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  1. == 2019-05-09 15:25:45,564 easyblock.py:279 INFO This is EasyBuild 3.9.1.dev0 (framework: 3.9.1.dev0, easyblocks: 3.9.1.dev0) on host nic72.
  2. == 2019-05-09 15:25:45,564 easyblock.py:285 INFO This is easyblock Tarball from module easybuild.easyblocks.generic.tarball (/dev/shm/vsc10042/2090320/eb_sandbox_20190509_14-56-22_40FHR/easybuild-easyblocks/easybuild/easyblocks/generic/tarball.py)
  3. == 2019-05-09 15:25:45,564 easyblock.py:840 INFO Build dir set to /dev/shm/vsc10042/2090320/eb_sandbox_20190509_14-56-22_40FHR/prokka/1.13.4/foss-2018b
  4. == 2019-05-09 15:25:45,564 easyblock.py:900 INFO Software install dir set to /dev/shm/vsc10042/2090320/eb_sandbox_20190509_14-56-22_40FHR/software/prokka/1.13.4-foss-2018b
  5. == 2019-05-09 15:25:45,565 easyblock.py:905 INFO Module install dir set to /dev/shm/vsc10042/2090320/eb_sandbox_20190509_14-56-22_40FHR/modules/all
  6. == 2019-05-09 15:25:45,565 easyblock.py:264 INFO Init completed for application name prokka version 1.13.4
  7. == 2019-05-09 15:25:45,565 easyblock.py:2999 INFO Obtained application instance of for prokka (easyblock: Tarball)
  8. == 2019-05-09 15:25:45,565 one.py:146 INFO Skipping reformatting value for parameter 'toolchain'
  9. == 2019-05-09 15:25:45,568 filetools.py:1207 INFO Creating directory /dev/shm/vsc10042/2090320/eb-qF5pjw/reprod_20190509152545_1961 (parents: True, set_gid: False, sticky: False)
  10. == 2019-05-09 15:25:45,568 easyblock.py:3169 INFO Dumped easyconfig instance to /dev/shm/vsc10042/2090320/eb-qF5pjw/reprod_20190509152545_1961/prokka-1.13.4-foss-2018b.eb
  11. == 2019-05-09 15:25:45,568 filetools.py:1207 INFO Creating directory /dev/shm/vsc10042/2090320/eb-qF5pjw/reprod_20190509152545_1961/easyblocks (parents: True, set_gid: False, sticky: False)
  12. == 2019-05-09 15:25:45,568 filetools.py:1677 INFO /dev/shm/vsc10042/2090320/eb_sandbox_20190509_14-56-22_40FHR/easybuild-easyblocks/easybuild/easyblocks/generic/tarball.py copied to /dev/shm/vsc10042/2090320/eb-qF5pjw/reprod_20190509152545_1961/easyblocks/tarball.py
  13. == 2019-05-09 15:25:45,568 easyblock.py:3184 INFO Dumped easyblock tarball.py required for reproduction to /dev/shm/vsc10042/2090320/eb-qF5pjw/reprod_20190509152545_1961/easyblocks
  14. == 2019-05-09 15:25:45,568 easyblock.py:1599 INFO Number of iterations to perform for central part of installation procedure: 1
  15. == 2019-05-09 15:25:45,568 build_log.py:252 INFO building and installing prokka/1.13.4-foss-2018b...
  16. == 2019-05-09 15:25:45,569 build_log.py:252 INFO fetching files...
