It seems the flag checkratios is making the run to crash...
Gates 2016-08-18 16:49:44 ~/gDrive2/projects/TREES-C/PfuEGRIN/src/cmonkeyRuns : cmonkey2 --checkratios --num_cores 4 --organism pfu --out /Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/cmonkeyRuns/39samplesx2045genesRun1 /Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/expression/ratios/ratios.39samplesx2045genes.2016aug.txt
2016-08-18 16:50:02 INFO checking MEME...
2016-08-18 16:50:03 INFO Input matrix has # rows: 2040, # columns: 39
2016-08-18 16:50:03 INFO # clusters/row: 2
2016-08-18 16:50:03 INFO # clusters/column: 136
2016-08-18 16:50:03 INFO # CLUSTERS: 204
2016-08-18 16:50:03 INFO use operons: 1
2016-08-18 16:50:03 INFO using MEME version 4.10.0
2016-08-18 16:50:03 INFO attempting automatic download of operons from Microbes Online
2016-08-18 16:50:03 INFO NCBI CODE IS: 186497
2016-08-18 16:50:03 INFO Automatically using STRING file in 'cache/186497.gz' (URL: http://networks.systemsbiology.net/string9/186497.gz)
2016-08-18 16:50:16 WARNING can't find the correct RSAT mapping !
2016-08-18 16:50:16 INFO KEGG = 'Pyrococcus furiosus DSM 3638' -> RSAT = 'Pyrococcus_furiosus'
2016-08-18 16:50:16 INFO Creating networks...
2016-08-18 16:50:16 INFO stringdb.read_edges2()
2016-08-18 16:50:17 INFO Finished loading cache/186497.gz
2016-08-18 16:50:18 WARNING 36 (out of 375528) nodes not found in synonyms
2016-08-18 16:50:18 WARNING 23 (out of 375528) nodes not found in canonical gene names
2016-08-18 16:50:18 INFO stringdb.read_edges2(), 185414 edges read, 2350 edges ignored
2016-08-18 16:50:18 INFO MicrobesOnline - make_network()
2016-08-18 16:50:18 INFO MicrobesOnline.get_operon_predictions_for(186497)
2016-08-18 16:50:18 INFO 852 prediction pairs read
2016-08-18 16:50:19 INFO 440 operons created
2016-08-18 16:50:19 INFO 2105 edges computed
2016-08-18 16:50:19 INFO Finished creating networks.
2016-08-18 16:50:19 INFO Checking the quality of the input matrix names...
Traceback (most recent call last):
File "/Users/alomana/anaconda/bin/cmonkey2", line 36, in
cmonkey_run.run()
File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/cmonkey_run.py", line 512, in run
self.prepare_run()
File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/cmonkey_run.py", line 457, in prepare_run
self.__create_output_database()
File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/cmonkey_run.py", line 118, in __create_output_database
num_columns int, num_clusters int, git_sha text)''')
sqlite3.OperationalError: table run_infos already exists
Gates 2016-08-18 16:50:19 ~/gDrive2/projects/TREES-C/PfuEGRIN/src/cmonkeyRuns :
Gates 2016-08-18 16:48:09 ~/gDrive2/projects/TREES-C/PfuEGRIN/src/cmonkeyRuns : cmonkey2 --num_cores 4 --organism pfu --out /Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/cmonkeyRuns/39samplesx2045genesRun1 /Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/expression/ratios/ratios.39samplesx2045genes.2016aug.txt
2016-08-18 16:48:29 INFO checking MEME...
2016-08-18 16:48:29 INFO Input matrix has # rows: 2040, # columns: 39
2016-08-18 16:48:29 INFO # clusters/row: 2
2016-08-18 16:48:29 INFO # clusters/column: 136
2016-08-18 16:48:29 INFO # CLUSTERS: 204
2016-08-18 16:48:29 INFO use operons: 1
2016-08-18 16:48:29 INFO using MEME version 4.10.0
2016-08-18 16:48:30 INFO attempting automatic download of operons from Microbes Online
2016-08-18 16:48:30 INFO NCBI CODE IS: 186497
2016-08-18 16:48:30 INFO Automatically using STRING file in 'cache/186497.gz' (URL: http://networks.systemsbiology.net/string9/186497.gz)
2016-08-18 16:48:43 WARNING can't find the correct RSAT mapping !
2016-08-18 16:48:43 INFO KEGG = 'Pyrococcus furiosus DSM 3638' -> RSAT = 'Pyrococcus_furiosus'
2016-08-18 16:48:43 INFO Creating networks...
2016-08-18 16:48:43 INFO stringdb.read_edges2()
2016-08-18 16:48:44 INFO Finished loading cache/186497.gz
2016-08-18 16:48:45 WARNING 36 (out of 375528) nodes not found in synonyms
2016-08-18 16:48:45 WARNING 23 (out of 375528) nodes not found in canonical gene names
2016-08-18 16:48:45 INFO stringdb.read_edges2(), 185414 edges read, 2350 edges ignored
2016-08-18 16:48:45 INFO MicrobesOnline - make_network()
2016-08-18 16:48:45 INFO MicrobesOnline.get_operon_predictions_for(186497)
2016-08-18 16:48:45 INFO 852 prediction pairs read
2016-08-18 16:48:46 INFO 440 operons created
2016-08-18 16:48:46 INFO 2105 edges computed
2016-08-18 16:48:46 INFO Finished creating networks.
