
Clock type: CPU
Ordered by: totaltime, desc

name                                                                                                                      ncall       tsub      ttot      tavg      
/home/johannes/scms/snakemake/snakemake/__init__.py:40 snakemake                                                          1           0.000000  105.2874  105.2874
/home/johannes/scms/snakemake/snakemake/workflow.py:475 Workflow.execute                                                  1           0.000000  103.6026  103.6026
/home/johannes/scms/snakemake/snakemake/dag.py:171 DAG.init                                                               1           0.063296  44.32311  44.32311
/home/johannes/scms/snakemake/snakemake/scheduler.py:392 JobScheduler.schedule                                            1           0.003332  43.46730  43.46730
/home/johannes/scms/snakemake/snakemake/scheduler.py:471 JobScheduler.run                                                 10          0.000000  43.28077  4.328077
/home/johannes/scms/snakemake/snakemake/executors/__init__.py:123 DryrunExecutor.run_jobs                                 10          0.053250  43.28077  4.328077
/home/johannes/scms/snakemake/snakemake/executors/__init__.py:138 DryrunExecutor.run                                      27002       0.143087  43.22752  0.001601
/home/johannes/scms/snakemake/snakemake/executors/__init__.py:149 DryrunExecutor._run                                     27002       0.136432  31.76622  0.001176
/home/johannes/scms/snakemake/snakemake/executors/__init__.py:170 DryrunExecutor.printjob                                 27002       0.183023  29.86677  0.001106
/home/johannes/scms/snakemake/snakemake/executors/__init__.py:156 DryrunExecutor.printjob                                 27002       0.036610  29.54733  0.001094
/home/johannes/scms/snakemake/snakemake/jobs.py:909 Job.log_info                                                          27002       0.788440  29.51072  0.001093
/home/johannes/scms/snakemake/snakemake/dag.py:697 DAG.update                                                             36001/1     0.492546  23.61831  0.000656
/home/johannes/scms/snakemake/snakemake/dag.py:785 DAG.update_                                                            36001/1     0.696418  23.58500  0.000655
/home/johannes/scms/snakemake/snakemake/logging.py:166 Logger.handler                                                     144010      0.358959  21.82057  0.000152
/home/johannes/scms/snakemake/snakemake/logging.py:274 Logger.text_handler                                                144010      0.782913  21.46161  0.000149
/home/johannes/scms/snakemake/snakemake/logging.py:217 Logger.job_info                                                    27002       0.069891  21.06764  0.000780
/home/johannes/scms/snakemake/snakemake/dag.py:875 DAG.update_needrun                                                     2           1.129070  19.66191  9.830955
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:1424 Logger.info                90008       0.346061  17.45015  0.000194
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:1553 Logger._log                90012       0.392644  17.00756  0.000189
/home/johannes/scms/snakemake/snakemake/dag.py:1458 DAG.collect_potential_dependencies                                    27002       0.386047  13.93144  0.000516
/home/johannes/scms/snakemake/snakemake/dag.py:1568 DAG.file2jobs                                                         36000       0.266249  13.09318  0.000364
/home/johannes/scms/snakemake/snakemake/dag.py:1320 DAG.new_job                                                           36001       0.255472  12.11772  0.000337
/home/johannes/scms/snakemake/snakemake/dag.py:1143 DAG.postprocess                                                       1           0.000000  11.82137  11.82137
/home/johannes/scms/snakemake/snakemake/scheduler.py:495 JobScheduler._proceed                                            27002       1.813197  11.31822  0.000419
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:1579 Logger.handle              90012       0.322805  10.92071  0.000121
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:1633 Logger.callHandlers        90012       0.432601  10.50139  0.000117
..johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:937 ColorizingStreamHandler.handle  180024      0.851785  10.06879  0.000056
/home/johannes/scms/snakemake/snakemake/jobs.py:82 JobFactory.new                                                         27002       0.149802  9.822229  0.000364
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/asyncio/runners.py:8 run                            9001        0.139766  9.684455  0.001076
/home/johannes/scms/snakemake/snakemake/jobs.py:149 Job.__init__                                                          27002       0.539194  9.635812  0.000357
/home/johannes/scms/snakemake/snakemake/io.py:427 _IOFile.exists                                                          207003      0.609529  8.727441  0.000042
/home/johannes/scms/snakemake/snakemake/io.py:225 _IOFile.wrapper                                                         234004      0.992464  8.506260  0.000036
/home/johannes/scms/snakemake/snakemake/scheduler.py:368 JobScheduler.open_jobs                                           18004       7.028315  7.051611  0.000392
/home/johannes/scms/snakemake/snakemake/dag.py:1495 DAG.bfs                                                               648074      3.718099  6.931671  0.000011