  17. == 2019-05-09 15:25:45,569 easyblock.py:2779 INFO Starting fetch step
  18. == 2019-05-09 15:25:45,569 easyblock.py:2785 INFO Running method fetch_step part of step fetch
  19. == 2019-05-09 15:25:45,569 easyblock.py:1680 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version
  20. == 2019-05-09 15:25:45,569 filetools.py:394 INFO Command eb found at /dev/shm/vsc10042/2090320/eb_sandbox_20190509_14-56-22_40FHR/easybuild-framework/eb
  21. == 2019-05-09 15:25:45,584 easyblock.py:668 INFO Found file v1.13.4.zip at /apps/gent/source/p/prokka/v1.13.4.zip
  22. == 2019-05-09 15:25:45,589 easyblock.py:393 INFO Added sources: [{'path': '/apps/gent/source/p/prokka/v1.13.4.zip', 'cmd': None, 'finalpath': '/dev/shm/vsc10042/2090320/eb_sandbox_20190509_14-56-22_40FHR/prokka/1.13.4/foss-2018b', 'name': 'v1.13.4.zip', 'checksum': 'b5621af689ffb5348eab699a378d45d7566cd63a7da52845229b484af33ea8e2'}]
  23. == 2019-05-09 15:25:45,589 easyblock.py:1721 INFO no patches provided
  24. == 2019-05-09 15:25:47,242 easyblock.py:1731 INFO md5 checksum for /apps/gent/source/p/prokka/v1.13.4.zip: 62028c89ebaad46bbdf3f2da4a0dc898
  25. == 2019-05-09 15:25:47,632 easyblock.py:1731 INFO sha256 checksum for /apps/gent/source/p/prokka/v1.13.4.zip: b5621af689ffb5348eab699a378d45d7566cd63a7da52845229b484af33ea8e2
  26. == 2019-05-09 15:25:47,632 easyblock.py:1766 INFO Checking dirs that need to be created: ['/dev/shm/vsc10042/2090320/eb_sandbox_20190509_14-56-22_40FHR/software/prokka/1.13.4-foss-2018b', '/dev/shm/vsc10042/2090320/eb_sandbox_20190509_14-56-22_40FHR/modules/all/prokka', '/dev/shm/vsc10042/2090320/eb_sandbox_20190509_14-56-22_40FHR/modules/bio/prokka']
  27. == 2019-05-09 15:25:47,632 filetools.py:1207 INFO Creating directory /dev/shm/vsc10042/2090320/eb_sandbox_20190509_14-56-22_40FHR/software/prokka/1.13.4-foss-2018b (parents: True, set_gid: False, sticky: False)
  28. == 2019-05-09 15:25:47,633 filetools.py:1207 INFO Creating directory /dev/shm/vsc10042/2090320/eb_sandbox_20190509_14-56-22_40FHR/modules/all/prokka (parents: True, set_gid: False, sticky: False)
  29. == 2019-05-09 15:25:47,633 filetools.py:1207 INFO Creating directory /dev/shm/vsc10042/2090320/eb_sandbox_20190509_14-56-22_40FHR/modules/bio/prokka (parents: True, set_gid: False, sticky: False)
  30. == 2019-05-09 15:25:47,633 build_log.py:252 INFO creating build dir, resetting environment...
  31. == 2019-05-09 15:25:47,633 easyblock.py:2779 INFO Starting ready step
  32. == 2019-05-09 15:25:47,633 easyblock.py:2785 INFO Running method check_readiness_step part of step ready
  33. == 2019-05-09 15:25:47,635 easyblock.py:1618 INFO Setting parallelism: 4
  34. == 2019-05-09 15:25:47,691 environment.py:97 INFO Environment variable LD_LIBRARY_PATH set to (previous value: '')
  35. == 2019-05-09 15:25:47,691 environment.py:97 INFO Environment variable LD_PRELOAD set to (previous value: '')
  36. == 2019-05-09 15:25:47,691 easyblock.py:2785 INFO Running method make_builddir part of step ready
  37. == 2019-05-09 15:25:47,692 filetools.py:1207 INFO Creating directory /dev/shm/vsc10042/2090320/eb_sandbox_20190509_14-56-22_40FHR/prokka/1.13.4/foss-2018b (parents: True, set_gid: False, sticky: False)
  38. == 2019-05-09 15:25:47,692 easyblock.py:2785 INFO Running method reset_env part of step ready
  39. == 2019-05-09 15:25:47,692 easyblock.py:2785 INFO Running method handle_iterate_opts part of step ready
  40. == 2019-05-09 15:25:47,692 build_log.py:252 INFO unpacking...
