfiles/com_google_protobuf/python/google/protobuf/pyext/_message.so)
parallel: This job failed:
/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-2/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr8/THOMAS-chr8_76425463_107108006-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 1.
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
[2020-03-30T13:21Z]   File "/tmp/Bazel.runfiles_95qw0fdt/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 44, in <module>
[2020-03-30T13:21Z]     import tensorflow as tf
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
[2020-03-30T13:21Z]     from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 52, in <module>
[2020-03-30T13:21Z]     from tensorflow.core.framework.graph_pb2 import *
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/core/framework/graph_pb2.py", line 6, in <module>
[2020-03-30T13:21Z]     from google.protobuf import descriptor as _descriptor
[2020-03-30T13:21Z]   File "/tmp/Bazel.runfiles_95qw0fdt/runfiles/com_google_protobuf/python/google/protobuf/descriptor.py", line 47, in <module>
[2020-03-30T13:21Z]     from google.protobuf.pyext import _message
[2020-03-30T13:21Z] ImportError: /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/Bazel.runfiles_95qw0fdt/runfiles/com_google_protobuf/python/google/protobuf/pyext/_message.so)
[2020-03-30T13:21Z] parallel: This job failed:
[2020-03-30T13:21Z] /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-2/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
[2020-03-30T13:21Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr9/THOMAS-chr9_33213907_60550632-regions-nolcr.bed --logdir /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr9/THOMAS-chr9_33213907_60550632-work/log --examples /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/bcbiotx/tmpx939j5cc --sample THOMAS
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
  File "/tmp/Bazel.runfiles_0ypk43co/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 44, in <module>
    import tensorflow as tf
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
    from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 52, in <module>
    from tensorflow.core.framework.graph_pb2 import *
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/core/framework/graph_pb2.py", line 6, in <module>
    from google.protobuf import descriptor as _descriptor
  File "/tmp/Bazel.runfiles_0ypk43co/runfiles/com_google_protobuf/python/google/protobuf/descriptor.py", line 47, in <module>
    from google.protobuf.pyext import _message
ImportError: /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/Bazel.runfiles_0ypk43co/runfiles/com_google_protobuf/python/google/protobuf/pyext/_message.so)
parallel: This job failed:
/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-2/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr9/THOMAS-chr9_33213907_60550632-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 1.
[2020-03-30T13:21Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-regions-nolcr.bed --logdir /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-work/log --examples /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/bcbiotx/tmpv_fyoxfj --sample THOMAS
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
  File "/tmp/Bazel.runfiles_95qw0fdt/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 44, in <module>
    import tensorflow as tf
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
    from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 52, in <module>
    from tensorflow.core.framework.graph_pb2 import *
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/core/framework/graph_pb2.py", line 6, in <module>
    from google.protobuf import descriptor as _descriptor
  File "/tmp/Bazel.runfiles_95qw0fdt/runfiles/com_google_protobuf/python/google/protobuf/descriptor.py", line 47, in <module>
    from google.protobuf.pyext import _message
ImportError: /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/Bazel.runfiles_95qw0fdt/runfiles/com_google_protobuf/python/google/protobuf/pyext/_message.so)
parallel: This job failed:
/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-2/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 1.
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
[2020-03-30T13:21Z]   File "/tmp/Bazel.runfiles_f49csoj5/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 44, in <module>
[2020-03-30T13:21Z]     import tensorflow as tf
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
[2020-03-30T13:21Z]     from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 52, in <module>
[2020-03-30T13:21Z]     from tensorflow.core.framework.graph_pb2 import *
[2020-03-30T13:21Z]   File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/core/framework/graph_pb2.py", line 6, in <module>
[2020-03-30T13:21Z]     from google.protobuf import descriptor as _descriptor
[2020-03-30T13:21Z]   File "/tmp/Bazel.runfiles_f49csoj5/runfiles/com_google_protobuf/python/google/protobuf/descriptor.py", line 47, in <module>
[2020-03-30T13:21Z]     from google.protobuf.pyext import _message
[2020-03-30T13:21Z] ImportError: /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/Bazel.runfiles_f49csoj5/runfiles/com_google_protobuf/python/google/protobuf/pyext/_message.so)
[2020-03-30T13:21Z] parallel: This job failed:
[2020-03-30T13:21Z] /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-2/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr17/THOMAS-chr17_36173568_59584229-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
[2020-03-30T13:21Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr17/THOMAS-chr17_36173568_59584229-regions-nolcr.bed --logdir /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr17/THOMAS-chr17_36173568_59584229-work/log --examples /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/bcbiotx/tmpyfmbd3gf --sample THOMAS
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
  File "/tmp/Bazel.runfiles_f49csoj5/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 44, in <module>
    import tensorflow as tf
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
    from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 52, in <module>
    from tensorflow.core.framework.graph_pb2 import *
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/core/framework/graph_pb2.py", line 6, in <module>