2016-08-18 16:48:47 INFO MicrobesOnline.get_operon_predictions_for(186497)
2016-08-18 16:48:47 INFO 852 prediction pairs read
2016-08-18 16:48:47 INFO 440 operons created
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s003' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0033' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t001' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t002' not found in RSAT features
2016-08-18 16:48:47 WARNING Operon did not contain any available genes
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s004' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0222.1n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s007' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0298.1n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s008' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s009' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0328' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0355.1n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s011' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0551' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s014' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0706.1n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0720' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0732.2n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0776.1n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t015' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t016' not found in RSAT features
2016-08-18 16:48:47 WARNING Operon did not contain any available genes
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0841.1n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s017' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0855.1n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0879' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0882' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0897.1n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1015.1n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s020' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1093.1n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1112.1n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1162' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1226' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1255' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1309' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1319' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s026' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1357.1n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t026' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t027' not found in RSAT features
2016-08-18 16:48:47 WARNING Operon did not contain any available genes
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s030' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t036' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t037' not found in RSAT features
2016-08-18 16:48:47 WARNING Operon did not contain any available genes
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s035' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1633' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t039' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t042' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s039' not found in RSAT features
2016-08-18 16:48:47 WARNING Operon did not contain any available genes
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s041' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s044' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1940.1n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s045' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s046' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s049' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s050' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF2048.1n' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s053' not found in RSAT features
2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF2054.1n' not found in RSAT features
2016-08-18 16:48:51 WARNING 39 genes not found in synonyms.
2016-08-18 16:48:51 INFO cmonkey_run config_params:
2016-08-18 16:48:51 INFO operon_file=None
2016-08-18 16:48:51 INFO memb.min_cluster_rows_allowed=3
2016-08-18 16:48:51 INFO add_fuzz=rows
2016-08-18 16:48:51 INFO search_distances={'upstream': (-20, 150)}
2016-08-18 16:48:51 INFO result_freq=10
2016-08-18 16:48:51 INFO num_iterations=2000
2016-08-18 16:48:51 INFO rsat_organism=None
2016-08-18 16:48:51 INFO interactive=False
2016-08-18 16:48:51 INFO case_sensitive=False
2016-08-18 16:48:51 INFO start_iteration=1
2016-08-18 16:48:51 INFO ncbi_code=186497
2016-08-18 16:48:51 INFO logfile=None
2016-08-18 16:48:51 INFO normalize_ratios=True
2016-08-18 16:48:51 INFO memb.prob_row_change=0.5
2016-08-18 16:48:51 INFO MEME={'use_revcomp': 'True', 'version': '4.10.0', 'schedule': 1,100, 'arg_mod': 'zoops', 'global_background': 'True', 'nmotifs_rvec': 'c(rep(1, num_iterations/3), rep(2, num_iterations/3))', 'background_order': '3', 'max_width': '24'}
2016-08-18 16:48:51 INFO memb.clusters_per_col=136
2016-08-18 16:48:51 INFO pipeline={'row-scoring': {'args': {'functions': [{'function': {'module': 'cmonkey.microarray', 'class': 'RowScoringFunction'}, 'id': 'Rows'}, {'function': {'module': 'cmonkey.network', 'class': 'ScoringFunction'}, 'id': 'Networks'}, {'function': {'module': 'cmonkey.motif', 'class': 'MemeScoringFunction'}, 'id': 'Motifs'}]}, 'function': {'module': 'cmonkey.scoring', 'class': 'ScoringFunctionCombiner'}, 'id': 'combiner'}, 'column-scoring': {'function': {'module': 'cmonkey.scoring', 'class': 'ColumnScoringFunction'}, 'id': 'Columns'}}
