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Error when no enriched features? #5

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SeppeDeWinter opened this issue Apr 29, 2022 · 0 comments
Open

Error when no enriched features? #5

SeppeDeWinter opened this issue Apr 29, 2022 · 0 comments

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@SeppeDeWinter
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Run pycistarget

run_without_promoters = True, will run the methods in all regions + the region sets without promoters

#import os

#os.chdir('/staging/leuven/stg_00002/lcb/cbravo/Multiomics_pipeline/scenicplus/src/')

from scenicplus.wrappers.run_pycistarget import *

run_pycistarget(region_sets_nonzero,

             ctx_db_path = '/lustre1/project/stg_00002/lcb/nhecker/cross_species/snare_seq/human/pycistarget_v10_2022_04_27/dbs/SNAREseq_human_cortex.regions_vs_motifs.rankings.feather',

             species = 'homo_sapiens',

             save_path = '/lustre1/project/stg_00002/lcb/nhecker/cross_species/snare_seq/human/pycistarget_v10_2022_04_27/',

             dem_db_path = '/lustre1/project/stg_00002/lcb/nhecker/cross_species/snare_seq/human/pycistarget_v10_2022_04_27/dbs/SNAREseq_human_cortex.regions_vs_motifs.scores.feather',

             run_without_promoters = True,

             biomart_host = 'http://jul2018.archive.ensembl.org/',

             promoter_space = 500,

             ctx_auc_threshold = 0.005,

             ctx_nes_threshold = 3.0,

             ctx_rank_threshold = 0.05,

             dem_log2fc_thr = 0.5,

             dem_motif_hit_thr = 3.0,

             dem_max_bg_regions = 500,

             path_to_motif_annotations = '/staging/leuven/stg_00002/lcb/cbravo/cluster_motif_collection_V10_no_desso_no_factorbook/snapshots/motifs-v10-nr.more_orthology.hgnc-mm0.00001-o0.0_clust.tsv',

             annotation_version = 'v10nr_clust',

             annotation = ['Direct_annot', 'Orthology_annot'],

             n_cpu = 1,

             _temp_dir = '/scratch/leuven/339/vsc33943/ray_spill')

2022-04-29 13:25:41,912 pycisTarget_wrapper INFO /lustre1/project/stg_00002/lcb/nhecker/cross_species/snare_seq/human/pycistarget_v10_2022_04_27/ folder already exists.

/opt/venv/lib/python3.8/site-packages/scenicplus/wrappers/run_pycistarget.py:126: FutureWarning: The default value of regex will change from True to False in a future version.
annot['Chromosome'] = annot['Chromosome'].str.replace(r'(\b\S)', r'chr\1')