    from google.protobuf import descriptor as _descriptor
  File "/tmp/Bazel.runfiles_f49csoj5/runfiles/com_google_protobuf/python/google/protobuf/descriptor.py", line 47, in <module>
    from google.protobuf.pyext import _message
ImportError: /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/Bazel.runfiles_f49csoj5/runfiles/com_google_protobuf/python/google/protobuf/pyext/_message.so)
parallel: This job failed:
/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-2/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chr17/THOMAS-chr17_36173568_59584229-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 1.
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 600, in __call__
    return self.func(*args, **kwargs)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 256, in __call__
    for func, args, kwargs in self.items]
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 256, in <listcomp>
    for func, args, kwargs in self.items]
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/utils.py", line 55, in wrapper
    return f(*args, **kwargs)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/multitasks.py", line 315, in variantcall_sample
    return genotype.variantcall_sample(*args)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/genotype.py", line 377, in variantcall_sample
    out_file = caller_fn(align_bams, items, ref_file, assoc_files, region, out_file)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/deepvariant.py", line 24, in run
    region, out_file)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/deepvariant.py", line 32, in _run_germline
    example_dir = _make_examples(bam_file, data, ref_file, region_bed, out_file, work_dir)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/deepvariant.py", line 52, in _make_examples
    do.run(cmd, "DeepVariant make_examples %s" % dd.get_sample_name(data))
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-regions-nolcr.bed --logdir /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-work/log --examples /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/bcbiotx/tmpv_fyoxfj --sample THOMAS
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
  File "/tmp/Bazel.runfiles_95qw0fdt/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 44, in <module>
    import tensorflow as tf
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
    from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 52, in <module>
    from tensorflow.core.framework.graph_pb2 import *
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/core/framework/graph_pb2.py", line 6, in <module>
    from google.protobuf import descriptor as _descriptor
  File "/tmp/Bazel.runfiles_95qw0fdt/runfiles/com_google_protobuf/python/google/protobuf/descriptor.py", line 47, in <module>
    from google.protobuf.pyext import _message
ImportError: /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/Bazel.runfiles_95qw0fdt/runfiles/com_google_protobuf/python/google/protobuf/pyext/_message.so)
parallel: This job failed:
/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-2/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 1.
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/bcbio_nextgen.py", line 245, in <module>
    main(**kwargs)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/bcbio_nextgen.py", line 46, in main
    run_main(**kwargs)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 50, in run_main
    fc_dir, run_info_yaml)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 91, in _run_toplevel
    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 154, in variant2pipeline
    samples = genotype.parallel_variantcall_region(samples, run_parallel)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/genotype.py", line 208, in parallel_variantcall_region
    "vrn_file", ["region", "sam_ref", "config"]))
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/split.py", line 35, in grouped_parallel_split_combine
    final_output = parallel_fn(parallel_name, split_args)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
    return run_multicore(fn, items, config, parallel=parallel)
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
    for data in joblib.Parallel(parallel["num_jobs"], batch_size=1, backend="multiprocessing")(joblib.delayed(fn)(*x) for x in items):
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 1016, in __call__
    self.retrieve()
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 908, in retrieve
    self._output.extend(job.get(timeout=self.timeout))
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/multiprocessing/pool.py", line 644, in get
    raise self._value
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-regions-nolcr.bed --logdir /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-work/log --examples /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/bcbiotx/tmpv_fyoxfj --sample THOMAS
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s Traceback (most recent call last):
  File "/tmp/Bazel.runfiles_95qw0fdt/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 44, in <module>
    import tensorflow as tf
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/__init__.py", line 22, in <module>
    from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 52, in <module>
    from tensorflow.core.framework.graph_pb2 import *
  File "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/tensorflow/core/framework/graph_pb2.py", line 6, in <module>
    from google.protobuf import descriptor as _descriptor
  File "/tmp/Bazel.runfiles_95qw0fdt/runfiles/com_google_protobuf/python/google/protobuf/descriptor.py", line 47, in <module>
    from google.protobuf.pyext import _message
ImportError: /RED/BCBIO/RESOURCES/bcbio/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/Bazel.runfiles_95qw0fdt/runfiles/com_google_protobuf/python/google/protobuf/pyext/_message.so)
parallel: This job failed:
/RED/BCBIO/RESOURCES/bcbio/anaconda/bin/python /RED/BCBIO/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.10.0-2/binaries/DeepVariant/0.10.0/DeepVariant-0.10.0/make_examples.zip --mode calling --ref /RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/prealign/THOMAS/THOMAS-prealign.bam --regions /media/kokyriakidis/PRODUCTION/BCBIO_RUNS/THOMAS/work/deepvariant/chrY/THOMAS-chrY_16091111_56678506-regions-nolcr.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 1.