  41. == 2019-05-09 15:25:47,693 easyblock.py:2779 INFO Starting source step
  42. == 2019-05-09 15:25:47,693 easyblock.py:2785 INFO Running method checksum_step part of step source
  43. == 2019-05-09 15:25:48,070 easyblock.py:1782 INFO Checksum verification for /apps/gent/source/p/prokka/v1.13.4.zip using b5621af689ffb5348eab699a378d45d7566cd63a7da52845229b484af33ea8e2 passed.
  44. == 2019-05-09 15:25:48,070 easyblock.py:2785 INFO Running method extract_step part of step source
  45. == 2019-05-09 15:25:48,070 easyblock.py:1850 INFO Unpacking source v1.13.4.zip
  46. == 2019-05-09 15:25:48,070 run.py:141 INFO Auto-enabling streaming output of 'unzip -qq /apps/gent/source/p/prokka/v1.13.4.zip' command because logging to stdout is enabled
  47. == 2019-05-09 15:25:48,071 run.py:192 INFO running cmd: unzip -qq /apps/gent/source/p/prokka/v1.13.4.zip
  48. == 2019-05-09 15:25:51,072 build_log.py:252 INFO patching...
  49. == 2019-05-09 15:25:51,072 easyblock.py:2779 INFO Starting patch step
  50. == 2019-05-09 15:25:51,072 easyblock.py:2785 INFO Running method patch_step part of step patch
  51. == 2019-05-09 15:25:51,072 build_log.py:252 INFO preparing...
  52. == 2019-05-09 15:25:51,072 easyblock.py:2779 INFO Starting prepare step
  53. == 2019-05-09 15:25:51,073 easyblock.py:2785 INFO Running method prepare_step part of step prepare
  54. == 2019-05-09 15:25:51,867 environment.py:97 INFO Environment variable LD_LIBRARY_PATH set to (previous value: '')
  55. == 2019-05-09 15:25:51,867 environment.py:97 INFO Environment variable LD_PRELOAD set to (previous value: '')
  56. == 2019-05-09 15:25:52,550 environment.py:97 INFO Environment variable LD_LIBRARY_PATH set to (previous value: '')
  57. == 2019-05-09 15:25:52,551 environment.py:97 INFO Environment variable LD_PRELOAD set to (previous value: '')
  58. == 2019-05-09 15:25:53,285 environment.py:97 INFO Environment variable LD_LIBRARY_PATH set to /apps/brussel/CO7/broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/lib:/apps/brussel/CO7/broadwell/software/FFTW/3.3.8-gompi-2018b/lib:/apps/brussel/CO7/broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/lib:/apps/brussel/CO7/broadwell/software/OpenMPI/3.1.1-GCC-7.3.0-2.30/lib:/apps/brussel/CO7/broadwell/software/hwloc/1.11.10-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/numactl/2.0.11-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/zlib/1.2.11-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/binutils/2.30-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/GCCcore/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0:/apps/brussel/CO7/broadwell/software/GCCcore/7.3.0/lib64:/apps/brussel/CO7/broadwell/software/GCCcore/7.3.0/lib (previous value: '/apps/brussel/CO7/broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/lib:/apps/brussel/CO7/broadwell/software/FFTW/3.3.8-gompi-2018b/lib:/apps/brussel/CO7/broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/lib:/apps/brussel/CO7/broadwell/software/OpenMPI/3.1.1-GCC-7.3.0-2.30/lib:/apps/brussel/CO7/broadwell/software/hwloc/1.11.10-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/numactl/2.0.11-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/zlib/1.2.11-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/binutils/2.30-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/GCCcore/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0:/apps/brussel/CO7/broadwell/software/GCCcore/7.3.0/lib64:/apps/brussel/CO7/broadwell/software/GCCcore/7.3.0/lib')
  59. == 2019-05-09 15:25:53,285 environment.py:97 INFO Environment variable LD_PRELOAD set to (previous value: '')