2016-08-18 16:48:51 INFO pipeline_file=
2016-08-18 16:48:51 INFO quantile_normalize=False
2016-08-18 16:48:51 INFO remap_network_nodes=False
2016-08-18 16:48:51 INFO output_dir=/Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/cmonkeyRuns/39samplesx2045genesRun1
2016-08-18 16:48:51 INFO memb.clusters_per_row=2
2016-08-18 16:48:51 INFO minimize_io=False
2016-08-18 16:48:51 INFO memb.prob_col_change=1.0
2016-08-18 16:48:51 INFO rsat_base_url=http://rsat01.biologie.ens.fr/rsat/
2016-08-18 16:48:51 INFO tmp_dir=
2016-08-18 16:48:51 INFO use_operons=True
2016-08-18 16:48:51 INFO dbfile_name=cmonkey_run.db
2016-08-18 16:48:51 INFO postadjust=True
2016-08-18 16:48:51 INFO rsat_dir=None
2016-08-18 16:48:51 INFO memb.max_changes_per_row=1
2016-08-18 16:48:51 INFO Rows={'scaling': ('scaling_const', 0.3), 'schedule': 1,2}
2016-08-18 16:48:51 INFO sequence_types=['upstream']
2016-08-18 16:48:51 INFO Motifs={'scaling': ('scaling_rvec', 'c(rep(1e-5, 100), seq(1e-5, 1, length=num_iterations_3/4))'), 'sequence_types': 'upstream', 'schedule': 2,10}
2016-08-18 16:48:51 INFO num_clusters=204
2016-08-18 16:48:51 INFO new_data_file=False
2016-08-18 16:48:51 INFO log_subresults=True
2016-08-18 16:48:51 INFO nomotifs=False
2016-08-18 16:48:51 INFO debug=set()
2016-08-18 16:48:51 INFO ratios_file=/Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/expression/ratios/ratios.39samplesx2045genes.2016aug.txt
2016-08-18 16:48:51 INFO random_seed=537810168
2016-08-18 16:48:51 INFO use_BSCM=False
2016-08-18 16:48:51 INFO resume=False
2016-08-18 16:48:51 INFO string_file=cache/186497.gz
2016-08-18 16:48:51 INFO rsat_features=feature
2016-08-18 16:48:51 INFO multiprocessing=True
2016-08-18 16:48:51 INFO command_line=/Users/alomana/anaconda/bin/cmonkey2 --num_cores 4 --organism pfu --out /Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/cmonkeyRuns/39samplesx2045genesRun1 /Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/expression/ratios/ratios.39samplesx2045genes.2016aug.txt
2016-08-18 16:48:51 INFO debug_freq=50
2016-08-18 16:48:51 INFO memb.max_changes_per_col=5
2016-08-18 16:48:51 INFO memb.max_cluster_rows_allowed=70
2016-08-18 16:48:51 INFO use_string=True
2016-08-18 16:48:51 INFO Columns={'schedule': 1,5}
2016-08-18 16:48:51 INFO fasta_file=None
2016-08-18 16:48:51 INFO Weeder={'freqfile_dir': '', 'top': '50', 'schedule': 1,100, 'global_background': 'True', 'nmotifs_rvec': 'c(rep(1, num_iterations/3), rep(2, num_iterations/3))', 'analysis': 'small', 'orgcode': ''}
2016-08-18 16:48:51 INFO organism_code=pfu
2016-08-18 16:48:51 INFO use_chi2=False
2016-08-18 16:48:51 INFO num_cores=4
2016-08-18 16:48:51 INFO scan_distances={'upstream': (-30, 250)}
2016-08-18 16:48:51 INFO synonym_file=None
2016-08-18 16:48:51 INFO SequenceType-upstream={'search_distance': '-20,150', 'scan_distance': '-30,250'}
2016-08-18 16:48:51 INFO Networks={'scaling': ('scaling_rvec', 'seq(1e-5, 0.5, length=num_iterations_3/4)'), 'schedule': 1,7}
2016-08-18 16:48:51 INFO Postprocessing={'run_tomtom': 'False'}
2016-08-18 16:48:51 INFO nonetworks=False
2016-08-18 16:48:51 INFO checkratios=False
2016-08-18 16:48:51 INFO cache_dir=cache
2016-08-18 16:48:51 INFO stats_freq=10
2016-08-18 16:48:51 INFO out_database=/Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/cmonkeyRuns/39samplesx2045genesRun1/cmonkey_run.db
2016-08-18 16:48:51 INFO Iteration # 1
2016-08-18 16:48:57 INFO running meme/mast on cluster 1, # sequences: 6
2016-08-18 16:48:57 INFO running meme/mast on cluster 14, # sequences: 3
2016-08-18 16:48:57 INFO running meme/mast on cluster 27, # sequences: 13
2016-08-18 16:48:57 INFO running meme/mast on cluster 40, # sequences: 14
2016-08-18 16:48:57 INFO running meme/mast on cluster 15, # sequences: 17
2016-08-18 16:48:57 INFO running meme/mast on cluster 2, # sequences: 14
2016-08-18 16:48:58 INFO running meme/mast on cluster 28, # sequences: 15
2016-08-18 16:48:59 INFO running meme/mast on cluster 41, # sequences: 18
2016-08-18 16:48:59 INFO running meme/mast on cluster 3, # sequences: 6
2016-08-18 16:49:00 INFO running meme/mast on cluster 16, # sequences: 5
2016-08-18 16:49:00 INFO running meme/mast on cluster 4, # sequences: 3
2016-08-18 16:49:01 INFO running meme/mast on cluster 29, # sequences: 11
2016-08-18 16:49:01 INFO running meme/mast on cluster 17, # sequences: 14
2016-08-18 16:49:01 INFO running meme/mast on cluster 5, # sequences: 4
2016-08-18 16:49:01 INFO running meme/mast on cluster 6, # sequences: 4
2016-08-18 16:49:02 INFO running meme/mast on cluster 42, # sequences: 7
2016-08-18 16:49:02 INFO running meme/mast on cluster 30, # sequences: 11
2016-08-18 16:49:02 INFO running meme/mast on cluster 7, # sequences: 7
2016-08-18 16:49:02 INFO running meme/mast on cluster 43, # sequences: 8
2016-08-18 16:49:03 INFO running meme/mast on cluster 8, # sequences: 6
2016-08-18 16:49:03 INFO running meme/mast on cluster 18, # sequences: 15
2016-08-18 16:49:04 INFO running meme/mast on cluster 31, # sequences: 5
2016-08-18 16:49:04 INFO running meme/mast on cluster 44, # sequences: 8
2016-08-18 16:49:04 INFO running meme/mast on cluster 9, # sequences: 21
2016-08-18 16:49:04 INFO running meme/mast on cluster 32, # sequences: 3
2016-08-18 16:49:05 INFO running meme/mast on cluster 45, # sequences: 7
2016-08-18 16:49:05 INFO running meme/mast on cluster 33, # sequences: 11
2016-08-18 16:49:05 INFO running meme/mast on cluster 46, # sequences: 15
2016-08-18 16:49:05 INFO running meme/mast on cluster 19, # sequences: 5
2016-08-18 16:49:06 INFO running meme/mast on cluster 20, # sequences: 10
2016-08-18 16:49:06 INFO running meme/mast on cluster 34, # sequences: 8
2016-08-18 16:49:07 INFO running meme/mast on cluster 35, # sequences: 9
