run_pycistarget() starts but never delivers results (local run)

Sebdumas commented 1 year ago

Hello,

Very excited with the Scenicplus package. I am trying to finalise processing of my cistopic objet but I have an issue for the run_pycistarget() step.

Here is the code I run and the output

>>> db_fpath = "/media/sdb1/scenicplus/Analysis_aging/Database"
>>> motif_annot_fpath = "/media/sdb1/scenicplus/Analysis_aging/Database"
>>> 
>>> rankings_db = os.path.join(db_fpath, 'mm10_screen_v10_clust.regions_vs_motifs.rankings.feather')
>>> scores_db =  os.path.join(db_fpath, 'mm10_screen_v10_clust.regions_vs_motifs.scores.feather')
>>> motif_annotation = os.path.join(motif_annot_fpath, 'motifs-v10nr_clust-nr.mgi-m0.001-o0.0.tbl')
>>> if not os.path.exists(os.path.join(work_dir, 'motifs')):
...     os.makedirs(os.path.join(work_dir, 'motifs'))
... 
>>> tmp_dir="/media/sdb1/Tmp"
>>> from scenicplus.wrappers.run_pycistarget import run_pycistarget

>>> sys.stderr = open(os.devnull, "w")  # silence stderr
>>> run_pycistarget(
...     region_sets = region_sets,
...     species = 'mus_musculus',
...     save_path = os.path.join(work_dir, 'motifs'),
...     ctx_db_path = rankings_db,
...     dem_db_path = scores_db,
...     path_to_motif_annotations = motif_annotation,
...     run_without_promoters = True,
...     n_cpu = 10,
...     _temp_dir = os.path.join(tmp_dir, 'ray_spill'),
...     annotation_version = 'v10nr_clust')
2023-08-09 03:31:21,836 pycisTarget_wrapper INFO     /media/sdb1/scenicplus/Analysis_aging/pycisTopic/output/motifs folder already exists.
2023-08-09 03:31:22,128 pycisTarget_wrapper INFO     Loading cisTarget database for topics_otsu
2023-08-09 03:31:22,129 cisTarget    INFO     Reading cisTarget database
2023-08-09 03:33:50,111 pycisTarget_wrapper INFO     Running cisTarget for topics_otsu
2023-08-09 03:34:04,254 INFO worker.py:1612 -- Started a local Ray instance. View the dashboard at http://127.0.0.1:8265 
(ctx_internal_ray pid=30068) 2023-08-09 03:34:08,113 cisTarget    INFO     Running cisTarget for Topic1 which has 24544 regions
(ctx_internal_ray pid=30061) 2023-08-09 03:34:13,788 cisTarget    INFO     Running cisTarget for Topic4 which has 30197 regions [repeated 3x across cluster]
(ctx_internal_ray pid=30068) 2023-08-09 03:34:25,503 cisTarget    INFO     Annotating motifs for Topic1
(ctx_internal_ray pid=30069) 2023-08-09 03:34:15,904 cisTarget    INFO     Running cisTarget for Topic5 which has 29703 regions
>>>

I don't get any error message but even though it looks like the calculation is over in the Terminal, it is actually still ongoing in the background, with "Ray" processes still opened. And it seems they have entered in some kind of loops, calculating over and over. I can stop most of this calculation with the ray. shutdown() command.

Do you have any suggestion to solve that please?

Thank you very much for your help,

Kind regards, Sébastien

Versions

Python: 3.8.8
SCENIC+: 1.0.1.dev3+g3741a4b
Ray: 2.6.2

SeppeDeWinter commented 1 year ago

Hi Sébastien

Ray might be supressing the error. Can you try running using a single core, that way you should be able to see the error message.

Best,

Seppe

Sebdumas commented 1 year ago

OK, I'm doing it. So far it seems to run properly (see below). It didn't get stuck at the first steps as when using multiple cores.

