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  1. == 2019-03-14 14:25:31,405 easyblock.py:273 INFO This is EasyBuild 3.9.0.dev0-r068366858a642595b1b0279e1ce0712534b74ffe (framework: 3.9.0.dev0-r068366858a642595b1b0279e1ce0712534b74ffe, easyblocks: 3.9.0.dev0-r6099ff6ae85bb249b79df540c3e5ff5e382b29cc) on host cermis.
  2. == 2019-03-14 14:25:31,405 easyblock.py:279 INFO This is easyblock MakeCp from module easybuild.easyblocks.generic.makecp (/opt/easybuild/EB-develop/easybuild-easyblocks/easybuild/easyblocks/generic/makecp.pyo)
  3. == 2019-03-14 14:25:31,405 easyblock.py:833 INFO Build dir set to /tmp/bmtagger/3.101/foss-2018b
  4. == 2019-03-14 14:25:31,405 config.py:506 DEBUG software install path as specified by 'installpath_software': /opt/easybuild/software
  5. == 2019-03-14 14:25:31,406 easyconfig.py:1995 DEBUG Determining software installation subdir for <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x7fa5377247d0>
  6. == 2019-03-14 14:25:31,406 toolchain.py:445 DEBUG Toolchain definition for {'dummy': True, 'versionsuffix': '', 'version': '2018b', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'foss', 'full_mod_name': 'Core/foss/2018b', 'hidden': False, 'parsed': True, 'short_mod_name': 'foss/2018b'}: {'LAPACK': ['OpenBLAS'], 'SCALAPACK': ['ScaLAPACK'], 'BLAS': ['OpenBLAS'], 'FFT': ['FFTW'], 'BLACS': ['BLACS'], 'MPI': ['OpenMPI'], 'COMPILER': ['GCC']}
  7. == 2019-03-14 14:25:31,406 toolchain.py:59 DEBUG Obtained details for 'GCC' in toolchain '{'dummy': True, 'versionsuffix': '', 'version': '2018b', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'foss', 'full_mod_name': 'Core/foss/2018b', 'hidden': False, 'parsed': True, 'short_mod_name': 'foss/2018b'}' from cache
  8. == 2019-03-14 14:25:31,406 toolchain.py:106 DEBUG Found compilers [{'external_module_metadata': {}, 'full_mod_name': 'Core/GCC/7.3.0-2.30', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'GCC', 'dummy': True, 'short_mod_name': 'GCC/7.3.0-2.30', 'external_module': False, 'versionsuffix': '', 'version': '7.3.0-2.30', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}] for toolchain foss ({'dummy': True, 'versionsuffix': '', 'version': '2018b', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'foss', 'full_mod_name': 'Core/foss/2018b', 'hidden': False, 'parsed': True, 'short_mod_name': 'foss/2018b'})
  9. == 2019-03-14 14:25:31,407 toolchain.py:445 DEBUG Toolchain definition for {'dummy': True, 'versionsuffix': '', 'version': '2018b', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'foss', 'full_mod_name': 'Core/foss/2018b', 'hidden': False, 'parsed': True, 'short_mod_name': 'foss/2018b'}: {'LAPACK': ['OpenBLAS'], 'SCALAPACK': ['ScaLAPACK'], 'BLAS': ['OpenBLAS'], 'FFT': ['FFTW'], 'BLACS': ['BLACS'], 'MPI': ['OpenMPI'], 'COMPILER': ['GCC']}
  10. == 2019-03-14 14:25:31,407 toolchain.py:59 DEBUG Obtained details for 'OpenMPI' in toolchain '{'dummy': True, 'versionsuffix': '', 'version': '2018b', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'foss', 'full_mod_name': 'Core/foss/2018b', 'hidden': False, 'parsed': True, 'short_mod_name': 'foss/2018b'}' from cache
  11. == 2019-03-14 14:25:31,407 easyconfig.py:2001 DEBUG Obtained subdir MPI/GCC/7.3.0-2.30/OpenMPI/3.1.1/bmtagger/3.101
  12. == 2019-03-14 14:25:31,407 easyblock.py:878 INFO Software install dir set to /opt/easybuild/software/MPI/GCC/7.3.0-2.30/OpenMPI/3.1.1/bmtagger/3.101
  13. == 2019-03-14 14:25:31,407 config.py:506 DEBUG modules install path as specified by 'installpath_modules': /opt/easybuild/modules