..l/opt/miniconda3/envs/snakemake-dev/lib/python3.8/asyncio/base_events.py:580 _UnixSelectorEventLoop.run_until_complete  18002       0.159703  6.856731  0.000381
/home/johannes/scms/snakemake/snakemake/io.py:254 _IOFile.inventory                                                       9000        0.069885  6.274084  0.000697
/home/johannes/scms/snakemake/snakemake/io.py:120 ExistsDict.__contains__                                                 243004      0.566107  6.067750  0.000025
..s/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/asyncio/base_events.py:557 _UnixSelectorEventLoop.run_forever  18002       0.286145  5.978273  0.000332
/home/johannes/scms/snakemake/snakemake/logging.py:326 timestamp                                                          27002       0.185980  5.974592  0.000221
/home/johannes/scms/snakemake/snakemake/dag.py:199 DAG.check_directory_outputs                                            1           0.069963  5.829276  5.829276
..es/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/asyncio/base_events.py:1784 _UnixSelectorEventLoop._run_once  36010       0.329386  5.402622  0.000150
/home/johannes/scms/snakemake/snakemake/jobs.py:554 Job.missing_output                                                    72000       0.769804  5.242754  0.000073
/home/johannes/scms/snakemake/snakemake/io.py:1357 InputFiles.__init__                                                    189035      1.357385  5.064775  0.000027
/home/johannes/scms/snakemake/snakemake/io.py:245 _IOFile.wrapper                                                         252045      0.736431  5.038771  0.000020
/home/johannes/scms/snakemake/snakemake/rules.py:771 Rule.expand_input                                                    27002       0.325341  4.878998  0.000181
/home/johannes/scms/snakemake/snakemake/logging.py:60 ColorizingStreamHandler.emit                                        90012       0.682128  4.801462  0.000053
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:1538 Logger.makeRecord          90012       0.252958  4.719547  0.000052
/home/johannes/scms/snakemake/snakemake/rules.py:690 Rule._apply_wildcards                                                90007       0.535894  4.567020  0.000051
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/asyncio/events.py:79 Handle._run                    36024       0.089853  4.561725  0.000127
/home/johannes/scms/snakemake/snakemake/dag.py:202 <setcomp>                                                              1           0.139887  4.503453  4.503453
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:284 LogRecord.__init__          90012       1.570175  4.466589  0.000050
/home/johannes/scms/snakemake/snakemake/dag.py:358 DAG.needrun_jobs                                                       270031      0.621690  4.282503  0.000016
/home/johannes/scms/snakemake/snakemake/dag.py:898 update_needrun                                                         54004       0.432660  3.804345  0.000070
/home/johannes/scms/snakemake/snakemake/io.py:938 is_flagged                                                              873117      2.020436  3.801445  0.000004
/home/johannes/scms/snakemake/snakemake/io.py:659 _IOFile.apply_wildcards                                                 63001       0.411920  3.734627  0.000059
/home/johannes/scms/snakemake/snakemake/io.py:136 IOCache.mtime_inventory                                                 1           0.000000  3.500229  3.500229
/home/johannes/scms/snakemake/snakemake/io.py:139 IOCache._mtime_inventory                                                1           0.169848  3.496899  3.496899
/home/johannes/scms/snakemake/snakemake/dag.py:884 update_output_mintime                                                  54004       0.189876  3.460878  0.000064
/home/johannes/scms/snakemake/snakemake/dag.py:352 DAG.jobs                                                               324036      0.516355  3.460741  0.000011
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:1174 FileHandler.emit           90012       0.202913  3.384360  0.000038
..johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:1058 ColorizingStreamHandler.flush  180025      0.881863  3.358496  0.000019
/home/johannes/scms/snakemake/snakemake/jobs.py:534 Job.output_mintime                                                    54004       0.175287  3.271002  0.000061
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:1069 FileHandler.emit           90012       0.386019  3.181447  0.000035
/home/johannes/scms/snakemake/snakemake/io.py:315 _IOFile.get_inventory_parent                                            243004      0.515745  3.177102  0.000013
/home/johannes/scms/snakemake/snakemake/common.py:117 lazy_property.__get__                                               684043      1.941845  3.164268  0.000005
/home/johannes/scms/snakemake/snakemake/jobs.py:406 Job.shellcmd                                                          27002       0.063222  2.982556  0.000110
..johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:914 ColorizingStreamHandler.format  180024      0.316137  2.957370  0.000016
/home/johannes/scms/snakemake/snakemake/jobs.py:830 Job.format_wildcards                                                  9001        0.256143  2.919334  0.000324
/home/johannes/scms/snakemake/snakemake/jobs.py:1505 Reason.__bool__                                                      189014      0.633461  2.865297  0.000015