>>> run_pycistarget(
...     region_sets = region_sets,
...     species = 'mus_musculus',
...     save_path = os.path.join(work_dir, 'motifs'),
...     ctx_db_path = rankings_db,
...     dem_db_path = scores_db,
...     path_to_motif_annotations = motif_annotation,
...     run_without_promoters = True,
...     n_cpu = 1,
...     _temp_dir = os.path.join(tmp_dir, 'ray_spill'),
...     annotation_version = 'v10nr_clust')
2023-08-09 13:18:25,876 pycisTarget_wrapper INFO     Created folder : /media/sdb1/scenicplus/Analysis_aging/pycisTopic/output/motifs
2023-08-09 13:18:26,158 pycisTarget_wrapper INFO     Loading cisTarget database for topics_otsu
2023-08-09 13:18:26,158 cisTarget    INFO     Reading cisTarget database
2023-08-09 13:23:11,364 pycisTarget_wrapper INFO     Running cisTarget for topics_otsu
2023-08-09 13:23:11,365 cisTarget    INFO     Running cisTarget for Topic1 which has 24544 regions
2023-08-09 13:23:33,656 cisTarget    INFO     Annotating motifs for Topic1
2023-08-09 13:23:37,651 cisTarget    INFO     Getting cistromes for Topic1
2023-08-09 13:23:37,985 cisTarget    INFO     Running cisTarget for Topic2 which has 25617 regions
2023-08-09 13:23:51,290 cisTarget    INFO     Annotating motifs for Topic2
2023-08-09 13:23:54,816 cisTarget    INFO     Getting cistromes for Topic2
2023-08-09 13:23:55,176 cisTarget    INFO     Running cisTarget for Topic3 which has 21667 regions
2023-08-09 13:24:03,898 cisTarget    INFO     Annotating motifs for Topic3
2023-08-09 13:24:06,039 cisTarget    INFO     Getting cistromes for Topic3
2023-08-09 13:24:06,226 cisTarget    INFO     Running cisTarget for Topic4 which has 30197 regions
2023-08-09 13:24:19,968 cisTarget    INFO     Annotating motifs for Topic4
2023-08-09 13:24:24,406 cisTarget    INFO     Getting cistromes for Topic4
2023-08-09 13:24:24,887 cisTarget    INFO     Running cisTarget for Topic5 which has 29703 regions
2023-08-09 13:24:36,840 cisTarget    INFO     Annotating motifs for Topic5
2023-08-09 13:24:40,163 cisTarget    INFO     Getting cistromes for Topic5
2023-08-09 13:24:40,448 cisTarget    INFO     Running cisTarget for Topic6 which has 36107 regions
2023-08-09 13:24:58,515 cisTarget    INFO     Annotating motifs for Topic6
2023-08-09 13:25:03,159 cisTarget    INFO     Getting cistromes for Topic6
2023-08-09 13:25:03,620 cisTarget    INFO     Running cisTarget for Topic7 which has 15838 regions
2023-08-09 13:25:13,423 cisTarget    INFO     Annotating motifs for Topic7
2023-08-09 13:25:16,470 cisTarget    INFO     Getting cistromes for Topic7
2023-08-09 13:25:16,734 cisTarget    INFO     Running cisTarget for Topic8 which has 13123 regions
2023-08-09 13:25:25,076 cisTarget    INFO     Annotating motifs for Topic8
2023-08-09 13:25:27,533 cisTarget    INFO     Getting cistromes for Topic8
2023-08-09 13:25:27,802 cisTarget    INFO     Running cisTarget for Topic9 which has 9883 regions
2023-08-09 13:25:35,563 cisTarget    INFO     Annotating motifs for Topic9
2023-08-09 13:25:37,801 cisTarget    INFO     Getting cistromes for Topic9
2023-08-09 13:25:38,059 cisTarget    INFO     Running cisTarget for Topic10 which has 10181 regions
2023-08-09 13:25:47,562 cisTarget    INFO     Annotating motifs for Topic10
2023-08-09 13:25:49,904 cisTarget    INFO     Getting cistromes for Topic10
2023-08-09 13:25:50,114 cisTarget    INFO     Running cisTarget for Topic11 which has 30502 regions
2023-08-09 13:26:03,316 cisTarget    INFO     Annotating motifs for Topic11
2023-08-09 13:26:07,031 cisTarget    INFO     Getting cistromes for Topic11
2023-08-09 13:26:07,370 cisTarget    INFO     Running cisTarget for Topic12 which has 30939 regions