2016-08-18 16:49:07 INFO running meme/mast on cluster 47, # sequences: 9
2016-08-18 16:49:07 INFO running meme/mast on cluster 21, # sequences: 5
2016-08-18 16:49:08 INFO running meme/mast on cluster 10, # sequences: 5
2016-08-18 16:49:08 INFO running meme/mast on cluster 22, # sequences: 7
2016-08-18 16:49:08 INFO running meme/mast on cluster 11, # sequences: 9
2016-08-18 16:49:08 INFO running meme/mast on cluster 48, # sequences: 7
2016-08-18 16:49:08 INFO running meme/mast on cluster 36, # sequences: 7
2016-08-18 16:49:09 INFO running meme/mast on cluster 23, # sequences: 5
2016-08-18 16:49:09 INFO running meme/mast on cluster 49, # sequences: 8
2016-08-18 16:49:09 INFO running meme/mast on cluster 37, # sequences: 5
2016-08-18 16:49:10 INFO running meme/mast on cluster 24, # sequences: 10
2016-08-18 16:49:10 INFO running meme/mast on cluster 12, # sequences: 5
2016-08-18 16:49:10 INFO running meme/mast on cluster 38, # sequences: 6
2016-08-18 16:49:10 INFO running meme/mast on cluster 50, # sequences: 5
2016-08-18 16:49:10 INFO running meme/mast on cluster 13, # sequences: 5
2016-08-18 16:49:11 INFO running meme/mast on cluster 51, # sequences: 10
2016-08-18 16:49:11 INFO running meme/mast on cluster 39, # sequences: 5
2016-08-18 16:49:11 INFO running meme/mast on cluster 25, # sequences: 5
2016-08-18 16:49:11 INFO running meme/mast on cluster 53, # sequences: 8
2016-08-18 16:49:12 INFO running meme/mast on cluster 26, # sequences: 10
2016-08-18 16:49:12 INFO running meme/mast on cluster 66, # sequences: 2
2016-08-18 16:49:12 INFO running meme/mast on cluster 67, # sequences: 18
2016-08-18 16:49:12 INFO running meme/mast on cluster 54, # sequences: 12
2016-08-18 16:49:12 INFO running meme/mast on cluster 52, # sequences: 5
2016-08-18 16:49:13 INFO running meme/mast on cluster 79, # sequences: 13
2016-08-18 16:49:13 INFO running meme/mast on cluster 92, # sequences: 18
2016-08-18 16:49:14 INFO running meme/mast on cluster 55, # sequences: 8
2016-08-18 16:49:15 INFO running meme/mast on cluster 56, # sequences: 17
2016-08-18 16:49:15 INFO running meme/mast on cluster 68, # sequences: 7
2016-08-18 16:49:15 INFO running meme/mast on cluster 80, # sequences: 16
2016-08-18 16:49:16 INFO running meme/mast on cluster 69, # sequences: 14
2016-08-18 16:49:16 INFO running meme/mast on cluster 93, # sequences: 13
2016-08-18 16:49:17 INFO running meme/mast on cluster 81, # sequences: 8
2016-08-18 16:49:18 INFO running meme/mast on cluster 57, # sequences: 12
2016-08-18 16:49:18 INFO running meme/mast on cluster 70, # sequences: 11
2016-08-18 16:49:18 INFO running meme/mast on cluster 94, # sequences: 11
2016-08-18 16:49:18 INFO running meme/mast on cluster 82, # sequences: 6
2016-08-18 16:49:19 INFO running meme/mast on cluster 83, # sequences: 8
2016-08-18 16:49:19 INFO running meme/mast on cluster 71, # sequences: 7
2016-08-18 16:49:20 INFO running meme/mast on cluster 58, # sequences: 6
2016-08-18 16:49:20 INFO running meme/mast on cluster 95, # sequences: 4
2016-08-18 16:49:20 INFO running meme/mast on cluster 84, # sequences: 7
2016-08-18 16:49:20 INFO running meme/mast on cluster 96, # sequences: 22
2016-08-18 16:49:20 INFO running meme/mast on cluster 72, # sequences: 10
2016-08-18 16:49:20 INFO running meme/mast on cluster 59, # sequences: 15
2016-08-18 16:49:21 INFO running meme/mast on cluster 85, # sequences: 17
2016-08-18 16:49:22 INFO running meme/mast on cluster 73, # sequences: 11
2016-08-18 16:49:23 INFO running meme/mast on cluster 60, # sequences: 5
2016-08-18 16:49:23 INFO running meme/mast on cluster 74, # sequences: 8
2016-08-18 16:49:23 INFO running meme/mast on cluster 61, # sequences: 8
2016-08-18 16:49:24 INFO running meme/mast on cluster 86, # sequences: 6
2016-08-18 16:49:24 INFO running meme/mast on cluster 75, # sequences: 7
2016-08-18 16:49:25 INFO running meme/mast on cluster 87, # sequences: 7
2016-08-18 16:49:25 INFO running meme/mast on cluster 62, # sequences: 9
2016-08-18 16:49:25 INFO running meme/mast on cluster 97, # sequences: 7
2016-08-18 16:49:26 INFO running meme/mast on cluster 88, # sequences: 8
2016-08-18 16:49:26 INFO running meme/mast on cluster 76, # sequences: 6
2016-08-18 16:49:26 INFO running meme/mast on cluster 98, # sequences: 4
2016-08-18 16:49:26 INFO running meme/mast on cluster 63, # sequences: 27
2016-08-18 16:49:26 INFO running meme/mast on cluster 77, # sequences: 11
2016-08-18 16:49:27 INFO running meme/mast on cluster 89, # sequences: 10
2016-08-18 16:49:27 INFO running meme/mast on cluster 99, # sequences: 8
2016-08-18 16:49:28 INFO running meme/mast on cluster 100, # sequences: 8
2016-08-18 16:49:28 INFO running meme/mast on cluster 90, # sequences: 17
2016-08-18 16:49:28 INFO running meme/mast on cluster 78, # sequences: 8
2016-08-18 16:49:29 INFO running meme/mast on cluster 101, # sequences: 7
2016-08-18 16:49:29 INFO running meme/mast on cluster 105, # sequences: 11
2016-08-18 16:49:30 INFO running meme/mast on cluster 102, # sequences: 8
2016-08-18 16:49:31 INFO running meme/mast on cluster 106, # sequences: 7
2016-08-18 16:49:31 INFO running meme/mast on cluster 103, # sequences: 10
2016-08-18 16:49:32 INFO running meme/mast on cluster 91, # sequences: 4
2016-08-18 16:49:32 INFO running meme/mast on cluster 107, # sequences: 10
2016-08-18 16:49:32 INFO running meme/mast on cluster 118, # sequences: 2
2016-08-18 16:49:32 INFO running meme/mast on cluster 119, # sequences: 9
2016-08-18 16:49:33 INFO running meme/mast on cluster 104, # sequences: 9
2016-08-18 16:49:33 INFO running meme/mast on cluster 64, # sequences: 10
2016-08-18 16:49:33 INFO running meme/mast on cluster 108, # sequences: 8