2022-04-29 13:25:43,314 pycisTarget_wrapper INFO Loading cisTarget database for Topics
2022-04-29 13:25:43,315 cisTarget INFO Reading cisTarget database
2022-04-29 13:57:42,246 pycisTarget_wrapper INFO Running cisTarget for Topics
2022-04-29 13:57:42,249 cisTarget INFO Running cisTarget for Topic1 which has 13703 regions
2022-04-29 13:57:50,594 cisTarget INFO Annotating motifs for Topic1
2022-04-29 13:57:54,408 cisTarget INFO Getting cistromes for Topic1
2022-04-29 13:57:54,993 cisTarget INFO Running cisTarget for Topic2 which has 22851 regions
2022-04-29 13:58:03,400 cisTarget INFO Annotating motifs for Topic2
2022-04-29 13:58:05,728 cisTarget INFO Getting cistromes for Topic2
2022-04-29 13:58:06,050 cisTarget INFO Running cisTarget for Topic3 which has 12525 regions
2022-04-29 13:58:15,149 cisTarget INFO Annotating motifs for Topic3
2022-04-29 13:58:18,656 cisTarget INFO Getting cistromes for Topic3
2022-04-29 13:58:19,562 cisTarget INFO Running cisTarget for Topic4 which has 29276 regions
2022-04-29 13:58:30,937 cisTarget INFO Annotating motifs for Topic4
2022-04-29 13:58:35,664 cisTarget INFO Getting cistromes for Topic4
2022-04-29 13:58:35,710 cisTarget INFO Running cisTarget for Topic5 which has 20833 regions
2022-04-29 13:58:49,814 cisTarget INFO Annotating motifs for Topic5
2022-04-29 13:58:54,014 cisTarget INFO Getting cistromes for Topic5
2022-04-29 13:58:54,927 cisTarget INFO Running cisTarget for Topic6 which has 9009 regions
2022-04-29 13:59:10,030 cisTarget INFO Annotating motifs for Topic6
2022-04-29 13:59:19,402 cisTarget INFO Getting cistromes for Topic6
2022-04-29 13:59:21,111 cisTarget INFO Running cisTarget for Topic7 which has 20533 regions
2022-04-29 13:59:39,514 cisTarget INFO Annotating motifs for Topic7
2022-04-29 13:59:43,824 cisTarget INFO Getting cistromes for Topic7
2022-04-29 13:59:44,516 cisTarget INFO Running cisTarget for Topic8 which has 21334 regions
2022-04-29 14:00:00,030 cisTarget INFO Annotating motifs for Topic8
2022-04-29 14:00:04,598 cisTarget INFO Getting cistromes for Topic8
2022-04-29 14:00:05,119 cisTarget INFO Running cisTarget for Topic9 which has 11720 regions
2022-04-29 14:00:17,639 cisTarget INFO Annotating motifs for Topic9
2022-04-29 14:00:24,213 cisTarget INFO Getting cistromes for Topic9
2022-04-29 14:00:25,233 cisTarget INFO Running cisTarget for Topic10 which has 17882 regions
2022-04-29 14:00:39,513 cisTarget INFO Annotating motifs for Topic10
2022-04-29 14:00:45,221 cisTarget INFO Getting cistromes for Topic10
2022-04-29 14:00:46,307 cisTarget INFO Running cisTarget for Topic11 which has 21465 regions
2022-04-29 14:00:59,618 cisTarget INFO Annotating motifs for Topic11
2022-04-29 14:01:03,915 cisTarget INFO Getting cistromes for Topic11
2022-04-29 14:01:04,762 cisTarget INFO Running cisTarget for Topic12 which has 24535 regions
2022-04-29 14:01:17,754 cisTarget INFO Annotating motifs for Topic12
2022-04-29 14:01:22,358 cisTarget INFO Getting cistromes for Topic12
2022-04-29 14:01:22,686 cisTarget INFO Running cisTarget for Topic13 which has 9546 regions
2022-04-29 14:01:34,595 cisTarget INFO Annotating motifs for Topic13
2022-04-29 14:01:39,015 cisTarget INFO Getting cistromes for Topic13
2022-04-29 14:01:39,907 cisTarget INFO Running cisTarget for Topic14 which has 25595 regions
2022-04-29 14:01:52,319 cisTarget INFO Annotating motifs for Topic14
2022-04-29 14:01:54,653 cisTarget INFO Getting cistromes for Topic14
2022-04-29 14:01:54,982 cisTarget INFO Running cisTarget for Topic15 which has 15535 regions
2022-04-29 14:02:08,233 cisTarget INFO Annotating motifs for Topic15
2022-04-29 14:02:11,835 cisTarget INFO Getting cistromes for Topic15
2022-04-29 14:02:12,351 cisTarget INFO Running cisTarget for Topic16 which has 24957 regions
2022-04-29 14:02:28,204 cisTarget INFO Annotating motifs for Topic16
2022-04-29 14:02:31,016 cisTarget INFO Getting cistromes for Topic16
2022-04-29 14:02:31,198 cisTarget INFO Running cisTarget for Topic17 which has 26710 regions
2022-04-29 14:02:48,637 cisTarget INFO Annotating motifs for Topic17
2022-04-29 14:02:51,332 cisTarget INFO Getting cistromes for Topic17
2022-04-29 14:02:51,469 cisTarget INFO Running cisTarget for Topic18 which has 26376 regions
2022-04-29 14:03:08,772 cisTarget INFO Annotating motifs for Topic18
2022-04-29 14:03:11,462 cisTarget INFO Getting cistromes for Topic18
2022-04-29 14:03:11,611 cisTarget INFO Running cisTarget for Topic19 which has 19155 regions
2022-04-29 14:03:30,404 cisTarget INFO Annotating motifs for Topic19
2022-04-29 14:03:33,681 cisTarget INFO Getting cistromes for Topic19
2022-04-29 14:03:34,131 cisTarget INFO Running cisTarget for Topic20 which has 9452 regions
2022-04-29 14:03:58,447 cisTarget INFO Annotating motifs for Topic20
2022-04-29 14:04:03,393 cisTarget INFO Getting cistromes for Topic20
2022-04-29 14:04:04,244 cisTarget INFO Running cisTarget for Topic21 which has 15810 regions
2022-04-29 14:04:20,538 cisTarget INFO Annotating motifs for Topic21
2022-04-29 14:04:24,970 cisTarget INFO Getting cistromes for Topic21
2022-04-29 14:04:25,741 cisTarget INFO Running cisTarget for Topic23 which has 8929 regions
2022-04-29 14:04:41,679 cisTarget INFO Annotating motifs for Topic23
2022-04-29 14:04:47,329 cisTarget INFO Getting cistromes for Topic23
2022-04-29 14:04:47,904 cisTarget INFO Running cisTarget for Topic24 which has 21878 regions
2022-04-29 14:05:00,513 cisTarget INFO Annotating motifs for Topic24
2022-04-29 14:05:03,450 cisTarget INFO Getting cistromes for Topic24
2022-04-29 14:05:03,523 cisTarget INFO Running cisTarget for Topic25 which has 24046 regions
2022-04-29 14:05:22,142 cisTarget INFO Annotating motifs for Topic25
2022-04-29 14:05:28,328 cisTarget INFO Getting cistromes for Topic25
2022-04-29 14:05:29,422 cisTarget INFO Running cisTarget for Topic26 which has 24751 regions
2022-04-29 14:05:45,133 cisTarget INFO Annotating motifs for Topic26
2022-04-29 14:05:48,675 cisTarget INFO Getting cistromes for Topic26
2022-04-29 14:05:48,834 cisTarget INFO Running cisTarget for Topic27 which has 9241 regions
2022-04-29 14:06:02,600 cisTarget INFO Annotating motifs for Topic27
2022-04-29 14:06:08,380 cisTarget INFO Getting cistromes for Topic27
2022-04-29 14:06:09,169 cisTarget INFO Running cisTarget for Topic28 which has 27115 regions
2022-04-29 14:06:24,154 cisTarget INFO Annotating motifs for Topic28
2022-04-29 14:06:26,910 cisTarget INFO Getting cistromes for Topic28
2022-04-29 14:06:27,162 cisTarget INFO Running cisTarget for Topic29 which has 27363 regions
2022-04-29 14:06:39,134 cisTarget INFO Annotating motifs for Topic29
2022-04-29 14:06:42,268 cisTarget INFO Getting cistromes for Topic29
2022-04-29 14:06:42,356 cisTarget INFO Running cisTarget for Topic30 which has 26642 regions
2022-04-29 14:07:01,434 cisTarget INFO Annotating motifs for Topic30
2022-04-29 14:07:03,590 cisTarget INFO Getting cistromes for Topic30
2022-04-29 14:07:03,652 cisTarget INFO Running cisTarget for Topic31 which has 21479 regions
2022-04-29 14:07:17,671 cisTarget INFO Annotating motifs for Topic31
2022-04-29 14:07:21,258 cisTarget INFO Getting cistromes for Topic31
2022-04-29 14:07:22,394 cisTarget INFO Running cisTarget for Topic32 which has 27629 regions
2022-04-29 14:07:37,279 cisTarget INFO Annotating motifs for Topic32
2022-04-29 14:07:40,085 cisTarget INFO Getting cistromes for Topic32
2022-04-29 14:07:40,159 cisTarget INFO Running cisTarget for Topic33 which has 22747 regions
2022-04-29 14:07:54,661 cisTarget INFO Annotating motifs for Topic33
2022-04-29 14:07:59,084 cisTarget INFO Getting cistromes for Topic33
2022-04-29 14:07:59,464 cisTarget INFO Running cisTarget for Topic34 which has 16364 regions
2022-04-29 14:08:14,224 cisTarget INFO Annotating motifs for Topic34
2022-04-29 14:08:22,705 cisTarget INFO Getting cistromes for Topic34
2022-04-29 14:08:23,373 cisTarget INFO Running cisTarget for Topic35 which has 10618 regions
2022-04-29 14:08:36,511 cisTarget INFO Annotating motifs for Topic35
2022-04-29 14:08:43,026 cisTarget INFO Getting cistromes for Topic35
2022-04-29 14:08:44,198 cisTarget INFO Running cisTarget for Topic36 which has 26167 regions
2022-04-29 14:09:00,697 cisTarget INFO Annotating motifs for Topic36
2022-04-29 14:09:04,061 cisTarget INFO Getting cistromes for Topic36
2022-04-29 14:09:04,170 cisTarget INFO Running cisTarget for Topic37 which has 25079 regions
2022-04-29 14:09:17,970 cisTarget INFO Annotating motifs for Topic37
2022-04-29 14:09:20,537 cisTarget INFO Getting cistromes for Topic37
2022-04-29 14:09:20,617 cisTarget INFO Running cisTarget for Topic38 which has 22859 regions
2022-04-29 14:09:39,921 cisTarget INFO Annotating motifs for Topic38
2022-04-29 14:09:46,333 cisTarget INFO Getting cistromes for Topic38
2022-04-29 14:09:46,849 cisTarget INFO Running cisTarget for Topic39 which has 30127 regions
2022-04-29 14:09:56,855 cisTarget INFO Annotating motifs for Topic39
2022-04-29 14:09:59,336 cisTarget INFO Getting cistromes for Topic39
2022-04-29 14:09:59,437 cisTarget INFO Running cisTarget for Topic40 which has 8236 regions
2022-04-29 14:10:10,454 cisTarget INFO Annotating motifs for Topic40
2022-04-29 14:10:14,337 cisTarget INFO Getting cistromes for Topic40
2022-04-29 14:10:14,971 cisTarget INFO Running cisTarget for Topic41 which has 19666 regions
2022-04-29 14:10:26,792 cisTarget INFO Annotating motifs for Topic41
2022-04-29 14:10:31,816 cisTarget INFO Getting cistromes for Topic41
2022-04-29 14:10:32,644 cisTarget INFO Running cisTarget for Topic42 which has 25090 regions