2023-08-09 13:26:22,807 cisTarget    INFO     Annotating motifs for Topic12
2023-08-09 13:26:26,831 cisTarget    INFO     Getting cistromes for Topic12
2023-08-09 13:26:27,223 cisTarget    INFO     Running cisTarget for Topic13 which has 11168 regions
2023-08-09 13:26:37,354 cisTarget    INFO     Annotating motifs for Topic13
2023-08-09 13:26:39,933 cisTarget    INFO     Getting cistromes for Topic13
2023-08-09 13:26:40,195 cisTarget    INFO     Running cisTarget for Topic14 which has 23236 regions
2023-08-09 13:26:53,093 cisTarget    INFO     Annotating motifs for Topic14
2023-08-09 13:26:56,184 cisTarget    INFO     Getting cistromes for Topic14
2023-08-09 13:26:56,521 cisTarget    INFO     Running cisTarget for Topic15 which has 30982 regions
2023-08-09 13:27:11,491 cisTarget    INFO     Annotating motifs for Topic15
2023-08-09 13:27:14,794 cisTarget    INFO     Getting cistromes for Topic15
2023-08-09 13:27:15,113 cisTarget    INFO     Running cisTarget for Topic16 which has 18137 regions
2023-08-09 13:27:26,281 cisTarget    INFO     Annotating motifs for Topic16
2023-08-09 13:27:28,870 cisTarget    INFO     Getting cistromes for Topic16
2023-08-09 13:27:29,154 cisTarget    INFO     Running cisTarget for Topic17 which has 20259 regions
2023-08-09 13:27:40,390 cisTarget    INFO     Annotating motifs for Topic17
2023-08-09 13:27:43,594 cisTarget    INFO     Getting cistromes for Topic17
2023-08-09 13:27:43,933 cisTarget    INFO     Running cisTarget for Topic18 which has 15953 regions
2023-08-09 13:27:54,293 cisTarget    INFO     Annotating motifs for Topic18
2023-08-09 13:27:56,686 cisTarget    INFO     Getting cistromes for Topic18
2023-08-09 13:27:56,886 cisTarget    INFO     Running cisTarget for Topic19 which has 20365 regions
2023-08-09 13:28:08,580 cisTarget    INFO     Annotating motifs for Topic19
2023-08-09 13:28:11,062 cisTarget    INFO     Getting cistromes for Topic19
2023-08-09 13:28:11,404 cisTarget    INFO     Running cisTarget for Topic20 which has 14298 regions
2023-08-09 13:28:22,104 cisTarget    INFO     Annotating motifs for Topic20
2023-08-09 13:28:24,652 cisTarget    INFO     Getting cistromes for Topic20
2023-08-09 13:28:24,914 cisTarget    INFO     Running cisTarget for Topic21 which has 16927 regions
2023-08-09 13:28:33,627 cisTarget    INFO     Annotating motifs for Topic21
2023-08-09 13:28:35,814 cisTarget    INFO     Getting cistromes for Topic21
2023-08-09 13:28:36,071 cisTarget    INFO     Running cisTarget for Topic22 which has 33478 regions
2023-08-09 13:28:52,310 cisTarget    INFO     Annotating motifs for Topic22
2023-08-09 13:28:55,666 cisTarget    INFO     Getting cistromes for Topic22
2023-08-09 13:28:56,014 cisTarget    INFO     Running cisTarget for Topic23 which has 21312 regions
2023-08-09 13:29:07,265 cisTarget    INFO     Annotating motifs for Topic23
2023-08-09 13:29:09,505 cisTarget    INFO     Getting cistromes for Topic23
2023-08-09 13:29:09,709 cisTarget    INFO     Running cisTarget for Topic24 which has 13934 regions
2023-08-09 13:29:20,334 cisTarget    INFO     Annotating motifs for Topic24
2023-08-09 13:29:22,943 cisTarget    INFO     Getting cistromes for Topic24
2023-08-09 13:29:23,183 cisTarget    INFO     Running cisTarget for Topic25 which has 14559 regions
2023-08-09 13:29:32,008 cisTarget    INFO     Annotating motifs for Topic25
2023-08-09 13:29:34,600 cisTarget    INFO     Getting cistromes for Topic25
2023-08-09 13:29:34,884 cisTarget    INFO     Running cisTarget for Topic26 which has 19671 regions