2016-08-18 16:49:34 INFO running meme/mast on cluster 120, # sequences: 6
2016-08-18 16:49:34 INFO running meme/mast on cluster 131, # sequences: 9
2016-08-18 16:49:34 INFO running meme/mast on cluster 109, # sequences: 11
2016-08-18 16:49:34 INFO running meme/mast on cluster 65, # sequences: 3
2016-08-18 16:49:35 INFO running meme/mast on cluster 121, # sequences: 8
2016-08-18 16:49:35 INFO running meme/mast on cluster 144, # sequences: 21
2016-08-18 16:49:35 INFO running meme/mast on cluster 132, # sequences: 8
2016-08-18 16:49:36 INFO running meme/mast on cluster 122, # sequences: 10
2016-08-18 16:49:36 INFO running meme/mast on cluster 110, # sequences: 3
2016-08-18 16:49:36 INFO running meme/mast on cluster 133, # sequences: 2
2016-08-18 16:49:36 INFO running meme/mast on cluster 134, # sequences: 8
2016-08-18 16:49:36 INFO running meme/mast on cluster 111, # sequences: 5
2016-08-18 16:49:37 INFO running meme/mast on cluster 123, # sequences: 12
2016-08-18 16:49:37 INFO running meme/mast on cluster 112, # sequences: 8
2016-08-18 16:49:37 INFO running meme/mast on cluster 135, # sequences: 10
2016-08-18 16:49:38 INFO running meme/mast on cluster 113, # sequences: 11
2016-08-18 16:49:38 INFO running meme/mast on cluster 124, # sequences: 6
2016-08-18 16:49:39 INFO running meme/mast on cluster 136, # sequences: 3
2016-08-18 16:49:39 INFO running meme/mast on cluster 145, # sequences: 6
2016-08-18 16:49:39 INFO running meme/mast on cluster 125, # sequences: 3
2016-08-18 16:49:39 INFO running meme/mast on cluster 137, # sequences: 4
2016-08-18 16:49:40 INFO running meme/mast on cluster 126, # sequences: 12
2016-08-18 16:49:40 INFO running meme/mast on cluster 114, # sequences: 6
2016-08-18 16:49:40 INFO running meme/mast on cluster 146, # sequences: 4
2016-08-18 16:49:40 INFO running meme/mast on cluster 138, # sequences: 4
2016-08-18 16:49:41 INFO running meme/mast on cluster 147, # sequences: 8
2016-08-18 16:49:41 INFO running meme/mast on cluster 115, # sequences: 9
2016-08-18 16:49:41 INFO running meme/mast on cluster 139, # sequences: 9
2016-08-18 16:49:42 INFO running meme/mast on cluster 127, # sequences: 6
2016-08-18 16:49:42 INFO running meme/mast on cluster 148, # sequences: 10
It seems the flag checkratios is making the run to crash...
Gates 2016-08-18 16:49:44 ~/gDrive2/projects/TREES-C/PfuEGRIN/src/cmonkeyRuns : cmonkey2 --checkratios --num_cores 4 --organism pfu --out /Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/cmonkeyRuns/39samplesx2045genesRun1 /Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/expression/ratios/ratios.39samplesx2045genes.2016aug.txt 2016-08-18 16:50:02 INFO checking MEME... 2016-08-18 16:50:03 INFO Input matrix has # rows: 2040, # columns: 39 2016-08-18 16:50:03 INFO # clusters/row: 2 2016-08-18 16:50:03 INFO # clusters/column: 136 2016-08-18 16:50:03 INFO # CLUSTERS: 204 2016-08-18 16:50:03 INFO use operons: 1 2016-08-18 16:50:03 INFO using MEME version 4.10.0 2016-08-18 16:50:03 INFO attempting automatic download of operons from Microbes Online 2016-08-18 16:50:03 INFO NCBI CODE IS: 186497 2016-08-18 16:50:03 INFO Automatically using STRING file in 'cache/186497.gz' (URL: http://networks.systemsbiology.net/string9/186497.gz) 2016-08-18 16:50:16 WARNING can't find the correct RSAT mapping ! 2016-08-18 16:50:16 INFO KEGG = 'Pyrococcus furiosus DSM 3638' -> RSAT = 'Pyrococcus_furiosus' 2016-08-18 16:50:16 INFO Creating networks... 2016-08-18 16:50:16 INFO stringdb.read_edges2() 2016-08-18 16:50:17 INFO Finished loading cache/186497.gz 2016-08-18 16:50:18 WARNING 36 (out of 375528) nodes not found in synonyms 2016-08-18 16:50:18 WARNING 23 (out of 375528) nodes not found in canonical gene names 2016-08-18 16:50:18 INFO stringdb.read_edges2(), 185414 edges read, 2350 edges ignored 2016-08-18 16:50:18 INFO MicrobesOnline - make_network() 2016-08-18 16:50:18 INFO MicrobesOnline.get_operon_predictions_for(186497) 2016-08-18 16:50:18 INFO 852 prediction pairs read 2016-08-18 16:50:19 INFO 440 operons created 2016-08-18 16:50:19 INFO 2105 edges computed 2016-08-18 16:50:19 INFO Finished creating networks. 2016-08-18 16:50:19 INFO Checking the quality of the input matrix names... Traceback (most recent call last): File "/Users/alomana/anaconda/bin/cmonkey2", line 36, in
cmonkey_run.run()
File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/cmonkey_run.py", line 512, in run
self.prepare_run()
File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/cmonkey_run.py", line 457, in prepare_run
self.__create_output_database()
File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/cmonkey_run.py", line 118, in __create_output_database
num_columns int, num_clusters int, git_sha text)''')
sqlite3.OperationalError: table run_infos already exists
Gates 2016-08-18 16:50:19 ~/gDrive2/projects/TREES-C/PfuEGRIN/src/cmonkeyRuns :
Gates 2016-08-18 16:48:09 ~/gDrive2/projects/TREES-C/PfuEGRIN/src/cmonkeyRuns : cmonkey2 --num_cores 4 --organism pfu --out /Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/cmonkeyRuns/39samplesx2045genesRun1 /Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/expression/ratios/ratios.39samplesx2045genes.2016aug.txt 2016-08-18 16:48:29 INFO checking MEME... 2016-08-18 16:48:29 INFO Input matrix has # rows: 2040, # columns: 39 2016-08-18 16:48:29 INFO # clusters/row: 2 2016-08-18 16:48:29 INFO # clusters/column: 136 2016-08-18 16:48:29 INFO # CLUSTERS: 204 2016-08-18 16:48:29 INFO use operons: 1 2016-08-18 16:48:29 INFO using MEME version 4.10.0 2016-08-18 16:48:30 INFO attempting automatic download of operons from Microbes Online 2016-08-18 16:48:30 INFO NCBI CODE IS: 186497 2016-08-18 16:48:30 INFO Automatically using STRING file in 'cache/186497.gz' (URL: http://networks.systemsbiology.net/string9/186497.gz) 2016-08-18 16:48:43 WARNING can't find the correct RSAT mapping ! 