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/posixpath.py:372 abspath                            54016       0.349746  2.816693  0.000052
/home/johannes/scms/snakemake/snakemake/rules.py:874 Rule.expand_output                                                   27002       0.329491  2.792948  0.000103
/home/johannes/scms/snakemake/snakemake/jobs.py:538 <genexpr>                                                             54004       0.209862  2.775986  0.000051
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/posixpath.py:150 dirname                            243015      1.385766  2.661357  0.000011
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:651 Formatter.format            180024      0.687681  2.641233  0.000015
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/posixpath.py:387 realpath                           27001       0.113262  2.618103  0.000097
/home/johannes/scms/snakemake/snakemake/io.py:345 _IOFile.is_remote                                                       540058      0.935844  2.473501  0.000005
/home/johannes/scms/snakemake/snakemake/rules.py:772 concretize_iofile                                                    36000       0.109855  2.323480  0.000065
/home/johannes/scms/snakemake/snakemake/logging.py:283 job_info                                                           162008      0.557339  2.247656  0.000014
/home/johannes/scms/snakemake/snakemake/jobs.py:304 Job.resources                                                         108009      0.206751  1.987082  0.000018
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/string.py:165 Formatter.vformat                     18001       0.029954  1.901534  0.000106
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/string.py:171 Formatter._vformat                    63002/18..  0.570691  1.861601  0.000030
/home/johannes/scms/snakemake/snakemake/jobs.py:673 Job.check_protected_output                                            27002       0.179692  1.763016  0.000065
/home/johannes/scms/snakemake/snakemake/rules.py:932 Rule.expand_resources                                                27002       0.210400  1.757029  0.000065
/home/johannes/scms/snakemake/snakemake/utils.py:382 format                                                               9001        0.186668  1.755108  0.000195
/home/johannes/scms/snakemake/snakemake/io.py:745 _IOFile.__hash__                                                        1755032     1.754161  1.754161  0.000001
/home/johannes/scms/snakemake/snakemake/io.py:187 IOFile                                                                  72010       0.169778  1.624525  0.000023
/home/johannes/scms/snakemake/snakemake/rules.py:875 <genexpr>                                                            54003       0.059892  1.604193  0.000030
/home/johannes/scms/snakemake/snakemake/workflow.py:1047 Workflow.include                                                 1           0.000000  1.501817  1.501817
/home/johannes/scms/snakemake-paper-2020/resources/hello-world/Snakefile:1 <module>                                       1           0.000000  1.458545  1.458545
/home/johannes/scms/snakemake/snakemake/io.py:201 __new__                                                                 72010       0.429406  1.454747  0.000020
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/asyncio/events.py:756 new_event_loop                9001        0.019953  1.437595  0.000160
..local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/asyncio/events.py:650 _UnixDefaultEventLoopPolicy.new_event_loop  9001        0.009988  1.407663  0.000156
/home/johannes/scms/snakemake/snakemake/io.py:1412 Wildcards._add_name                                                    99004       0.296196  1.404271  0.000014
..annes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/asyncio/unix_events.py:53 _UnixSelectorEventLoop.__init__  9001        0.026621  1.397675  0.000155
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/string.py:162 SequenceFormatter.format              9001        0.033271  1.388816  0.000154
..s/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/asyncio/selector_events.py:54 _UnixSelectorEventLoop.__init__  9001        0.086512  1.371054  0.000152
/home/johannes/scms/snakemake/snakemake/jobs.py:674 <lambda>                                                              27001       0.043278  1.340440  0.000050
/home/johannes/scms/snakemake/snakemake/dag.py:1263 DAG.finish                                                            27002       0.216268  1.326658  0.000049
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/collections/__init__.py:608 Counter.update          6           0.000000  1.325822  0.220970
/home/johannes/scms/snakemake/snakemake/dag.py:2034 DAG.stats                                                             18          0.000000  1.325822  0.073657
/home/johannes/scms/snakemake/snakemake/io.py:113 ExistsDict.__getitem__                                                  225003      0.419618  1.319252  0.000006
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/posixpath.py:334 normpath                           54018       0.771046  1.317343  0.000024
/home/johannes/scms/snakemake/snakemake/io.py:453 _IOFile.protected                                                       27001       0.063223  1.297162  0.000048