2023-08-09 13:29:46,909 cisTarget    INFO     Annotating motifs for Topic26
2023-08-09 13:29:49,707 cisTarget    INFO     Getting cistromes for Topic26
2023-08-09 13:29:49,936 cisTarget    INFO     Running cisTarget for Topic27 which has 25750 regions
2023-08-09 13:30:04,480 cisTarget    INFO     Annotating motifs for Topic27
2023-08-09 13:30:07,903 cisTarget    INFO     Getting cistromes for Topic27
2023-08-09 13:30:08,212 cisTarget    INFO     Running cisTarget for Topic28 which has 26867 regions
2023-08-09 13:30:23,357 cisTarget    INFO     Annotating motifs for Topic28
2023-08-09 13:30:26,896 cisTarget    INFO     Getting cistromes for Topic28
2023-08-09 13:30:27,272 cisTarget    INFO     Running cisTarget for Topic29 which has 16301 regions
2023-08-09 13:30:38,036 cisTarget    INFO     Annotating motifs for Topic29
2023-08-09 13:30:40,359 cisTarget    INFO     Getting cistromes for Topic29
2023-08-09 13:30:40,598 cisTarget    INFO     Running cisTarget for Topic30 which has 28571 regions
2023-08-09 13:30:52,272 cisTarget    INFO     Annotating motifs for Topic30
2023-08-09 13:30:55,074 cisTarget    INFO     Getting cistromes for Topic30
2023-08-09 13:30:55,335 cisTarget    INFO     Running cisTarget for Topic31 which has 17171 regions
2023-08-09 13:31:06,502 cisTarget    INFO     Annotating motifs for Topic31
2023-08-09 13:31:08,952 cisTarget    INFO     Getting cistromes for Topic31
2023-08-09 13:31:09,169 cisTarget    INFO     Running cisTarget for Topic32 which has 22109 regions
2023-08-09 13:31:20,957 cisTarget    INFO     Annotating motifs for Topic32
2023-08-09 13:31:23,340 cisTarget    INFO     Getting cistromes for Topic32
2023-08-09 13:31:23,563 cisTarget    INFO     Running cisTarget for Topic33 which has 16113 regions
2023-08-09 13:31:31,957 cisTarget    INFO     Annotating motifs for Topic33
2023-08-09 13:31:34,184 cisTarget    INFO     Getting cistromes for Topic33
2023-08-09 13:31:34,424 cisTarget    INFO     Running cisTarget for Topic34 which has 18823 regions
2023-08-09 13:31:49,486 cisTarget    INFO     Annotating motifs for Topic34
2023-08-09 13:31:52,695 cisTarget    INFO     Getting cistromes for Topic34
2023-08-09 13:31:53,089 cisTarget    INFO     Running cisTarget for Topic35 which has 25920 regions
2023-08-09 13:32:07,246 cisTarget    INFO     Annotating motifs for Topic35
2023-08-09 13:32:10,808 cisTarget    INFO     Getting cistromes for Topic35
2023-08-09 13:32:11,142 cisTarget    INFO     Running cisTarget for Topic36 which has 19400 regions
2023-08-09 13:32:22,659 cisTarget    INFO     Annotating motifs for Topic36
2023-08-09 13:32:25,195 cisTarget    INFO     Getting cistromes for Topic36
2023-08-09 13:32:25,386 cisTarget    INFO     Running cisTarget for Topic37 which has 22135 regions
2023-08-09 13:32:39,317 cisTarget    INFO     Annotating motifs for Topic37
2023-08-09 13:32:42,215 cisTarget    INFO     Getting cistromes for Topic37
2023-08-09 13:32:42,528 cisTarget    INFO     Running cisTarget for Topic38 which has 33110 regions
2023-08-09 13:33:02,286 cisTarget    INFO     Annotating motifs for Topic38
2023-08-09 13:33:05,988 cisTarget    INFO     Getting cistromes for Topic38
2023-08-09 13:33:06,261 cisTarget    INFO     Running cisTarget for Topic39 which has 34319 regions
2023-08-09 13:33:24,308 cisTarget    INFO     Annotating motifs for Topic39
2023-08-09 13:33:28,886 cisTarget    INFO     Getting cistromes for Topic39
2023-08-09 13:33:29,379 cisTarget    INFO     Running cisTarget for Topic40 which has 37839 regions
2023-08-09 13:33:47,196 cisTarget    INFO     Annotating motifs for Topic40