2016-08-18 16:48:43 INFO KEGG = 'Pyrococcus furiosus DSM 3638' -> RSAT = 'Pyrococcus_furiosus' 2016-08-18 16:48:43 INFO Creating networks... 2016-08-18 16:48:43 INFO stringdb.read_edges2() 2016-08-18 16:48:44 INFO Finished loading cache/186497.gz 2016-08-18 16:48:45 WARNING 36 (out of 375528) nodes not found in synonyms 2016-08-18 16:48:45 WARNING 23 (out of 375528) nodes not found in canonical gene names 2016-08-18 16:48:45 INFO stringdb.read_edges2(), 185414 edges read, 2350 edges ignored 2016-08-18 16:48:45 INFO MicrobesOnline - make_network() 2016-08-18 16:48:45 INFO MicrobesOnline.get_operon_predictions_for(186497) 2016-08-18 16:48:45 INFO 852 prediction pairs read 2016-08-18 16:48:46 INFO 440 operons created 2016-08-18 16:48:46 INFO 2105 edges computed 2016-08-18 16:48:46 INFO Finished creating networks. 2016-08-18 16:48:47 INFO MicrobesOnline.get_operon_predictions_for(186497) 2016-08-18 16:48:47 INFO 852 prediction pairs read 2016-08-18 16:48:47 INFO 440 operons created 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s003' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0033' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t001' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t002' not found in RSAT features 2016-08-18 16:48:47 WARNING Operon did not contain any available genes 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s004' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0222.1n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s007' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0298.1n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s008' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s009' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0328' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0355.1n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s011' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0551' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s014' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0706.1n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0720' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0732.2n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0776.1n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t015' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t016' not found in RSAT features 2016-08-18 16:48:47 WARNING Operon did not contain any available genes 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0841.1n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s017' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0855.1n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0879' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0882' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF0897.1n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1015.1n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s020' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1093.1n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1112.1n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1162' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1226' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1255' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1309' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1319' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s026' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1357.1n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t026' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t027' not found in RSAT features 2016-08-18 16:48:47 WARNING Operon did not contain any available genes 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s030' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t036' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t037' not found in RSAT features 2016-08-18 16:48:47 WARNING Operon did not contain any available genes 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s035' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1633' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t039' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_t042' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s039' not found in RSAT features 2016-08-18 16:48:47 WARNING Operon did not contain any available genes 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s041' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s044' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF1940.1n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s045' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s046' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s049' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s050' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF2048.1n' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF_s053' not found in RSAT features 2016-08-18 16:48:47 WARNING Microbes Online operon gene 'PF2054.1n' not found in RSAT features 2016-08-18 16:48:51 WARNING 39 genes not found in synonyms. 