2022-04-29 14:10:42,421 cisTarget INFO Annotating motifs for Topic42
2022-04-29 14:10:44,150 cisTarget INFO Getting cistromes for Topic42
2022-04-29 14:10:44,253 cisTarget INFO Running cisTarget for Topic43 which has 28680 regions
2022-04-29 14:10:53,066 cisTarget INFO Annotating motifs for Topic43
2022-04-29 14:10:55,974 cisTarget INFO Getting cistromes for Topic43
2022-04-29 14:10:56,072 cisTarget INFO Running cisTarget for Topic44 which has 25169 regions
2022-04-29 14:11:06,255 cisTarget INFO Annotating motifs for Topic44
2022-04-29 14:11:08,908 cisTarget INFO Getting cistromes for Topic44
2022-04-29 14:11:08,986 cisTarget INFO Running cisTarget for Topic45 which has 21862 regions
2022-04-29 14:11:20,843 cisTarget INFO Annotating motifs for Topic45
2022-04-29 14:11:23,265 cisTarget INFO Getting cistromes for Topic45
2022-04-29 14:11:23,697 cisTarget INFO Running cisTarget for Topic47 which has 11173 regions
2022-04-29 14:11:34,508 cisTarget INFO Annotating motifs for Topic47
2022-04-29 14:11:38,886 cisTarget INFO Getting cistromes for Topic47
2022-04-29 14:11:39,969 cisTarget INFO Running cisTarget for Topic48 which has 19915 regions
2022-04-29 14:11:53,137 cisTarget INFO Annotating motifs for Topic48
2022-04-29 14:11:56,239 cisTarget INFO Getting cistromes for Topic48
2022-04-29 14:11:57,036 cisTarget INFO Running cisTarget for Topic49 which has 28401 regions
2022-04-29 14:12:07,871 cisTarget INFO Annotating motifs for Topic49
2022-04-29 14:12:09,535 cisTarget INFO Getting cistromes for Topic49
2022-04-29 14:12:09,578 cisTarget INFO Running cisTarget for Topic50 which has 25767 regions
2022-04-29 14:12:16,319 cisTarget INFO Annotating motifs for Topic50
2022-04-29 14:12:17,923 cisTarget INFO Getting cistromes for Topic50
2022-04-29 14:12:17,988 cisTarget INFO Running cisTarget for Topic51 which has 16533 regions
2022-04-29 14:12:25,563 cisTarget INFO Annotating motifs for Topic51
2022-04-29 14:12:28,231 cisTarget INFO Getting cistromes for Topic51
2022-04-29 14:12:28,724 cisTarget INFO Running cisTarget for Topic53 which has 23574 regions
2022-04-29 14:12:38,047 cisTarget INFO Annotating motifs for Topic53
2022-04-29 14:12:40,782 cisTarget INFO Getting cistromes for Topic53
2022-04-29 14:12:41,284 cisTarget INFO Running cisTarget for Topic54 which has 24723 regions
2022-04-29 14:12:48,951 cisTarget INFO Annotating motifs for Topic54
2022-04-29 14:12:51,001 cisTarget INFO Getting cistromes for Topic54
2022-04-29 14:12:51,179 cisTarget INFO Running cisTarget for Topic55 which has 26636 regions
2022-04-29 14:12:58,170 cisTarget INFO Annotating motifs for Topic55
2022-04-29 14:12:59,738 cisTarget INFO Getting cistromes for Topic55
2022-04-29 14:12:59,778 cisTarget INFO Running cisTarget for Topic56 which has 26835 regions
2022-04-29 14:13:07,245 cisTarget INFO Annotating motifs for Topic56
2022-04-29 14:13:09,112 cisTarget INFO Getting cistromes for Topic56
2022-04-29 14:13:09,186 cisTarget INFO Running cisTarget for Topic57 which has 25292 regions
2022-04-29 14:13:19,112 cisTarget INFO Annotating motifs for Topic57
2022-04-29 14:13:21,795 cisTarget INFO Getting cistromes for Topic57
2022-04-29 14:13:22,099 cisTarget INFO Running cisTarget for Topic58 which has 23763 regions
2022-04-29 14:13:28,715 cisTarget INFO Annotating motifs for Topic58
2022-04-29 14:13:30,418 cisTarget INFO Getting cistromes for Topic58
2022-04-29 14:13:30,514 cisTarget INFO Running cisTarget for Topic59 which has 24669 regions
2022-04-29 14:13:39,284 cisTarget INFO Annotating motifs for Topic59
2022-04-29 14:13:41,563 cisTarget INFO Getting cistromes for Topic59
2022-04-29 14:13:41,856 cisTarget INFO Running cisTarget for Topic60 which has 17206 regions
2022-04-29 14:13:49,370 cisTarget INFO Annotating motifs for Topic60
2022-04-29 14:13:51,786 cisTarget INFO Getting cistromes for Topic60
2022-04-29 14:13:52,160 cisTarget INFO Running cisTarget for Topic61 which has 24594 regions
2022-04-29 14:13:59,076 cisTarget INFO Annotating motifs for Topic61
2022-04-29 14:14:00,819 cisTarget INFO Getting cistromes for Topic61
2022-04-29 14:14:00,983 cisTarget INFO Running cisTarget for Topic62 which has 27029 regions
2022-04-29 14:14:08,249 cisTarget INFO Annotating motifs for Topic62
2022-04-29 14:14:09,909 cisTarget INFO Getting cistromes for Topic62
2022-04-29 14:14:09,999 cisTarget INFO Running cisTarget for Topic64 which has 20551 regions
2022-04-29 14:14:23,046 cisTarget INFO Annotating motifs for Topic64
2022-04-29 14:14:26,184 cisTarget INFO Getting cistromes for Topic64
2022-04-29 14:14:26,686 cisTarget INFO Running cisTarget for Topic65 which has 21205 regions
2022-04-29 14:14:41,025 cisTarget INFO Annotating motifs for Topic65
2022-04-29 14:14:44,513 cisTarget INFO Getting cistromes for Topic65
2022-04-29 14:14:45,209 cisTarget INFO Running cisTarget for Topic66 which has 26952 regions
2022-04-29 14:14:56,792 cisTarget INFO Annotating motifs for Topic66
2022-04-29 14:14:58,810 cisTarget INFO Getting cistromes for Topic66
2022-04-29 14:14:58,856 cisTarget INFO Running cisTarget for Topic67 which has 25319 regions
2022-04-29 14:15:11,348 cisTarget INFO Annotating motifs for Topic67
2022-04-29 14:15:13,786 cisTarget INFO Getting cistromes for Topic67
2022-04-29 14:15:13,882 cisTarget INFO Running cisTarget for Topic68 which has 21984 regions
2022-04-29 14:15:27,494 cisTarget INFO Annotating motifs for Topic68
2022-04-29 14:15:30,466 cisTarget INFO Getting cistromes for Topic68
2022-04-29 14:15:30,722 cisTarget INFO Running cisTarget for Topic69 which has 23334 regions
2022-04-29 14:15:44,849 cisTarget INFO Annotating motifs for Topic69
2022-04-29 14:15:48,824 cisTarget INFO Getting cistromes for Topic69
2022-04-29 14:15:49,362 cisTarget INFO Running cisTarget for Topic70 which has 22904 regions
2022-04-29 14:16:10,648 cisTarget INFO Annotating motifs for Topic70
2022-04-29 14:16:13,852 cisTarget INFO Getting cistromes for Topic70
2022-04-29 14:16:14,237 cisTarget INFO Running cisTarget for Topic71 which has 22941 regions
2022-04-29 14:16:28,951 cisTarget INFO Annotating motifs for Topic71
2022-04-29 14:16:31,649 cisTarget INFO Getting cistromes for Topic71
2022-04-29 14:16:32,054 cisTarget INFO Running cisTarget for Topic72 which has 7798 regions
2022-04-29 14:16:44,786 cisTarget INFO Annotating motifs for Topic72
2022-04-29 14:16:48,328 cisTarget INFO Getting cistromes for Topic72
2022-04-29 14:16:49,079 cisTarget INFO Running cisTarget for Topic73 which has 21751 regions
2022-04-29 14:17:06,071 cisTarget INFO Annotating motifs for Topic73
2022-04-29 14:17:09,964 cisTarget INFO Getting cistromes for Topic73
2022-04-29 14:17:10,644 cisTarget INFO Running cisTarget for Topic74 which has 19709 regions
2022-04-29 14:17:26,689 cisTarget INFO Annotating motifs for Topic74
2022-04-29 14:17:30,413 cisTarget INFO Getting cistromes for Topic74
2022-04-29 14:17:30,863 cisTarget INFO Done!
2022-04-29 14:17:30,877 pycisTarget_wrapper INFO Created folder : /lustre1/project/stg_00002/lcb/nhecker/cross_species/snare_seq/human/pycistarget_v10_2022_04_27/CTX_Topics_All
2022-04-29 14:17:32,182 pycisTarget_wrapper INFO Running cisTarget without promoters for Topics
2022-04-29 14:23:43,585 cisTarget INFO Running cisTarget for Topic1 which has 10036 regions
2022-04-29 14:23:49,248 cisTarget INFO Annotating motifs for Topic1
2022-04-29 14:23:51,037 cisTarget INFO Getting cistromes for Topic1
2022-04-29 14:23:51,199 cisTarget INFO Running cisTarget for Topic2 which has 20170 regions
2022-04-29 14:23:57,800 cisTarget INFO Annotating motifs for Topic2
2022-04-29 14:23:59,607 cisTarget INFO Getting cistromes for Topic2
2022-04-29 14:23:59,753 cisTarget INFO Running cisTarget for Topic3 which has 7814 regions
2022-04-29 14:24:05,563 cisTarget INFO Annotating motifs for Topic3
2022-04-29 14:24:07,792 cisTarget INFO Getting cistromes for Topic3
2022-04-29 14:24:08,095 cisTarget INFO Running cisTarget for Topic4 which has 27988 regions
2022-04-29 14:24:15,151 cisTarget INFO Annotating motifs for Topic4
2022-04-29 14:24:16,657 cisTarget INFO Getting cistromes for Topic4
2022-04-29 14:24:16,676 cisTarget INFO Running cisTarget for Topic5 which has 16985 regions
2022-04-29 14:24:24,020 cisTarget INFO Annotating motifs for Topic5
2022-04-29 14:24:26,403 cisTarget INFO Getting cistromes for Topic5
2022-04-29 14:24:26,774 cisTarget INFO Running cisTarget for Topic6 which has 3433 regions
2022-04-29 14:24:31,753 cisTarget INFO Annotating motifs for Topic6
2022-04-29 14:24:33,476 cisTarget INFO Getting cistromes for Topic6
2022-04-29 14:24:33,756 cisTarget INFO Running cisTarget for Topic7 which has 17095 regions
2022-04-29 14:24:41,373 cisTarget INFO Annotating motifs for Topic7
2022-04-29 14:24:43,703 cisTarget INFO Getting cistromes for Topic7
2022-04-29 14:24:44,011 cisTarget INFO Running cisTarget for Topic8 which has 19004 regions
2022-04-29 14:24:51,204 cisTarget INFO Annotating motifs for Topic8
2022-04-29 14:24:53,034 cisTarget INFO Getting cistromes for Topic8
2022-04-29 14:24:53,205 cisTarget INFO Running cisTarget for Topic9 which has 7317 regions
2022-04-29 14:24:58,808 cisTarget INFO Annotating motifs for Topic9
2022-04-29 14:25:00,974 cisTarget INFO Getting cistromes for Topic9
2022-04-29 14:25:01,271 cisTarget INFO Running cisTarget for Topic10 which has 13853 regions
2022-04-29 14:25:07,290 cisTarget INFO Annotating motifs for Topic10
2022-04-29 14:25:09,286 cisTarget INFO Getting cistromes for Topic10
2022-04-29 14:25:09,469 cisTarget INFO Running cisTarget for Topic11 which has 18680 regions