2023-08-09 13:33:51,248 cisTarget    INFO     Getting cistromes for Topic40
2023-08-09 13:33:51,696 cisTarget    INFO     Running cisTarget for Topic41 which has 16466 regions
2023-08-09 13:34:02,810 cisTarget    INFO     Annotating motifs for Topic41
2023-08-09 13:34:05,146 cisTarget    INFO     Getting cistromes for Topic41
2023-08-09 13:34:05,406 cisTarget    INFO     Running cisTarget for Topic42 which has 16819 regions
2023-08-09 13:34:15,573 cisTarget    INFO     Annotating motifs for Topic42
2023-08-09 13:34:17,769 cisTarget    INFO     Getting cistromes for Topic42
2023-08-09 13:34:17,976 cisTarget    INFO     Running cisTarget for Topic43 which has 25024 regions
2023-08-09 13:34:28,841 cisTarget    INFO     Annotating motifs for Topic43
2023-08-09 13:34:31,358 cisTarget    INFO     Getting cistromes for Topic43
2023-08-09 13:34:31,579 cisTarget    INFO     Running cisTarget for Topic44 which has 21406 regions
2023-08-09 13:34:43,109 cisTarget    INFO     Annotating motifs for Topic44
2023-08-09 13:34:45,457 cisTarget    INFO     Getting cistromes for Topic44
2023-08-09 13:34:45,770 cisTarget    INFO     Running cisTarget for Topic45 which has 17503 regions
2023-08-09 13:34:56,214 cisTarget    INFO     Annotating motifs for Topic45
2023-08-09 13:34:58,453 cisTarget    INFO     Getting cistromes for Topic45
2023-08-09 13:34:58,665 cisTarget    INFO     Done!
2023-08-09 13:34:58,665 pycisTarget_wrapper INFO     Created folder : /media/sdb1/scenicplus/Analysis_aging/pycisTopic/output/motifs/CTX_topics_otsu_All
2023-08-09 13:34:59,554 pycisTarget_wrapper INFO     Running cisTarget without promoters for topics_otsu
2023-08-09 13:36:13,761 cisTarget    INFO     Running cisTarget for Topic1 which has 23023 regions
2023-08-09 13:36:27,173 cisTarget    INFO     Annotating motifs for Topic1
2023-08-09 13:36:30,422 cisTarget    INFO     Getting cistromes for Topic1
2023-08-09 13:36:30,689 cisTarget    INFO     Running cisTarget for Topic2 which has 24141 regions
2023-08-09 13:36:42,432 cisTarget    INFO     Annotating motifs for Topic2
2023-08-09 13:36:45,868 cisTarget    INFO     Getting cistromes for Topic2
2023-08-09 13:36:46,202 cisTarget    INFO     Running cisTarget for Topic3 which has 20795 regions
2023-08-09 13:36:59,631 cisTarget    INFO     Annotating motifs for Topic3
2023-08-09 13:37:01,773 cisTarget    INFO     Getting cistromes for Topic3
2023-08-09 13:37:01,955 cisTarget    INFO     Running cisTarget for Topic4 which has 26687 regions
2023-08-09 13:37:16,274 cisTarget    INFO     Annotating motifs for Topic4
2023-08-09 13:37:20,574 cisTarget    INFO     Getting cistromes for Topic4
2023-08-09 13:37:21,047 cisTarget    INFO     Running cisTarget for Topic5 which has 28143 regions
2023-08-09 13:37:35,124 cisTarget    INFO     Annotating motifs for Topic5
2023-08-09 13:37:38,440 cisTarget    INFO     Getting cistromes for Topic5
2023-08-09 13:37:38,721 cisTarget    INFO     Running cisTarget for Topic6 which has 32531 regions
2023-08-09 13:37:55,667 cisTarget    INFO     Annotating motifs for Topic6
2023-08-09 13:38:00,055 cisTarget    INFO     Getting cistromes for Topic6
2023-08-09 13:38:00,508 cisTarget    INFO     Running cisTarget for Topic7 which has 14802 regions
2023-08-09 13:38:11,896 cisTarget    INFO     Annotating motifs for Topic7
2023-08-09 13:38:14,907 cisTarget    INFO     Getting cistromes for Topic7
2023-08-09 13:38:15,165 cisTarget    INFO     Running cisTarget for Topic8 which has 12521 regions
2023-08-09 13:38:25,397 cisTarget    INFO     Annotating motifs for Topic8
2023-08-09 13:38:27,861 cisTarget    INFO     Getting cistromes for Topic8