  14. == 2019-03-14 14:25:31,407 easyblock.py:883 INFO Module install dir set to /opt/easybuild/modules/all
  15. == 2019-03-14 14:25:31,407 easyblock.py:258 INFO Init completed for application name bmtagger version 3.101
  16. == 2019-03-14 14:25:31,408 easyblock.py:2840 INFO Obtained application instance of for bmtagger (easyblock: MakeCp)
  17. == 2019-03-14 14:25:31,408 easyblock.py:2853 DEBUG Skip set to False
  18. == 2019-03-14 14:25:31,408 templates.py:156 DEBUG config: <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x7fa5377247d0>
  19. == 2019-03-14 14:25:31,408 templates.py:183 DEBUG version found in easyconfig is 3.101
  20. == 2019-03-14 14:25:31,408 templates.py:227 DEBUG name: bitbucket_account, config: %(namelower)s
  21. == 2019-03-14 14:25:31,408 templates.py:227 DEBUG name: github_account, config: %(namelower)s
  22. == 2019-03-14 14:25:31,409 templates.py:227 DEBUG name: name, config: bmtagger
  23. == 2019-03-14 14:25:31,409 templates.py:227 DEBUG name: version, config: 3.101
  24. == 2019-03-14 14:25:31,409 templates.py:227 DEBUG name: versionsuffix, config:
  25. == 2019-03-14 14:25:31,409 templates.py:227 DEBUG name: versionprefix, config:
  26. == 2019-03-14 14:25:31,409 templates.py:156 DEBUG config: <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x7fa5377247d0>
  27. == 2019-03-14 14:25:31,409 templates.py:183 DEBUG version found in easyconfig is 3.101
  28. == 2019-03-14 14:25:31,409 templates.py:227 DEBUG name: bitbucket_account, config: %(namelower)s
  29. == 2019-03-14 14:25:31,409 templates.py:227 DEBUG name: github_account, config: %(namelower)s
  30. == 2019-03-14 14:25:31,410 templates.py:227 DEBUG name: name, config: bmtagger
  31. == 2019-03-14 14:25:31,410 templates.py:227 DEBUG name: version, config: 3.101
  32. == 2019-03-14 14:25:31,410 templates.py:227 DEBUG name: versionsuffix, config:
  33. == 2019-03-14 14:25:31,410 templates.py:227 DEBUG name: versionprefix, config:
  34. == 2019-03-14 14:25:31,410 one.py:145 INFO Skipping reformatting value for parameter 'toolchain'
  35. == 2019-03-14 14:25:31,410 one.py:145 INFO Skipping reformatting value for parameter 'toolchainopts'
  36. == 2019-03-14 14:25:31,412 easyconfig.py:933 DEBUG Dumped easyconfig: easyblock = 'MakeCp'
  37.  
  38. name = 'bmtagger'
  39. version = '3.101'
  40.  
  41. homepage = 'ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/'
  42. description = "Best Match Tagger for removing human reads from metagenomics datasets"
  43.  
  44. toolchain = {'name': 'foss', 'version': '2018b'}
  45. toolchainopts = {'cstd': 'c++98'}
  46.  
  47. source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/%(name)s/']
  48. sources = [{'download_filename': 'bmtools.tar.gz', 'filename': 'bmtools-%(version)s.tar.gz'}]
  49. patches = ['%(name)s-%(version)s_fix-hardcoding.patch']
  50. checksums = [
  51. '81ac6d47aa478c2e0ef760f15b9c71e1c52430c96a2c8d064667ebbef148e873', # bmtools-%(version)s.tar.gz
  52. '8779edd4dab6c0a3bc1bbcc5f265d61ccfd685972a0570bc3a84f5a131972195', # %(name)s-3.101_fix-hardcoding.patch
  53. ]
  54.  
  55. dependencies = [
  56. ('BLAST+', '2.7.1'),
  57. ('SRPRISM', '3.0.0'),
  58. ]
  59.  
  60. files_to_copy = [(['%(name)s/bmfilter', '%(name)s/%(name)s.sh', '%(name)s/bmtool', '%(name)s/extract_fullseq'], 'bin')]
  61. sanity_check_commands = ['bmtool -h', 'bmfilter -h']
  62.  
  63. sanity_check_paths = {
  64. 'files': ['bin/bmfilter', 'bin/%(name)s.sh', 'bin/bmtool', 'bin/extract_fullseq'],
  65. 'dirs': [],
  66. }
  67.  