/home/johannes/scms/snakemake/snakemake/dag.py:1094 DAG.update_ready                                                      27003       0.312929  1.281911  0.000047
/home/johannes/scms/snakemake/snakemake/jobs.py:42 format_files                                                           117005      0.309520  1.251021  0.000011
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/posixpath.py:490 commonpath                         54000       0.526762  1.232553  0.000023
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/posixpath.py:41 _get_sep                            522079      0.812621  1.172249  0.000002
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/posixpath.py:396 _joinrealpath                      27001       0.199846  1.153790  0.000043
/home/johannes/scms/snakemake/snakemake/dag.py:1031 DAG.update_priority                                                   1           0.069945  1.119196  1.119196
/home/johannes/scms/snakemake/snakemake/logging.py:229 Logger.dag_debug                                                   108003      0.299498  1.095698  0.000010
/home/johannes/scms/snakemake/snakemake/rules.py:887 Rule.expand_log                                                      54004       0.213089  1.092129  0.000020
/home/johannes/scms/snakemake/snakemake/dag.py:1338 DAG.cache_job                                                         27002       0.139808  1.085166  0.000040
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/posixpath.py:117 splitext                           90012       0.426838  1.082786  0.000012
/home/johannes/scms/snakemake/snakemake/output_index.py:40 OutputIndex.match                                              36000       0.435974  1.062537  0.000030
/home/johannes/scms/snakemake/snakemake/logging.py:455 format_dict                                                        54004       0.386010  1.054808  0.000020
/home/johannes/scms/snakemake/snakemake/io.py:1421 Wildcards._set_name                                                    99004       0.502469  1.051499  0.000011
/home/johannes/scms/snakemake/snakemake/io.py:879 apply_wildcards                                                         63001       0.103214  1.048539  0.000017
/home/johannes/scms/snakemake/snakemake/dag.py:391 DAG.noneedrun_finished                                                 270021      0.602503  1.022223  0.000004
/home/johannes/scms/snakemake/snakemake/dag.py:225 DAG.update_checkpoint_outputs                                          2           0.000000  0.992680  0.496340
/home/johannes/scms/snakemake/snakemake/dag.py:219 DAG.checkpoint_jobs                                                    2           0.073285  0.992680  0.496340
/home/johannes/scms/snakemake/snakemake/dag.py:226 <genexpr>                                                              2           0.000000  0.992680  0.496340
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:1502 Logger.findCaller          90012       0.445930  0.974651  0.000011
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/posixpath.py:71 join                                108023      0.503006  0.949363  0.000009
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/re.py:203 sub                                       63002       0.159759  0.945325  0.000015
/home/johannes/scms/snakemake/snakemake/io.py:1462 OutputFiles._allitems                                                  126015      0.362797  0.945324  0.000008
/home/johannes/scms/snakemake/snakemake/persistence.py:150 Persistence.lock_warn_only                                     1           0.000000  0.939414  0.939414
/home/johannes/scms/snakemake/snakemake/persistence.py:131 Persistence.locked                                             1           0.096608  0.939414  0.939414
/home/johannes/scms/snakemake/snakemake/dag.py:1560 DAG.rule2job                                                          1           0.000000  0.889195  0.889195
/home/johannes/scms/snakemake/snakemake/dag.py:1155 DAG.handle_pipes                                                      1           0.093266  0.886121  0.886121
/home/johannes/scms/snakemake/snakemake/jobs.py:273 Job.benchmark                                                         207012      0.416224  0.885816  0.000004
/home/johannes/scms/snakemake/snakemake/jobs.py:1032 Job.products                                                         27002       0.113186  0.885441  0.000033
..ohannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:901 ColorizingStreamHandler.release  360051      0.611708  0.884988  0.000002
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:635 Formatter.formatMessage     180024      0.289463  0.858534  0.000005
/home/johannes/scms/snakemake/snakemake/dag.py:1242 DAG.update_checkpoint_dependencies                                    1           0.000000  0.856133  0.856133
/home/johannes/scms/snakemake/snakemake/rules.py:346 Rule.set_input                                                       4           0.000000  0.855991  0.213998
/home/johannes/scms/snakemake/snakemake/rules.py:478 Rule._set_inoutput_item                                              9008/8      0.116571  0.855991  0.000095
/home/johannes/scms/snakemake/snakemake/workflow.py:1202 decorate                                                         5           0.000000  0.855991  0.171198
/home/johannes/.local/opt/miniconda3/envs/snakemake-dev/lib/python3.8/logging/__init__.py:629 Formatter.usesTime          180024      0.282792  0.852048  0.000005