2023-08-09 13:38:28,135 cisTarget    INFO     Running cisTarget for Topic9 which has 9525 regions
2023-08-09 13:38:37,588 cisTarget    INFO     Annotating motifs for Topic9
2023-08-09 13:38:39,773 cisTarget    INFO     Getting cistromes for Topic9
2023-08-09 13:38:40,002 cisTarget    INFO     Running cisTarget for Topic10 which has 9792 regions
2023-08-09 13:38:47,882 cisTarget    INFO     Annotating motifs for Topic10
2023-08-09 13:38:50,159 cisTarget    INFO     Getting cistromes for Topic10
2023-08-09 13:38:50,372 cisTarget    INFO     Running cisTarget for Topic11 which has 28552 regions
2023-08-09 13:39:04,831 cisTarget    INFO     Annotating motifs for Topic11
2023-08-09 13:39:08,405 cisTarget    INFO     Getting cistromes for Topic11
2023-08-09 13:39:08,734 cisTarget    INFO     Running cisTarget for Topic12 which has 29122 regions
2023-08-09 13:39:24,003 cisTarget    INFO     Annotating motifs for Topic12
2023-08-09 13:39:27,850 cisTarget    INFO     Getting cistromes for Topic12
2023-08-09 13:39:28,231 cisTarget    INFO     Running cisTarget for Topic13 which has 10458 regions
2023-08-09 13:39:39,319 cisTarget    INFO     Annotating motifs for Topic13
2023-08-09 13:39:41,815 cisTarget    INFO     Getting cistromes for Topic13
2023-08-09 13:39:42,065 cisTarget    INFO     Running cisTarget for Topic14 which has 21852 regions
2023-08-09 13:39:53,268 cisTarget    INFO     Annotating motifs for Topic14
2023-08-09 13:39:56,326 cisTarget    INFO     Getting cistromes for Topic14
2023-08-09 13:39:56,693 cisTarget    INFO     Running cisTarget for Topic15 which has 29334 regions
2023-08-09 13:40:11,518 cisTarget    INFO     Annotating motifs for Topic15
2023-08-09 13:40:14,784 cisTarget    INFO     Getting cistromes for Topic15
2023-08-09 13:40:15,178 cisTarget    INFO     Running cisTarget for Topic16 which has 16965 regions
2023-08-09 13:40:26,228 cisTarget    INFO     Annotating motifs for Topic16
2023-08-09 13:40:28,728 cisTarget    INFO     Getting cistromes for Topic16
2023-08-09 13:40:28,980 cisTarget    INFO     Running cisTarget for Topic17 which has 19313 regions
2023-08-09 13:40:41,636 cisTarget    INFO     Annotating motifs for Topic17
2023-08-09 13:40:44,665 cisTarget    INFO     Getting cistromes for Topic17
2023-08-09 13:40:44,961 cisTarget    INFO     Running cisTarget for Topic18 which has 15173 regions
2023-08-09 13:40:54,013 cisTarget    INFO     Annotating motifs for Topic18
2023-08-09 13:40:56,359 cisTarget    INFO     Getting cistromes for Topic18
2023-08-09 13:40:56,583 cisTarget    INFO     Running cisTarget for Topic19 which has 19284 regions
2023-08-09 13:41:08,276 cisTarget    INFO     Annotating motifs for Topic19
2023-08-09 13:41:10,785 cisTarget    INFO     Getting cistromes for Topic19
2023-08-09 13:41:11,108 cisTarget    INFO     Running cisTarget for Topic20 which has 13527 regions
2023-08-09 13:41:21,840 cisTarget    INFO     Annotating motifs for Topic20
2023-08-09 13:41:24,367 cisTarget    INFO     Getting cistromes for Topic20
2023-08-09 13:41:24,608 cisTarget    INFO     Running cisTarget for Topic21 which has 16145 regions
2023-08-09 13:41:33,127 cisTarget    INFO     Annotating motifs for Topic21
2023-08-09 13:41:35,304 cisTarget    INFO     Getting cistromes for Topic21
2023-08-09 13:41:35,533 cisTarget    INFO     Running cisTarget for Topic22 which has 31333 regions
2023-08-09 13:41:51,500 cisTarget    INFO     Annotating motifs for Topic22
2023-08-09 13:41:54,869 cisTarget    INFO     Getting cistromes for Topic22
2023-08-09 13:41:55,220 cisTarget    INFO     Running cisTarget for Topic23 which has 20358 regions