  68. moduleclass = 'bio'
  69.  
  70. == 2019-03-14 14:25:31,412 filetools.py:1200 INFO Creating directory /tmp/eb-ypvdUu/reprod_20190314142531_17164 (parents: True, set_gid: False, sticky: False)
  71. == 2019-03-14 14:25:31,412 easyblock.py:3010 INFO Dumped easyconfig instance to /tmp/eb-ypvdUu/reprod_20190314142531_17164/bmtagger-3.101-foss-2018b.eb
  72. == 2019-03-14 14:25:31,413 filetools.py:1200 INFO Creating directory /tmp/eb-ypvdUu/reprod_20190314142531_17164/easyblocks (parents: True, set_gid: False, sticky: False)
  73. == 2019-03-14 14:25:31,413 filetools.py:1670 INFO /opt/easybuild/EB-develop/easybuild-easyblocks/easybuild/easyblocks/generic/makecp.py copied to /tmp/eb-ypvdUu/reprod_20190314142531_17164/easyblocks/makecp.py
  74. == 2019-03-14 14:25:31,413 easyblock.py:3025 INFO Dumped easyblock makecp.py required for reproduction to /tmp/eb-ypvdUu/reprod_20190314142531_17164/easyblocks
  75. == 2019-03-14 14:25:31,413 filetools.py:1228 DEBUG Not creating existing path /tmp/eb-ypvdUu/reprod_20190314142531_17164/easyblocks
  76. == 2019-03-14 14:25:31,413 filetools.py:1670 INFO /opt/easybuild/EB-develop/easybuild-easyblocks/easybuild/easyblocks/generic/configuremake.py copied to /tmp/eb-ypvdUu/reprod_20190314142531_17164/easyblocks/configuremake.py
  77. == 2019-03-14 14:25:31,413 easyblock.py:3025 INFO Dumped easyblock configuremake.py required for reproduction to /tmp/eb-ypvdUu/reprod_20190314142531_17164/easyblocks
  78. == 2019-03-14 14:25:31,414 build_log.py:252 INFO building and installing MPI/GCC/7.3.0-2.30/OpenMPI/3.1.1/bmtagger/3.101...
  79. == 2019-03-14 14:25:31,414 easyblock.py:2608 DEBUG Not skipping fetch step (skippable: False, skip: None, skipsteps: [], module_only: False, force: True
  80. == 2019-03-14 14:25:31,414 build_log.py:252 INFO fetching files...
  81. == 2019-03-14 14:25:31,414 easyblock.py:2616 INFO Starting fetch step
  82. == 2019-03-14 14:25:31,414 templates.py:156 DEBUG config: <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x7fa5377247d0>
  83. == 2019-03-14 14:25:31,414 templates.py:183 DEBUG version found in easyconfig is 3.101
  84. == 2019-03-14 14:25:31,414 templates.py:227 DEBUG name: bitbucket_account, config: %(namelower)s
  85. == 2019-03-14 14:25:31,415 templates.py:227 DEBUG name: github_account, config: %(namelower)s
  86. == 2019-03-14 14:25:31,415 templates.py:227 DEBUG name: name, config: bmtagger
  87. == 2019-03-14 14:25:31,415 templates.py:227 DEBUG name: version, config: 3.101
  88. == 2019-03-14 14:25:31,415 templates.py:227 DEBUG name: versionsuffix, config:
  89. == 2019-03-14 14:25:31,415 templates.py:227 DEBUG name: versionprefix, config:
  90. == 2019-03-14 14:25:31,415 templates.py:156 DEBUG config: <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x7fa5377247d0>
  91. == 2019-03-14 14:25:31,415 templates.py:183 DEBUG version found in easyconfig is 3.101
  92. == 2019-03-14 14:25:31,415 templates.py:227 DEBUG name: bitbucket_account, config: %(namelower)s
  93. == 2019-03-14 14:25:31,416 templates.py:227 DEBUG name: github_account, config: %(namelower)s
  94. == 2019-03-14 14:25:31,416 templates.py:227 DEBUG name: name, config: bmtagger
  95. == 2019-03-14 14:25:31,416 templates.py:227 DEBUG name: version, config: 3.101
  96. == 2019-03-14 14:25:31,416 templates.py:227 DEBUG name: versionsuffix, config:
  97. == 2019-03-14 14:25:31,416 templates.py:227 DEBUG name: versionprefix, config:
  98. == 2019-03-14 14:25:31,416 easyblock.py:2622 INFO Running method fetch_step part of step fetch
  99. == 2019-03-14 14:25:31,416 easyblock.py:1597 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version
  100. == 2019-03-14 14:25:31,417 filetools.py:394 INFO Command eb found at /opt/easybuild/EB-develop/easybuild-framework/eb
  101. == 2019-03-14 14:25:31,417 tools.py:265 DEBUG Also considering installation prefix /opt/easybuild/EB-develop...