Konstantinos;
Sorry about the continued problems. The issue you're hitting with GLIBC_2.23 is that the DeepVariant package is pre-built so needs more recent machines with at least this version of glibc available. This has been true since the very first DeepVariant release, so isn't anything new in 0.10.0. I'm surprised you're only seeing it now and wondering if you're testing on different machines than previously. If you're able to run on more recent operating systems I hope it'll avoid the problem.
I also think we've finally worked out the issues you were seeing previously with 0.10.0_3, so hopefully if you can find a location to run it'll now work cleanly for you. Thanks again for all the patience and help debugging.


Enable Webpack tree shaking

Resolves #351
Impact: minor
Type: feature
Issue
Wepack tree shacking was not enabled due to the following setting being in our .babelrc,
modules: commonjs
This PR removes that setting to effectively enable tree shaking(dead code elimination)
Solution
Follow NextJS' example when using a custom web server: https://github.com/zeit/next.js/blob/canary/examples/custom-server-express/server.js
Testing

Rebuild app
Complete the checkout flow, both login and as an anonymous user.
Verify there are no errors

Okay this makes sense. So there are essentially two runtime contexts. One is the startup code (the server) and the other is the Next.js routes and associated code. You had to change everything in the server context, everything they import, and everything they export to use commonjs imports and exports, and then the Next.js context can be ES modules because Next imports them itself through webpack.
Nice work.

@willopez @rosshadden it looks like there are two lint errors that are being flagged in CI.

They might have come from the merge. I'll take a look.

Yeah my fault. I saw session in both sides of the diff and didn't notice express changed to cookie. Fixed.


Bug fix in Wifi AP selection:

on Android SDK 27, if location service is disabled, when we create a task with smb share, a prompt asks to set the WIFI AP to "Private address". If we answer ok, the Wifi AP was regardless set to "Any AP"

👍


Use .webmanifest as extension for Web App Manifests

As noted in specification: https://www.w3.org/TR/appmanifest/

It looks good to me.


The results are different everytime I run the same code, why is that?

It is because of this line on building skelton.
https://github.com/azamikram/rcd/blob/02a11f7399390a29c144efd4e086ffad428371d3/causallearn/utils/PCUtils/SkeletonDiscovery.py#L163


SmbShare module new compression parameters

The SmbShare Module | Microsoft Docs for Windows Server needs to be updated with new parameters for the Reset-SmbClientConfiguration, Reset-SmbServerConfiguration, Set-SmbClientConfiguration, and Set-SmbServerConfiguration commands.
More information can be found in the blog article: SMB compression behavior & settings changes - Microsoft Tech Community