/home/johannes/scms/snakemake/snakemake/io.py:715 _IOFile.clone_flags                                                     63001       0.198883  0.829513  0.000013
/home/johannes/scms/snakemake/snakemake/rules.py:1030 Rule.get_wildcards                                                  27002       0.192634  0.825055  0.000031
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/home/johannes/scms/snakemake/snakemake/io.py:257 _IOFile._inventory                                                      9000        0.059896  0.415947  0.000046
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/home/johannes/scms/snakemake/snakemake/rules.py:935 apply                                                                54004       0.232889  0.369395  0.000007
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/home/johannes/scms/snakemake/snakemake/dag.py:1137 DAG.close_remote_objects                                              1           0.036639  0.359762  0.359762
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/home/johannes/scms/snakemake/snakemake/logging.py:320 indent                                                             162008      0.232866  0.349353  0.000002
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/home/johannes/scms/snakemake/snakemake/dag.py:539 DAG.check_periodic_wildcards                                           36001       0.136427  0.346118  0.000010
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/home/johannes/scms/snakemake/snakemake/rules.py:982 Rule.expand_group                                                    81006       0.213121  0.342968  0.000004
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/home/johannes/scms/snakemake/snakemake/dag.py:398 DAG.reason                                                             279010      0.306458  0.333113  0.000001
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<frozen importlib._bootstrap>:956 _find_and_load_unlocked                                                                 139/4       0.000000  0.222938  0.001604
<frozen importlib._bootstrap>:986 _find_and_load                                                                          140/4       0.000000  0.222938  0.001592
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<frozen importlib._bootstrap>:650 _load_unlocked                                                                          135/4       0.000000  0.219606  0.001627
<frozen importlib._bootstrap>:211 _call_with_frames_removed                                                               150/5       0.000000  0.219606  0.001464
<frozen importlib._bootstrap_external>:777 SourceFileLoader.exec_module                                                   125/3       0.000000  0.219606  0.001757
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/home/johannes/scms/snakemake/snakemake/dag.py:1234 DAG._ready                                                            63002       0.146470  0.193084  0.000003
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/home/johannes/scms/snakemake/snakemake/dag.py:991 DAG.in_until                                                           36000       0.069855  0.179699  0.000005
/home/johannes/scms/snakemake/snakemake/logging.py:484 setup_logger                                                       1           0.000000  0.179681  0.179681
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/home/johannes/scms/snakemake/snakemake/rules.py:1053 get_wildcard_len                                                    27001       0.096513  0.156425  0.000006
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/home/johannes/scms/snakemake/snakemake/dag.py:690 DAG.jobid                                                              36003       0.103160  0.126449  0.000004
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<frozen importlib._bootstrap>:1017 _handle_fromlist                                                                       47/33       0.000000  0.056555  0.001203
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/home/johannes/scms/snakemake/snakemake/parser.py:873 parse                                                               1           0.006655  0.043272  0.043272
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<frozen importlib._bootstrap>:890 _find_spec                                                                              138         0.003326  0.033263  0.000241
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<frozen importlib._bootstrap_external>:1334 find_spec                                                                     138         0.000000  0.026621  0.000193
<frozen importlib._bootstrap_external>:1302 _get_spec                                                                     138         0.003320  0.026621  0.000193
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<frozen importlib._bootstrap_external>:1431 FileFinder.find_spec                                                          197         0.006660  0.023301  0.000118
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<string>:1 <module>                                                                                                       5           0.000000  0.000000  0.000000
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<frozen importlib._bootstrap>:881 _find_spec_legacy                                                                       7           0.000000  0.000000  0.000000
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