  102. == 2019-03-14 14:25:31,417 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /opt/easybuild/ebfiles_repo/easybuild/easyconfigs
  103. == 2019-03-14 14:25:31,417 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /opt/easybuild/EB-develop/easybuild-easyconfigs/easybuild/easyconfigs/easybuild/easyconfigs
  104. == 2019-03-14 14:25:31,417 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-ypvdUu/files_pr7890/easybuild/easyconfigs
  105. == 2019-03-14 14:25:31,417 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python2.7/dist-packages/git/ext/gitdb/easybuild/easyconfigs
  106. == 2019-03-14 14:25:31,418 tools.py:270 DEBUG Checking for easybuild/easyconfigs at easybuild/easyconfigs
  107. == 2019-03-14 14:25:31,418 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /opt/easybuild/EB-develop/easybuild-easyconfigs/easybuild/easyconfigs
  108. == 2019-03-14 14:25:31,418 tools.py:274 DEBUG Added /opt/easybuild/EB-develop/easybuild-easyconfigs/easybuild/easyconfigs to list of paths for easybuild/easyconfigs
  109. == 2019-03-14 14:25:31,418 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /opt/easybuild/EB-develop/easybuild-easyblocks/easybuild/easyconfigs
  110. == 2019-03-14 14:25:31,418 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /opt/easybuild/EB-develop/easybuild-framework/easybuild/easyconfigs
  111. == 2019-03-14 14:25:31,418 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /opt/easybuild/EB-develop/vsc-install/lib/easybuild/easyconfigs
  112. == 2019-03-14 14:25:31,418 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /opt/easybuild/EB-develop/vsc-base/lib/easybuild/easyconfigs
  113. == 2019-03-14 14:25:31,418 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python2.7/easybuild/easyconfigs
  114. == 2019-03-14 14:25:31,419 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python2.7/plat-x86_64-linux-gnu/easybuild/easyconfigs
  115. == 2019-03-14 14:25:31,419 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python2.7/lib-tk/easybuild/easyconfigs
  116. == 2019-03-14 14:25:31,419 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python2.7/lib-old/easybuild/easyconfigs
  117. == 2019-03-14 14:25:31,419 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python2.7/lib-dynload/easybuild/easyconfigs
  118. == 2019-03-14 14:25:31,419 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib/python2.7/dist-packages/easybuild/easyconfigs
  119. == 2019-03-14 14:25:31,419 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python2.7/dist-packages/easybuild/easyconfigs
  120. == 2019-03-14 14:25:31,419 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python2.7/dist-packages/gitdb/ext/smmap/easybuild/easyconfigs
  121. == 2019-03-14 14:25:31,419 tools.py:270 DEBUG Checking for easybuild/easyconfigs at /opt/easybuild/EB-develop/easybuild/easyconfigs
  122. == 2019-03-14 14:25:31,420 filetools.py:1200 INFO Creating directory /opt/easybuild/sources/b/bmtagger (parents: True, set_gid: False, sticky: False)
  123. == 2019-03-14 14:25:31,420 easyblock.py:732 DEBUG Trying to download file bmtools-3.101.tar.gz from ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz to /opt/easybuild/sources/b/bmtagger/bmtools-3.101.tar.gz ...
  124. == 2019-03-14 14:25:31,420 filetools.py:494 DEBUG Trying to download bmtools-3.101.tar.gz from ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz to /opt/easybuild/sources/b/bmtagger/bmtools-3.101.tar.gz
  125. == 2019-03-14 14:25:31,420 filetools.py:501 DEBUG Using timeout of 10 seconds for initiating download
  126. == 2019-03-14 14:25:31,420 filetools.py:1228 DEBUG Not creating existing path /opt/easybuild/sources/b/bmtagger
  127. == 2019-03-14 14:25:42,261 filetools.py:545 WARNING IOError occurred while trying to download ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz to /opt/easybuild/sources/b/bmtagger/bmtools-3.101.tar.gz: <urlopen error ftp error: timed out>
  128. == 2019-03-14 14:25:42,262 filetools.py:559 INFO Attempt 1 of downloading ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz to /opt/easybuild/sources/b/bmtagger/bmtools-3.101.tar.gz failed, trying again...