2023-08-09 13:42:06,220 cisTarget    INFO     Annotating motifs for Topic23
2023-08-09 13:42:08,458 cisTarget    INFO     Getting cistromes for Topic23
2023-08-09 13:42:08,613 cisTarget    INFO     Running cisTarget for Topic24 which has 13074 regions
2023-08-09 13:42:19,495 cisTarget    INFO     Annotating motifs for Topic24
2023-08-09 13:42:22,074 cisTarget    INFO     Getting cistromes for Topic24
2023-08-09 13:42:22,306 cisTarget    INFO     Running cisTarget for Topic25 which has 13734 regions
2023-08-09 13:42:31,129 cisTarget    INFO     Annotating motifs for Topic25
2023-08-09 13:42:33,604 cisTarget    INFO     Getting cistromes for Topic25
2023-08-09 13:42:33,872 cisTarget    INFO     Running cisTarget for Topic26 which has 18682 regions
2023-08-09 13:42:45,912 cisTarget    INFO     Annotating motifs for Topic26
2023-08-09 13:42:48,708 cisTarget    INFO     Getting cistromes for Topic26
2023-08-09 13:42:48,923 cisTarget    INFO     Running cisTarget for Topic27 which has 23924 regions
2023-08-09 13:43:02,893 cisTarget    INFO     Annotating motifs for Topic27
2023-08-09 13:43:06,237 cisTarget    INFO     Getting cistromes for Topic27
2023-08-09 13:43:06,540 cisTarget    INFO     Running cisTarget for Topic28 which has 25555 regions
2023-08-09 13:43:19,442 cisTarget    INFO     Annotating motifs for Topic28
2023-08-09 13:43:22,951 cisTarget    INFO     Getting cistromes for Topic28
2023-08-09 13:43:23,319 cisTarget    INFO     Running cisTarget for Topic29 which has 15541 regions
2023-08-09 13:43:33,645 cisTarget    INFO     Annotating motifs for Topic29
2023-08-09 13:43:35,926 cisTarget    INFO     Getting cistromes for Topic29
2023-08-09 13:43:36,157 cisTarget    INFO     Running cisTarget for Topic30 which has 26963 regions
2023-08-09 13:43:49,627 cisTarget    INFO     Annotating motifs for Topic30
2023-08-09 13:43:52,359 cisTarget    INFO     Getting cistromes for Topic30
2023-08-09 13:43:52,599 cisTarget    INFO     Running cisTarget for Topic31 which has 16462 regions
2023-08-09 13:44:04,111 cisTarget    INFO     Annotating motifs for Topic31
2023-08-09 13:44:06,627 cisTarget    INFO     Getting cistromes for Topic31
2023-08-09 13:44:06,849 cisTarget    INFO     Running cisTarget for Topic32 which has 21053 regions
2023-08-09 13:44:17,439 cisTarget    INFO     Annotating motifs for Topic32
2023-08-09 13:44:19,848 cisTarget    INFO     Getting cistromes for Topic32
2023-08-09 13:44:20,053 cisTarget    INFO     Running cisTarget for Topic33 which has 15382 regions
2023-08-09 13:44:30,175 cisTarget    INFO     Annotating motifs for Topic33
2023-08-09 13:44:32,382 cisTarget    INFO     Getting cistromes for Topic33
2023-08-09 13:44:32,582 cisTarget    INFO     Running cisTarget for Topic34 which has 17138 regions
2023-08-09 13:44:44,362 cisTarget    INFO     Annotating motifs for Topic34
2023-08-09 13:44:47,399 cisTarget    INFO     Getting cistromes for Topic34
2023-08-09 13:44:47,777 cisTarget    INFO     Running cisTarget for Topic35 which has 24767 regions
2023-08-09 13:45:01,644 cisTarget    INFO     Annotating motifs for Topic35
2023-08-09 13:45:05,174 cisTarget    INFO     Getting cistromes for Topic35
2023-08-09 13:45:05,507 cisTarget    INFO     Running cisTarget for Topic36 which has 18601 regions
2023-08-09 13:45:17,057 cisTarget    INFO     Annotating motifs for Topic36
2023-08-09 13:45:19,600 cisTarget    INFO     Getting cistromes for Topic36
2023-08-09 13:45:19,795 cisTarget    INFO     Running cisTarget for Topic37 which has 20711 regions
2023-08-09 13:45:32,253 cisTarget    INFO     Annotating motifs for Topic37