2022-04-29 14:25:16,147 cisTarget INFO Annotating motifs for Topic11
2022-04-29 14:25:17,913 cisTarget INFO Getting cistromes for Topic11
2022-04-29 14:25:18,131 cisTarget INFO Running cisTarget for Topic12 which has 22636 regions
2022-04-29 14:25:24,481 cisTarget INFO Annotating motifs for Topic12
2022-04-29 14:25:26,212 cisTarget INFO Getting cistromes for Topic12
2022-04-29 14:25:26,358 cisTarget INFO Running cisTarget for Topic13 which has 3981 regions
2022-04-29 14:25:31,130 cisTarget INFO Annotating motifs for Topic13
2022-04-29 14:25:32,857 cisTarget INFO Getting cistromes for Topic13
2022-04-29 14:25:33,065 cisTarget INFO Running cisTarget for Topic14 which has 23617 regions
2022-04-29 14:25:39,899 cisTarget INFO Annotating motifs for Topic14
2022-04-29 14:25:41,581 cisTarget INFO Getting cistromes for Topic14
2022-04-29 14:25:41,725 cisTarget INFO Running cisTarget for Topic15 which has 12132 regions
2022-04-29 14:25:47,296 cisTarget INFO Annotating motifs for Topic15
2022-04-29 14:25:49,136 cisTarget INFO Getting cistromes for Topic15
2022-04-29 14:25:49,326 cisTarget INFO Running cisTarget for Topic16 which has 23550 regions
2022-04-29 14:25:55,407 cisTarget INFO Annotating motifs for Topic16
2022-04-29 14:25:56,931 cisTarget INFO Getting cistromes for Topic16
2022-04-29 14:25:56,962 cisTarget INFO Running cisTarget for Topic17 which has 25106 regions
2022-04-29 14:26:03,198 cisTarget INFO Annotating motifs for Topic17
2022-04-29 14:26:04,699 cisTarget INFO Getting cistromes for Topic17
2022-04-29 14:26:04,739 cisTarget INFO Running cisTarget for Topic18 which has 24530 regions
2022-04-29 14:26:11,238 cisTarget INFO Annotating motifs for Topic18
2022-04-29 14:26:12,776 cisTarget INFO Getting cistromes for Topic18
2022-04-29 14:26:12,834 cisTarget INFO Running cisTarget for Topic19 which has 16612 regions
2022-04-29 14:26:19,465 cisTarget INFO Annotating motifs for Topic19
2022-04-29 14:26:21,572 cisTarget INFO Getting cistromes for Topic19
2022-04-29 14:26:21,774 cisTarget INFO Running cisTarget for Topic20 which has 4085 regions
2022-04-29 14:26:26,490 cisTarget INFO Annotating motifs for Topic20
2022-04-29 14:26:28,276 cisTarget INFO Getting cistromes for Topic20
2022-04-29 14:26:28,522 cisTarget INFO Running cisTarget for Topic21 which has 12764 regions
2022-04-29 14:26:35,260 cisTarget INFO Annotating motifs for Topic21
2022-04-29 14:26:37,325 cisTarget INFO Getting cistromes for Topic21
2022-04-29 14:26:37,559 cisTarget INFO Running cisTarget for Topic23 which has 4636 regions
2022-04-29 14:26:42,225 cisTarget INFO Annotating motifs for Topic23
2022-04-29 14:26:44,025 cisTarget INFO Getting cistromes for Topic23
2022-04-29 14:26:44,212 cisTarget INFO Running cisTarget for Topic24 which has 20657 regions
2022-04-29 14:26:49,817 cisTarget INFO Annotating motifs for Topic24
2022-04-29 14:26:51,317 cisTarget INFO Getting cistromes for Topic24
2022-04-29 14:26:51,334 cisTarget INFO Running cisTarget for Topic25 which has 21772 regions
2022-04-29 14:26:58,088 cisTarget INFO Annotating motifs for Topic25
2022-04-29 14:26:59,964 cisTarget INFO Getting cistromes for Topic25
2022-04-29 14:27:00,122 cisTarget INFO Running cisTarget for Topic26 which has 22711 regions
2022-04-29 14:27:06,383 cisTarget INFO Annotating motifs for Topic26
2022-04-29 14:27:07,946 cisTarget INFO Getting cistromes for Topic26
2022-04-29 14:27:08,015 cisTarget INFO Running cisTarget for Topic27 which has 5014 regions
2022-04-29 14:27:14,038 cisTarget INFO Annotating motifs for Topic27
2022-04-29 14:27:16,241 cisTarget INFO Getting cistromes for Topic27
2022-04-29 14:27:16,613 cisTarget INFO Running cisTarget for Topic28 which has 25777 regions
2022-04-29 14:27:23,033 cisTarget INFO Annotating motifs for Topic28
2022-04-29 14:27:24,514 cisTarget INFO Getting cistromes for Topic28
2022-04-29 14:27:24,574 cisTarget INFO Running cisTarget for Topic29 which has 25858 regions
2022-04-29 14:27:31,034 cisTarget INFO Annotating motifs for Topic29
2022-04-29 14:27:32,508 cisTarget INFO Getting cistromes for Topic29
2022-04-29 14:27:32,547 cisTarget INFO Running cisTarget for Topic30 which has 25152 regions
2022-04-29 14:27:38,926 cisTarget INFO Annotating motifs for Topic30
2022-04-29 14:27:40,395 cisTarget INFO Getting cistromes for Topic30
2022-04-29 14:27:40,411 cisTarget INFO Running cisTarget for Topic31 which has 19024 regions
2022-04-29 14:27:48,762 cisTarget INFO Annotating motifs for Topic31
2022-04-29 14:27:51,233 cisTarget INFO Getting cistromes for Topic31
2022-04-29 14:27:51,594 cisTarget INFO Running cisTarget for Topic32 which has 26255 regions
2022-04-29 14:27:57,892 cisTarget INFO Annotating motifs for Topic32
2022-04-29 14:27:59,440 cisTarget INFO Getting cistromes for Topic32
2022-04-29 14:27:59,456 cisTarget INFO Running cisTarget for Topic33 which has 21070 regions
2022-04-29 14:28:07,539 cisTarget INFO Annotating motifs for Topic33
2022-04-29 14:28:09,464 cisTarget INFO Getting cistromes for Topic33
2022-04-29 14:28:09,568 cisTarget INFO Running cisTarget for Topic34 which has 13529 regions
2022-04-29 14:28:17,105 cisTarget INFO Annotating motifs for Topic34
2022-04-29 14:28:19,702 cisTarget INFO Getting cistromes for Topic34
2022-04-29 14:28:19,795 cisTarget INFO Running cisTarget for Topic35 which has 5123 regions
2022-04-29 14:28:26,771 cisTarget INFO Annotating motifs for Topic35
2022-04-29 14:28:29,410 cisTarget INFO Getting cistromes for Topic35
2022-04-29 14:28:29,873 cisTarget INFO Running cisTarget for Topic36 which has 24609 regions
2022-04-29 14:28:36,877 cisTarget INFO Annotating motifs for Topic36
2022-04-29 14:28:39,058 cisTarget INFO Getting cistromes for Topic36
2022-04-29 14:28:39,072 cisTarget INFO Running cisTarget for Topic37 which has 23224 regions
2022-04-29 14:28:46,356 cisTarget INFO Annotating motifs for Topic37
2022-04-29 14:28:48,871 cisTarget INFO Getting cistromes for Topic37
2022-04-29 14:28:48,943 cisTarget INFO Running cisTarget for Topic38 which has 19551 regions
2022-04-29 14:28:58,086 cisTarget INFO Annotating motifs for Topic38
2022-04-29 14:29:01,336 cisTarget INFO Getting cistromes for Topic38
2022-04-29 14:29:01,545 cisTarget INFO Running cisTarget for Topic39 which has 28746 regions
2022-04-29 14:29:08,547 cisTarget INFO Annotating motifs for Topic39
2022-04-29 14:29:10,268 cisTarget INFO Getting cistromes for Topic39
2022-04-29 14:29:10,277 cisTarget INFO Running cisTarget for Topic40 which has 3009 regions
2022-04-29 14:29:15,117 cisTarget INFO Annotating motifs for Topic40
2022-04-29 14:29:17,037 cisTarget INFO Getting cistromes for Topic40
2022-04-29 14:29:17,728 cisTarget INFO Running cisTarget for Topic41 which has 15409 regions
2022-04-29 14:29:28,045 cisTarget INFO Annotating motifs for Topic41
2022-04-29 14:29:29,943 cisTarget INFO Getting cistromes for Topic41
2022-04-29 14:29:30,058 cisTarget INFO Running cisTarget for Topic42 which has 23341 regions
2022-04-29 14:29:36,471 cisTarget INFO Annotating motifs for Topic42
2022-04-29 14:29:38,246 cisTarget INFO Getting cistromes for Topic42
2022-04-29 14:29:38,336 cisTarget INFO Running cisTarget for Topic43 which has 27523 regions
2022-04-29 14:29:44,617 cisTarget INFO Annotating motifs for Topic43
2022-04-29 14:29:46,085 cisTarget INFO Getting cistromes for Topic43
2022-04-29 14:29:46,103 cisTarget INFO Running cisTarget for Topic44 which has 23053 regions
2022-04-29 14:29:52,720 cisTarget INFO Annotating motifs for Topic44
2022-04-29 14:29:54,390 cisTarget INFO Getting cistromes for Topic44
2022-04-29 14:29:54,532 cisTarget INFO Running cisTarget for Topic45 which has 20010 regions
2022-04-29 14:30:00,705 cisTarget INFO Annotating motifs for Topic45
2022-04-29 14:30:02,419 cisTarget INFO Getting cistromes for Topic45
2022-04-29 14:30:02,582 cisTarget INFO Running cisTarget for Topic47 which has 5580 regions
2022-04-29 14:30:10,318 cisTarget INFO Annotating motifs for Topic47
2022-04-29 14:30:13,679 cisTarget INFO Getting cistromes for Topic47
2022-04-29 14:30:14,381 cisTarget INFO Running cisTarget for Topic48 which has 15873 regions
2022-04-29 14:30:21,595 cisTarget INFO Annotating motifs for Topic48
2022-04-29 14:30:23,627 cisTarget INFO Getting cistromes for Topic48
2022-04-29 14:30:23,850 cisTarget INFO Running cisTarget for Topic49 which has 26984 regions
2022-04-29 14:30:30,767 cisTarget INFO Annotating motifs for Topic49
2022-04-29 14:30:32,245 cisTarget INFO Getting cistromes for Topic49
2022-04-29 14:30:32,273 cisTarget INFO Running cisTarget for Topic50 which has 23753 regions
2022-04-29 14:30:38,271 cisTarget INFO Annotating motifs for Topic50
2022-04-29 14:30:39,788 cisTarget INFO Getting cistromes for Topic50
2022-04-29 14:30:39,836 cisTarget INFO Running cisTarget for Topic51 which has 12827 regions
2022-04-29 14:30:45,536 cisTarget INFO Annotating motifs for Topic51
2022-04-29 14:30:47,247 cisTarget INFO Getting cistromes for Topic51
2022-04-29 14:30:47,417 cisTarget INFO Running cisTarget for Topic53 which has 20799 regions
2022-04-29 14:30:56,587 cisTarget INFO Annotating motifs for Topic53
2022-04-29 14:30:59,794 cisTarget INFO Getting cistromes for Topic53
2022-04-29 14:31:00,253 cisTarget INFO Running cisTarget for Topic54 which has 23012 regions
2022-04-29 14:31:09,952 cisTarget INFO Annotating motifs for Topic54
2022-04-29 14:31:12,177 cisTarget INFO Getting cistromes for Topic54
2022-04-29 14:31:12,322 cisTarget INFO Running cisTarget for Topic55 which has 25300 regions