  129. == 2019-03-14 14:25:52,774 filetools.py:545 WARNING IOError occurred while trying to download ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz to /opt/easybuild/sources/b/bmtagger/bmtools-3.101.tar.gz: <urlopen error ftp error: timed out>
  130. == 2019-03-14 14:25:52,775 filetools.py:559 INFO Attempt 2 of downloading ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz to /opt/easybuild/sources/b/bmtagger/bmtools-3.101.tar.gz failed, trying again...
  131. == 2019-03-14 14:26:03,148 filetools.py:545 WARNING IOError occurred while trying to download ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz to /opt/easybuild/sources/b/bmtagger/bmtools-3.101.tar.gz: <urlopen error ftp error: timed out>
  132. == 2019-03-14 14:26:03,148 filetools.py:565 WARNING Download of ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz to /opt/easybuild/sources/b/bmtagger/bmtools-3.101.tar.gz failed, done trying
  133. == 2019-03-14 14:26:03,149 build_log.py:163 ERROR EasyBuild crashed with an error (at easybuild/EB-develop/vsc-base/lib/vsc/utils/exceptions.py:124 in __init__): Couldn't find file bmtools-3.101.tar.gz anywhere, and downloading it didn't work either... Paths attempted (in order): /tmp/eb-ypvdUu/files_pr7890/b/bmtagger/b/bmtagger/bmtools-3.101.tar.gz, /tmp/eb-ypvdUu/files_pr7890/b/bmtagger/bmtagger/bmtools-3.101.tar.gz, /tmp/eb-ypvdUu/files_pr7890/b/bmtagger/bmtools-3.101.tar.gz, /opt/easybuild/ebfiles_repo/b/bmtagger/bmtools-3.101.tar.gz, /opt/easybuild/ebfiles_repo/bmtagger/bmtools-3.101.tar.gz, /opt/easybuild/ebfiles_repo/bmtools-3.101.tar.gz, /opt/easybuild/EB-develop/easybuild-easyconfigs/easybuild/easyconfigs/b/bmtagger/bmtools-3.101.tar.gz, /opt/easybuild/EB-develop/easybuild-easyconfigs/easybuild/easyconfigs/bmtagger/bmtools-3.101.tar.gz, /opt/easybuild/EB-develop/easybuild-easyconfigs/easybuild/easyconfigs/bmtools-3.101.tar.gz, /tmp/eb-ypvdUu/files_pr7890/b/bmtagger/bmtools-3.101.tar.gz, /tmp/eb-ypvdUu/files_pr7890/bmtagger/bmtools-3.101.tar.gz, /tmp/eb-ypvdUu/files_pr7890/bmtools-3.101.tar.gz, /opt/easybuild/EB-develop/easybuild-easyconfigs/easybuild/easyconfigs/b/bmtagger/bmtools-3.101.tar.gz, /opt/easybuild/EB-develop/easybuild-easyconfigs/easybuild/easyconfigs/bmtagger/bmtools-3.101.tar.gz, /opt/easybuild/EB-develop/easybuild-easyconfigs/easybuild/easyconfigs/bmtools-3.101.tar.gz, /opt/easybuild/sources/b/bmtagger/bmtools-3.101.tar.gz, /opt/easybuild/sources/bmtagger/bmtools-3.101.tar.gz, /opt/easybuild/sources/bmtools-3.101.tar.gz, ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtools.tar.gz (at easybuild/EB-develop/easybuild-framework/easybuild/framework/easyblock.py:755 in obtain_file)
  134. == 2019-03-14 14:26:03,150 easyblock.py:2870 WARNING build failed (first 300 chars): Couldn't find file bmtools-3.101.tar.gz anywhere, and downloading it didn't work either... Paths attempted (in order): /tmp/eb-ypvdUu/files_pr7890/b/bmtagger/b/bmtagger/bmtools-3.101.tar.gz, /tmp/eb-ypvdUu/files_pr7890/b/bmtagger/bmtagger/bmtools-3.101.tar.gz, /tmp/eb-ypvdUu/files_pr7890/b/bmtagger/
  135. == 2019-03-14 14:26:03,150 easyblock.py:288 INFO Closing log for application name bmtagger version 3.101
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