  60. == 2019-05-09 15:25:53,374 environment.py:97 INFO Environment variable LD_LIBRARY_PATH set to /apps/brussel/CO7/broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/lib:/apps/brussel/CO7/broadwell/software/FFTW/3.3.8-gompi-2018b/lib:/apps/brussel/CO7/broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/lib:/apps/brussel/CO7/broadwell/software/OpenMPI/3.1.1-GCC-7.3.0-2.30/lib:/apps/brussel/CO7/broadwell/software/hwloc/1.11.10-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/numactl/2.0.11-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/zlib/1.2.11-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/binutils/2.30-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/GCCcore/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0:/apps/brussel/CO7/broadwell/software/GCCcore/7.3.0/lib64:/apps/brussel/CO7/broadwell/software/GCCcore/7.3.0/lib (previous value: '/apps/brussel/CO7/broadwell/software/ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1/lib:/apps/brussel/CO7/broadwell/software/FFTW/3.3.8-gompi-2018b/lib:/apps/brussel/CO7/broadwell/software/OpenBLAS/0.3.1-GCC-7.3.0-2.30/lib:/apps/brussel/CO7/broadwell/software/OpenMPI/3.1.1-GCC-7.3.0-2.30/lib:/apps/brussel/CO7/broadwell/software/hwloc/1.11.10-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/numactl/2.0.11-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/zlib/1.2.11-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/binutils/2.30-GCCcore-7.3.0/lib:/apps/brussel/CO7/broadwell/software/GCCcore/7.3.0/lib/gcc/x86_64-pc-linux-gnu/7.3.0:/apps/brussel/CO7/broadwell/software/GCCcore/7.3.0/lib64:/apps/brussel/CO7/broadwell/software/GCCcore/7.3.0/lib')
  61. == 2019-05-09 15:25:53,374 environment.py:97 INFO Environment variable LD_PRELOAD set to (previous value: '')
  62. == 2019-05-09 15:26:07,842 build_log.py:163 ERROR EasyBuild crashed with an error (at ?:124 in __init__): Module command 'module load BioPerl/1.7.2-foss-2018b-Perl-5.28.0' failed with exit code 1; stderr: Lmod has detected the following error: The following module(s) are unknown:
  63. "Perl/5.28.0-GCCcore-7.3.0"
  64.  
  65. Please check the spelling or version number. Also try "module spider ..."
  66. It is also possible your cache file is out-of-date; it may help to try:
  67. $ module --ignore-cache load "Perl/5.28.0-GCCcore-7.3.0"
  68.  
  69. Also make sure that all modulefiles written in TCL start with the string
  70. #%Module
  71.  
  72. If you don't understand the warning or error, contact the helpdesk at
  73. hpc@vub.ac.be
  74. Executing this command requires loading "Perl/5.28.0-GCCcore-7.3.0" which
  75. failed while processing the following module(s):
  76.  
  77. Module fullname Module Filename
  78. --------------- ---------------
  79. BioPerl/1.7.2-foss-2018b-Perl-5.28.0 /apps/brussel/CO7/broadwell/modules/2018b/all/BioPerl/1.7.2-foss-2018b-Perl-5.28.0.luaExecuting this command requires loading "Perl/5.28.0-GCCcore-7.3.0" which
  80. failed while processing the following module(s):
  81.  
  82. Module fullname Module Filename
  83. --------------- ---------------
  84. XML-LibXML/2.0132-GCCcore-7.3.0-Perl-5.28.0 /apps/brussel/CO7/broadwell/modules/2018b/all/XML-LibXML/2.0132-GCCcore-7.3.0-Perl-5.28.0.lua
  85. BioPerl/1.7.2-foss-2018b-Perl-5.28.0 /apps/brussel/CO7/broadwell/modules/2018b/all/BioPerl/1.7.2-foss-2018b-Perl-5.28.0.lua
  86.  
  87.  
  88. ; stdout:
  89. false
  90. (at easybuild/tools/modules.py:738 in run_module)
  91. == 2019-05-09 15:26:07,844 easyblock.py:3029 WARNING build failed (first 300 chars): Module command 'module load BioPerl/1.7.2-foss-2018b-Perl-5.28.0' failed with exit code 1; stderr: Lmod has detected the following error: The following module(s) are unknown:
  92. "Perl/5.28.0-GCCcore-7.3.0"
  93.  
  94. Please check the spelling or version number. Also try "module spider ..."
  95. It is also possible yo
  96. == 2019-05-09 15:26:07,844 easyblock.py:294 INFO Closing log for application name prokka version 1.13.4
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