ValueError Traceback (most recent call last)
Input In [13], in <cell line: 6>()
1 # Run pycistarget
2 # run_without_promoters = True, will run the methods in all regions + the region sets without promoters
3 #import os
4 #os.chdir('/staging/leuven/stg_00002/lcb/cbravo/Multiomics_pipeline/scenicplus/src/')
5 from scenicplus.wrappers.run_pycistarget import *
----> 6 run_pycistarget(region_sets_nonzero,
7 ctx_db_path = '/lustre1/project/stg_00002/lcb/nhecker/cross_species/snare_seq/human/pycistarget_v10_2022_04_27/dbs/SNAREseq_human_cortex.regions_vs_motifs.rankings.feather',
8 species = 'homo_sapiens',
9 save_path = '/lustre1/project/stg_00002/lcb/nhecker/cross_species/snare_seq/human/pycistarget_v10_2022_04_27/',
10 dem_db_path = '/lustre1/project/stg_00002/lcb/nhecker/cross_species/snare_seq/human/pycistarget_v10_2022_04_27/dbs/SNAREseq_human_cortex.regions_vs_motifs.scores.feather',
11 run_without_promoters = True,
12 biomart_host = 'http://jul2018.archive.ensembl.org/ class="ansi-yellow-bg" style="color:rgb(175,0,0)">',
13 promoter_space = 500,
14 ctx_auc_threshold = 0.005,
15 ctx_nes_threshold = 3.0,
16 ctx_rank_threshold = 0.05,
17 dem_log2fc_thr = 0.5,
18 dem_motif_hit_thr = 3.0,
19 dem_max_bg_regions = 500,
20 path_to_motif_annotations = '/staging/leuven/stg_00002/lcb/cbravo/cluster_motif_collection_V10_no_desso_no_factorbook/snapshots/motifs-v10-nr.more_orthology.hgnc-mm0.00001-o0.0_clust.tsv',
21 annotation_version = 'v10nr_clust',
22 annotation = ['Direct_annot', 'Orthology_annot'],
23 n_cpu = 1,
24 _temp_dir = '/scratch/leuven/339/vsc33943/ray_spill')