2016-08-18 16:48:51 INFO cmonkey_run config_params: 2016-08-18 16:48:51 INFO operon_file=None 2016-08-18 16:48:51 INFO memb.min_cluster_rows_allowed=3 2016-08-18 16:48:51 INFO add_fuzz=rows 2016-08-18 16:48:51 INFO search_distances={'upstream': (-20, 150)} 2016-08-18 16:48:51 INFO result_freq=10 2016-08-18 16:48:51 INFO num_iterations=2000 2016-08-18 16:48:51 INFO rsat_organism=None 2016-08-18 16:48:51 INFO interactive=False 2016-08-18 16:48:51 INFO case_sensitive=False 2016-08-18 16:48:51 INFO start_iteration=1 2016-08-18 16:48:51 INFO ncbi_code=186497 2016-08-18 16:48:51 INFO logfile=None 2016-08-18 16:48:51 INFO normalize_ratios=True 2016-08-18 16:48:51 INFO memb.prob_row_change=0.5 2016-08-18 16:48:51 INFO MEME={'use_revcomp': 'True', 'version': '4.10.0', 'schedule': 1,100, 'arg_mod': 'zoops', 'global_background': 'True', 'nmotifs_rvec': 'c(rep(1, num_iterations/3), rep(2, num_iterations/3))', 'background_order': '3', 'max_width': '24'} 2016-08-18 16:48:51 INFO memb.clusters_per_col=136 2016-08-18 16:48:51 INFO pipeline={'row-scoring': {'args': {'functions': [{'function': {'module': 'cmonkey.microarray', 'class': 'RowScoringFunction'}, 'id': 'Rows'}, {'function': {'module': 'cmonkey.network', 'class': 'ScoringFunction'}, 'id': 'Networks'}, {'function': {'module': 'cmonkey.motif', 'class': 'MemeScoringFunction'}, 'id': 'Motifs'}]}, 'function': {'module': 'cmonkey.scoring', 'class': 'ScoringFunctionCombiner'}, 'id': 'combiner'}, 'column-scoring': {'function': {'module': 'cmonkey.scoring', 'class': 'ColumnScoringFunction'}, 'id': 'Columns'}} 2016-08-18 16:48:51 INFO pipeline_file= 2016-08-18 16:48:51 INFO quantile_normalize=False 2016-08-18 16:48:51 INFO remap_network_nodes=False 2016-08-18 16:48:51 INFO output_dir=/Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/cmonkeyRuns/39samplesx2045genesRun1 2016-08-18 16:48:51 INFO memb.clusters_per_row=2 2016-08-18 16:48:51 INFO minimize_io=False 2016-08-18 16:48:51 INFO memb.prob_col_change=1.0 2016-08-18 16:48:51 INFO rsat_base_url=http://rsat01.biologie.ens.fr/rsat/ 2016-08-18 16:48:51 INFO tmp_dir= 2016-08-18 16:48:51 INFO use_operons=True 2016-08-18 16:48:51 INFO dbfile_name=cmonkey_run.db 2016-08-18 16:48:51 INFO postadjust=True 2016-08-18 16:48:51 INFO rsat_dir=None 2016-08-18 16:48:51 INFO memb.max_changes_per_row=1 2016-08-18 16:48:51 INFO Rows={'scaling': ('scaling_const', 0.3), 'schedule': 1,2} 2016-08-18 16:48:51 INFO sequence_types=['upstream'] 2016-08-18 16:48:51 INFO Motifs={'scaling': ('scaling_rvec', 'c(rep(1e-5, 100), seq(1e-5, 1, length=num_iterations_3/4))'), 'sequence_types': 'upstream', 'schedule': 2,10} 2016-08-18 16:48:51 INFO num_clusters=204 2016-08-18 16:48:51 INFO new_data_file=False 2016-08-18 16:48:51 INFO log_subresults=True 2016-08-18 16:48:51 INFO nomotifs=False 2016-08-18 16:48:51 INFO debug=set() 2016-08-18 16:48:51 INFO ratios_file=/Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/expression/ratios/ratios.39samplesx2045genes.2016aug.txt 2016-08-18 16:48:51 INFO random_seed=537810168 2016-08-18 16:48:51 INFO use_BSCM=False 2016-08-18 16:48:51 INFO resume=False 2016-08-18 16:48:51 INFO string_file=cache/186497.gz 2016-08-18 16:48:51 INFO rsat_features=feature 2016-08-18 16:48:51 INFO multiprocessing=True 2016-08-18 16:48:51 INFO command_line=/Users/alomana/anaconda/bin/cmonkey2 --num_cores 4 --organism pfu --out /Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/cmonkeyRuns/39samplesx2045genesRun1 /Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/expression/ratios/ratios.39samplesx2045genes.2016aug.txt 2016-08-18 16:48:51 INFO debug_freq=50 2016-08-18 16:48:51 INFO memb.max_changes_per_col=5 2016-08-18 16:48:51 INFO memb.max_cluster_rows_allowed=70 2016-08-18 16:48:51 INFO use_string=True 2016-08-18 16:48:51 INFO Columns={'schedule': 1,5} 2016-08-18 16:48:51 INFO fasta_file=None 2016-08-18 16:48:51 INFO Weeder={'freqfile_dir': '', 'top': '50', 'schedule': 1,100, 'global_background': 'True', 'nmotifs_rvec': 'c(rep(1, num_iterations/3), rep(2, num_iterations/3))', 'analysis': 'small', 'orgcode': ''} 2016-08-18 16:48:51 INFO organism_code=pfu 2016-08-18 16:48:51 INFO use_chi2=False 2016-08-18 16:48:51 INFO num_cores=4 2016-08-18 16:48:51 INFO scan_distances={'upstream': (-30, 250)} 2016-08-18 16:48:51 INFO synonym_file=None 2016-08-18 16:48:51 INFO SequenceType-upstream={'search_distance': '-20,150', 'scan_distance': '-30,250'} 2016-08-18 16:48:51 INFO Networks={'scaling': ('scaling_rvec', 'seq(1e-5, 0.5, length=num_iterations_3/4)'), 'schedule': 1,7} 2016-08-18 16:48:51 INFO Postprocessing={'run_tomtom': 'False'} 2016-08-18 16:48:51 INFO nonetworks=False 2016-08-18 16:48:51 INFO checkratios=False 2016-08-18 16:48:51 INFO cache_dir=cache 2016-08-18 16:48:51 INFO stats_freq=10 2016-08-18 16:48:51 INFO out_database=/Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/cmonkeyRuns/39samplesx2045genesRun1/cmonkey_run.db 2016-08-18 16:48:51 INFO Iteration # 1 2016-08-18 16:48:57 INFO running meme/mast on cluster 1, # sequences: 6 2016-08-18 16:48:57 INFO running meme/mast on cluster 14, # sequences: 3 2016-08-18 16:48:57 INFO running meme/mast on cluster 27, # sequences: 13 2016-08-18 16:48:57 INFO running meme/mast on cluster 40, # sequences: 14 2016-08-18 16:48:57 INFO running meme/mast on cluster 15, # sequences: 17 2016-08-18 16:48:57 INFO running meme/mast on cluster 2, # sequences: 14 2016-08-18 16:48:58 INFO running meme/mast on cluster 28, # sequences: 15 2016-08-18 16:48:59 INFO running meme/mast on cluster 41, # sequences: 18 2016-08-18 16:48:59 INFO running meme/mast on cluster 3, # sequences: 6 2016-08-18 16:49:00 INFO running meme/mast on cluster 16, # sequences: 5 2016-08-18 16:49:00 INFO running meme/mast on cluster 4, # sequences: 3 2016-08-18 16:49:01 INFO running meme/mast on cluster 29, # sequences: 11 2016-08-18 16:49:01 INFO running meme/mast on cluster 17, # sequences: 14 2016-08-18 16:49:01 INFO running meme/mast on cluster 5, # sequences: 4 2016-08-18 16:49:01 INFO running meme/mast on cluster 6, # sequences: 4 2016-08-18 16:49:02 INFO running meme/mast on cluster 42, # sequences: 7 2016-08-18 16:49:02 INFO running meme/mast on cluster 30, # sequences: 11 2016-08-18 16:49:02 INFO running meme/mast on cluster 7, # sequences: 7 2016-08-18 16:49:02 INFO running meme/mast on cluster 43, # sequences: 