Docs Build status updates of commit d01d079:
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Hi @nedpyle - I can't assigned you for review in this repo but hopefully tagging you here will help. This is the PR to update the SMB compression parameters. Please let me know if you have a good example to add and let me know your thoughts on the parameter text. Of course, I'm happy for us to expand these as discussed.
Thanks,
Robin

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Hi @michaeltlombardi / @sdwheeler,
I believe this PR is release ready if you would be kind enough to review and if appropriate sign-off/merge 😊
The main update was to add in new compression parameters, I have also addressed some quality issues at the same time.
Please let me know if you have any questions or if I need to apply any other updates.
Thanks Robin

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Thanks @michaeltlombardi and @JohanFreelancer9 - Updates applied, I believe this is now ready to merge. #sign-off

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Hi @michaeltlombardi - I think all comments are now addressed. Thanks, Robin

Thanks for approving @michaeltlombardi - are you able to do the #sign-off and merge? I don't have the permissions for this repo.

@robinharwood sorry, thought I hit the button before closing the tab! 😣


Adding OAuth authentication

Description
I want to add sign in with google feature.
Screenshots
No response
Additional information
No response

Ok ...sorry @subhashis2204 my laptop was gone for repairing so didn't saw your message

Any update on this?

Hey! What's an update on this issue? Can I work on this?


Feature/core config

Let me know if you want to change the config for the orbs, but I've got them setup with ace config.

3x Roth_UI\units\player-Player.lua:28: bad argument #1 to 'pairs' (table expected, got nil)
[C]: in function `pairs'
Roth_UI\units\player-Player.lua:28: in main chunk
Locals:
(*temporary) = nil
(*temporary) = "table expected, got nil"
=  defined =[C]:-1


works on osx; not on linux

hi guys, any tips? I get this error when I try to run my app on a linux box. It works on osx however.
20170105-21:03:26.104(-6)? (STDERR)
W20170105-21:03:26.104(-6)? (STDERR) in the root directory of your application.
W20170105-21:03:28.901(-6)? (STDERR) /home/vu/.meteor/packages/meteor-tool/.1.4.2_3.17tso1e++os.linux.x86_64+web.browser+web.cordova/mt-os.linux.x86_64/dev_bundle/server-lib/node_modules/fibers/future.js:280
W20170105-21:03:28.901(-6)? (STDERR) 						throw(ex);
W20170105-21:03:28.901(-6)? (STDERR) 						^
W20170105-21:03:28.901(-6)? (STDERR)
W20170105-21:03:28.901(-6)? (STDERR) TypeError: applyContainerQuery is not a function
W20170105-21:03:28.901(-6)? (STDERR)     at meteorInstall.imports.ui.layouts.TopMenuComponent.js (imports/ui/layouts/TopMenuComponent.js:105:36)
W20170105-21:03:28.902(-6)? (STDERR)     at fileEvaluate (packages/modules-runtime.js:181:9)
W20170105-21:03:28.902(-6)? (STDERR)     at Module.require (packages/modules-runtime.js:106:16)
W20170105-21:03:28.902(-6)? (STDERR)     at Module.Mp.import (/home/vu/.meteor/packages/modules/.<IP_ADDRESS>m2ukcu++os+web.browser+web.cordova/npm/node_modules/reify/lib/runtime.js:70:16)
W20170105-21:03:28.902(-6)? (STDERR)     at meteorInstall.imports.ui.layouts.ConnectedTopMenuComponent.js (imports/ui/layouts/ConnectedTopMenuComponent.js:1:1)
W20170105-21:03:28.902(-6)? (STDERR)     at fileEvaluate (packages/modules-runtime.js:181:9)
W20170105-21:03:28.902(-6)? (STDERR)     at Module.require (packages/modules-runtime.js:106:16)
W20170105-21:03:28.902(-6)? (STDERR)     at Module.Mp.import (/home/vu/.meteor/packages/modules/.<IP_ADDRESS>m2ukcu++os+web.browser+web.cordova/npm/node_modules/reify/lib/runtime.js:70:16)
W20170105-21:03:28.902(-6)? (STDERR)     at meteorInstall.imports.ui.layouts.ConnectedMasterLayout.js (/home/vu/workspace/blackship/.meteor/local/build/programs/server/app/app.js:12789:2683)
W20170105-21:03:28.902(-6)? (STDERR)     at fileEvaluate (packages/modules-runtime.js:181:9)
W20170105-21:03:28.903(-6)? (STDERR)     at Module.require (packages/modules-runtime.js:106:16)
W20170105-21:03:28.903(-6)? (STDERR)     at Module.Mp.import (/home/vu/.meteor/packages/modules/.<IP_ADDRESS>m2ukcu++os+web.browser+web.cordova/npm/node_modules/reify/lib/runtime.js:70:16)
W20170105-21:03:28.903(-6)? (STDERR)     at meteorInstall.imports.routes.js (imports/routes.js:1:1)
W20170105-21:03:28.903(-6)? (STDERR)     at fileEvaluate (packages/modules-runtime.js:181:9)
W20170105-21:03:28.903(-6)? (STDERR)     at Module.require (packages/modules-runtime.js:106:16)
W20170105-21:03:28.903(-6)? (STDERR)     at Module.Mp.import (/home/vu/.meteor/packages/modules/.<IP_ADDRESS>m2ukcu++os+web.browser+web.cordova/npm/node_modules/reify/lib/runtime.js:70:16)
W20170105-21:03:28.903(-6)? (STDERR)     at meteorInstall.im