File /opt/venv/lib/python3.8/site-packages/scenicplus/wrappers/run_pycistarget.py:188, in run_pycistarget(region_sets, species, save_path, save_partial, ctx_db_path, dem_db_path, run_without_promoters, biomart_host, promoter_space, ctx_auc_threshold, ctx_nes_threshold, ctx_rank_threshold, dem_log2fc_thr, dem_motif_hit_thr, dem_max_bg_regions, annotation, motif_similarity_fdr, path_to_motif_annotations, annotation_version, n_cpu, temp_dir, exclude_motifs, exclude_collection)
186 db_regions = set(pd.concat([ctx_db.regions_to_db[x] for x in ctx_db.regions_to_db.keys()])['Query'])
187 ctx_db.regions_to_db = {x: target_to_query(regions_np[x], list(db_regions), fraction_overlap = 0.4) for x in regions_np.keys()}
--> 188 menr['CTX'+key+'_No_promoters'] = run_cistarget(ctx_db = ctx_db,
189 region_sets = regions_np,
190 specie = species,
191 auc_threshold = ctx_auc_threshold,
192 nes_threshold = ctx_nes_threshold,
193 rank_threshold = ctx_rank_threshold,
194 annotation = annotation,
195 motif_similarity_fdr = motif_similarity_fdr,
196 path_to_motif_annotations = path_to_motif_annotations,
197 n_cpu = n_cpu,
198 _temp_dir= temp_dir,
199 annotation_version = annotation_version)
200 out_folder = os.path.join(save_path,'CTX'+key+'_No_promoters')
201 check_folder = os.path.isdir(out_folder)