2023-08-09 13:45:35,042 cisTarget    INFO     Getting cistromes for Topic37
2023-08-09 13:45:35,358 cisTarget    INFO     Running cisTarget for Topic38 which has 30819 regions
2023-08-09 13:45:51,336 cisTarget    INFO     Annotating motifs for Topic38
2023-08-09 13:45:54,894 cisTarget    INFO     Getting cistromes for Topic38
2023-08-09 13:45:55,159 cisTarget    INFO     Running cisTarget for Topic39 which has 31114 regions
2023-08-09 13:46:12,063 cisTarget    INFO     Annotating motifs for Topic39
2023-08-09 13:46:16,339 cisTarget    INFO     Getting cistromes for Topic39
2023-08-09 13:46:16,862 cisTarget    INFO     Running cisTarget for Topic40 which has 35555 regions
2023-08-09 13:46:33,704 cisTarget    INFO     Annotating motifs for Topic40
2023-08-09 13:46:37,556 cisTarget    INFO     Getting cistromes for Topic40
2023-08-09 13:46:37,969 cisTarget    INFO     Running cisTarget for Topic41 which has 15724 regions
2023-08-09 13:46:49,010 cisTarget    INFO     Annotating motifs for Topic41
2023-08-09 13:46:51,332 cisTarget    INFO     Getting cistromes for Topic41
2023-08-09 13:46:51,576 cisTarget    INFO     Running cisTarget for Topic42 which has 16110 regions
2023-08-09 13:47:00,011 cisTarget    INFO     Annotating motifs for Topic42
2023-08-09 13:47:02,189 cisTarget    INFO     Getting cistromes for Topic42
2023-08-09 13:47:02,400 cisTarget    INFO     Running cisTarget for Topic43 which has 23891 regions
2023-08-09 13:47:14,722 cisTarget    INFO     Annotating motifs for Topic43
2023-08-09 13:47:17,164 cisTarget    INFO     Getting cistromes for Topic43
2023-08-09 13:47:17,368 cisTarget    INFO     Running cisTarget for Topic44 which has 20266 regions
2023-08-09 13:47:28,694 cisTarget    INFO     Annotating motifs for Topic44
2023-08-09 13:47:31,039 cisTarget    INFO     Getting cistromes for Topic44
2023-08-09 13:47:31,375 cisTarget    INFO     Running cisTarget for Topic45 which has 16861 regions
2023-08-09 13:47:40,768 cisTarget    INFO     Annotating motifs for Topic45
2023-08-09 13:47:42,981 cisTarget    INFO     Getting cistromes for Topic45
2023-08-09 13:47:43,180 cisTarget    INFO     Done!
2023-08-09 13:47:43,181 pycisTarget_wrapper INFO     Created folder:/media/sdb1/scenicplus/Analysis_aging/pycisTopic/output/motifs/CTX_topics_otsu_No_promoters
2023-08-09 13:47:44,098 pycisTarget_wrapper INFO     Running DEM for topics_otsu
2023-08-09 13:47:44,099 DEM          INFO     Reading DEM database
2023-08-09 13:51:29,252 DEM          INFO     Creating contrast groups
2023-08-09 13:53:13,580 DEM          INFO     Computing DEM for Topic1
2023-08-09 13:53:31,659 DEM          INFO     Computing DEM for Topic2
2023-08-09 13:53:56,392 DEM          INFO     Computing DEM for Topic3
2023-08-09 13:54:13,854 DEM          INFO     Computing DEM for Topic4
2023-08-09 13:57:25,882 DEM          INFO     Computing DEM for Topic5
2023-08-09 13:57:49,236 DEM          INFO     Computing DEM for Topic6

Best, Sébastien

Sebdumas commented 1 year ago

It finished properly using 1cpu in 2 hours. So it is probably an error only occurring with the parallelisation. Is there anything I could test to troubleshoot ?

2023-08-09 14:49:03,812 pycisTarget_wrapper INFO     Saving object
2023-08-09 15:18:40,132 pycisTarget_wrapper INFO     Finished! Took 120.23850954373678 minutes

Thank you,

Kind regards, Sébastien

SeppeDeWinter commented 1 year ago

Hi Sébastien

Great. Not sure what went wrong then ... Might be that your memory was running out.

Best,

Seppe

aertslab / scenicplus

run_pycistarget() starts but never delivers results (local run) #196