Sorry. I cannot really help this. I assume this is on meteor? Maybe the import wasn't correct?

ok yeah I guess it's something with npm or node or meteor or babel. Just thought i'd post instead it had come up before for someone.
Cheers

@Maxhodges thanks for the understanding. You can post the code you used to import react-container-query, maybe someone or I can spot the problem.

OK someone was importing like this
import {applyContainerQuery} from 'react-container-query';
but I've changed it to this
import {applyContainerQuery} from 'react-container-query';
now the error goes away!
I get a different error now, but probably unrelated
import {applyContainerQuery} from 'react-container-query';
...

Cheers!

like this with shrinkwrap

"react-container-query": {
     "version": "0.6.1",
     "from"<EMAIL_ADDRESS><0.7.0",
     "resolved": "https://registry.npmjs.org/react-container-query/-/react-container-query-0.6.1.tgz"
   },

The newest version is 0.8.0 now, it contains breaking changes since 0.6. So the doc might be different.

I'm closing this because I haven't receive any updates, and I don't use meteor myself. Please reopen if you have problem.


Log file filling up with errors

I have reinstalled Karabiner Elements 0.91.13 on OSX 10.12.6 to fix an issue where the config files weren’t sticking. Now I see an infinite stream of this in the Log:
 [error] [grabber] IOConnectCallStructMethod error: kIOReturnError (-536870212) @ bool krbn::virtual_hid_device_client::call_method(std::function<IOReturn ()>)

I had this too and was able to stop it by disabling several devices of unknown provenance (I don't know what any of the unchecked devices in the screenshot are supposed to be, as I only have one connected keyboard) in the preferences. Maybe try that?

I restarted and it went away. No more overflowing log file.

I just updated to .16 and because the Complex Modifications (read: Hyper Key) weren’t sticking again, and my console is still filling with
[[2017-09-12 14:42:12.996] [error] [grabber] IOConnectCallStructMethod error: kIOReturnError (-536870212) @ bool krbn::virtual_hid_device_client::call_method(std::function<IOReturn ()>)


Hello,One trace shows different images on two pages?

One trace in main page,show

But,in server map,show

Picture 1 show dubbo-profiderfunc10000 call dubbo-providerfunc20000 4 times,but Picture 1 show dubbo-profiderfunc10000 call dubbo-providerfunc20000 3 times and dubbo-providerfunc20000 call itself 1 time.
Actually,the picture 2 show the correct trace.

Hello, @edoc1991
I don't know much about dubbo.
But I can tell you that the first server-map includes all 7 transactions and the second server-map only shows the map of the selected transaction.


Document recent EXPLAIN changes.

This includes:

Query texts are logged when the VERBOSE flag is specified.
EXPLAIN ANALYZE contains statistics about intermediate result files.

@pykello thanks a lot!
I scanned to see if we have other examples of verbose or analyze that need updating, but it looks good. Merging!