File /opt/venv/lib/python3.8/site-packages/pycistarget/motif_enrichment_cistarget.py:526, in run_cistarget(ctx_db, region_sets, specie, name, fraction_overlap, auc_threshold, nes_threshold, rank_threshold, path_to_motif_annotations, annotation_version, annotation, motif_similarity_fdr, orthologous_identity_threshold, n_cpu, motifs_to_use, **kwargs)
524 sys.stderr = sys.stderr
525 else:
--> 526 ctx_dict = [ctx_internal(ctx_db = ctx_db,
527 region_set = region_sets[key],
528 name = key,
529 specie = specie,
530 auc_threshold = auc_threshold,
531 nes_threshold = nes_threshold,
532 rank_threshold = rank_threshold,
533 path_to_motif_annotations = path_to_motif_annotations,
534 annotation_version = annotation_version,
535 annotation = annotation,
536 motif_similarity_fdr = motif_similarity_fdr,
537 orthologous_identity_threshold = orthologous_identity_threshold,
538 motifs_to_use = motifs_to_use) for key in list(region_sets.keys())]
539 ctx_dict = {key: ctx_result for key, ctx_result in zip(list(region_sets.keys()), ctx_dict)}
540 log.info('Done!')

File /opt/venv/lib/python3.8/site-packages/pycistarget/motif_enrichment_cistarget.py:526, in (.0)
524 sys.stderr = sys.stderr
525 else:
--> 526 ctx_dict = [ctx_internal(ctx_db = ctx_db,
527 region_set = region_sets[key],
528 name = key,
529 specie = specie,
530 auc_threshold = auc_threshold,
531 nes_threshold = nes_threshold,
532 rank_threshold = rank_threshold,
533 path_to_motif_annotations = path_to_motif_annotations,
534 annotation_version = annotation_version,
535 annotation = annotation,
536 motif_similarity_fdr = motif_similarity_fdr,
537 orthologous_identity_threshold = orthologous_identity_threshold,
538 motifs_to_use = motifs_to_use) for key in list(region_sets.keys())]
539 ctx_dict = {key: ctx_result for key, ctx_result in zip(list(region_sets.keys()), ctx_dict)}
540 log.info('Done!')

File /opt/venv/lib/python3.8/site-packages/pycistarget/motif_enrichment_cistarget.py:690, in ctx_internal(ctx_db, region_set, name, specie, auc_threshold, nes_threshold, rank_threshold, path_to_motif_annotations, annotation_version, annotation, motif_similarity_fdr, orthologous_identity_threshold, motifs_to_use)
632 """
633 Internal function to run cistarget.
634
(...)
676 Nat Protoc. June 2020:1-30. doi:10.1038/s41596-020-0336-2
677 """
678 ctx_result = cisTarget(region_set,
679 name,
680 specie,
(...)
688 orthologous_identity_threshold,
689 motifs_to_use)
--> 690 ctx_result.run_ctx(ctx_db)
691 return ctx_result

File /opt/venv/lib/python3.8/site-packages/pycistarget/motif_enrichment_cistarget.py:351, in cisTarget.run_ctx(self, ctx_db)
349 # Calculate the leading edges for each row. Always return importance from gene inference phase.
350 weights = np.asarray([region_set_signature[region] for region in regions])
--> 351 enriched_features[[("Enrichment", COLUMN_NAME_TARGET_GENES), ("Enrichment", COLUMN_NAME_RANK_AT_MAX)]] = enriched_features.apply(
352 partial(leading_edge4row, avg2stdrcc=avg2stdrcc, genes=regions, weights=weights), axis=1)
353 enriched_features = enriched_features['Enrichment'].rename_axis(None)
354 # Format enriched features

File /opt/venv/lib/python3.8/site-packages/pandas/core/frame.py:3643, in DataFrame.setitem(self, key, value)
3641 self._setitem_frame(key, value)
3642 elif isinstance(key, (Series, np.ndarray, list, Index)):
-> 3643 self._setitem_array(key, value)
3644 elif isinstance(value, DataFrame):
3645 self._set_item_frame_value(key, value)

File /opt/venv/lib/python3.8/site-packages/pandas/core/frame.py:3685, in DataFrame._setitem_array(self, key, value)
3680 else:
3681 # Note: unlike self.iloc[:, indexer] = value, this will
3682 # never try to overwrite values inplace
3684 if isinstance(value, DataFrame):
-> 3685 check_key_length(self.columns, key, value)
3686 for k1, k2 in zip(key, value.columns):
3687 self[k1] = value[k2]

File /opt/venv/lib/python3.8/site-packages/pandas/core/indexers/utils.py:428, in check_key_length(columns, key, value)
426 if columns.is_unique:
427 if len(value.columns) != len(key):
--> 428 raise ValueError("Columns must be same length as key")
429 else:
430 # Missing keys in columns are represented as -1
431 if len(columns.get_indexer_non_unique(key)[0]) != len(value.columns):

ValueError: Columns must be same length as key
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