8 2016-08-18 16:49:03 INFO running meme/mast on cluster 8, # sequences: 6 2016-08-18 16:49:03 INFO running meme/mast on cluster 18, # sequences: 15 2016-08-18 16:49:04 INFO running meme/mast on cluster 31, # sequences: 5 2016-08-18 16:49:04 INFO running meme/mast on cluster 44, # sequences: 8 2016-08-18 16:49:04 INFO running meme/mast on cluster 9, # sequences: 21 2016-08-18 16:49:04 INFO running meme/mast on cluster 32, # sequences: 3 2016-08-18 16:49:05 INFO running meme/mast on cluster 45, # sequences: 7 2016-08-18 16:49:05 INFO running meme/mast on cluster 33, # sequences: 11 2016-08-18 16:49:05 INFO running meme/mast on cluster 46, # sequences: 15 2016-08-18 16:49:05 INFO running meme/mast on cluster 19, # sequences: 5 2016-08-18 16:49:06 INFO running meme/mast on cluster 20, # sequences: 10 2016-08-18 16:49:06 INFO running meme/mast on cluster 34, # sequences: 8 2016-08-18 16:49:07 INFO running meme/mast on cluster 35, # sequences: 9 2016-08-18 16:49:07 INFO running meme/mast on cluster 47, # sequences: 9 2016-08-18 16:49:07 INFO running meme/mast on cluster 21, # sequences: 5 2016-08-18 16:49:08 INFO running meme/mast on cluster 10, # sequences: 5 2016-08-18 16:49:08 INFO running meme/mast on cluster 22, # sequences: 7 2016-08-18 16:49:08 INFO running meme/mast on cluster 11, # sequences: 9 2016-08-18 16:49:08 INFO running meme/mast on cluster 48, # sequences: 7 2016-08-18 16:49:08 INFO running meme/mast on cluster 36, # sequences: 7 2016-08-18 16:49:09 INFO running meme/mast on cluster 23, # sequences: 5 2016-08-18 16:49:09 INFO running meme/mast on cluster 49, # sequences: 8 2016-08-18 16:49:09 INFO running meme/mast on cluster 37, # sequences: 5 2016-08-18 16:49:10 INFO running meme/mast on cluster 24, # sequences: 10 2016-08-18 16:49:10 INFO running meme/mast on cluster 12, # sequences: 5 2016-08-18 16:49:10 INFO running meme/mast on cluster 38, # sequences: 6 2016-08-18 16:49:10 INFO running meme/mast on cluster 50, # sequences: 5 2016-08-18 16:49:10 INFO running meme/mast on cluster 13, # sequences: 5 2016-08-18 16:49:11 INFO running meme/mast on cluster 51, # sequences: 10 2016-08-18 16:49:11 INFO running meme/mast on cluster 39, # sequences: 5 2016-08-18 16:49:11 INFO running meme/mast on cluster 25, # sequences: 5 2016-08-18 16:49:11 INFO running meme/mast on cluster 53, # sequences: 8 2016-08-18 16:49:12 INFO running meme/mast on cluster 26, # sequences: 10 2016-08-18 16:49:12 INFO running meme/mast on cluster 66, # sequences: 2 2016-08-18 16:49:12 INFO running meme/mast on cluster 67, # sequences: 18 2016-08-18 16:49:12 INFO running meme/mast on cluster 54, # sequences: 12 2016-08-18 16:49:12 INFO running meme/mast on cluster 52, # sequences: 5 2016-08-18 16:49:13 INFO running meme/mast on cluster 79, # sequences: 13 2016-08-18 16:49:13 INFO running meme/mast on cluster 92, # sequences: 18 2016-08-18 16:49:14 INFO running meme/mast on cluster 55, # sequences: 8 2016-08-18 16:49:15 INFO running meme/mast on cluster 56, # sequences: 17 2016-08-18 16:49:15 INFO running meme/mast on cluster 68, # sequences: 7 2016-08-18 16:49:15 INFO running meme/mast on cluster 80, # sequences: 16 2016-08-18 16:49:16 INFO running meme/mast on cluster 69, # sequences: 14 2016-08-18 16:49:16 INFO running meme/mast on cluster 93, # sequences: 13 2016-08-18 16:49:17 INFO running meme/mast on cluster 81, # sequences: 8 2016-08-18 16:49:18 INFO running meme/mast on cluster 57, # sequences: 12 2016-08-18 16:49:18 INFO running meme/mast on cluster 70, # sequences: 11 2016-08-18 16:49:18 INFO running meme/mast on cluster 94, # sequences: 11 2016-08-18 16:49:18 INFO running meme/mast on cluster 82, # sequences: 6 2016-08-18 16:49:19 INFO running meme/mast on cluster 83, # sequences: 8 2016-08-18 16:49:19 INFO running meme/mast on cluster 71, # sequences: 7 2016-08-18 16:49:20 INFO running meme/mast on cluster 58, # sequences: 6 2016-08-18 16:49:20 INFO running meme/mast on cluster 95, # sequences: 4 2016-08-18 16:49:20 INFO running meme/mast on cluster 84, # sequences: 7 2016-08-18 16:49:20 INFO running meme/mast on cluster 96, # sequences: 22 2016-08-18 16:49:20 INFO running meme/mast on cluster 72, # sequences: 10 2016-08-18 16:49:20 INFO running meme/mast on cluster 59, # sequences: 15 2016-08-18 16:49:21 INFO running meme/mast on cluster 85, # sequences: 17 2016-08-18 16:49:22 INFO running meme/mast on cluster 73, # sequences: 11 2016-08-18 16:49:23 INFO running meme/mast on cluster 60, # sequences: 5 2016-08-18 16:49:23 INFO running meme/mast on cluster 74, # sequences: 8 2016-08-18 16:49:23 INFO running meme/mast on cluster 61, # sequences: 8 2016-08-18 16:49:24 INFO running meme/mast on cluster 86, # sequences: 6 2016-08-18 16:49:24 INFO running meme/mast on cluster 75, # sequences: 7 2016-08-18 16:49:25 INFO running meme/mast on cluster 87, # sequences: 7 2016-08-18 16:49:25 INFO running meme/mast on cluster 62, # sequences: 9 2016-08-18 16:49:25 INFO running meme/mast on cluster 97, # sequences: 7 2016-08-18 16:49:26 INFO running meme/mast on cluster 88, # sequences: 8 2016-08-18 16:49:26 INFO running meme/mast on cluster 76, # sequences: 6 2016-08-18 16:49:26 INFO running meme/mast on cluster 98, # sequences: 4 2016-08-18 16:49:26 INFO running meme/mast on cluster 63, # sequences: 27 2016-08-18 16:49:26 INFO running meme/mast on cluster 77, # sequences: 11 2016-08-18 16:49:27 INFO running meme/mast on cluster 89, # sequences: 10 2016-08-18 16:49:27 INFO running meme/mast on cluster 99, # sequences: 8 2016-08-18 16:49:28 INFO running meme/mast on cluster 100, # sequences: 8 2016-08-18 16:49:28 INFO running meme/mast on cluster 90, # sequences: 17 2016-08-18 16:49:28 INFO running meme/mast on cluster 78, # sequences: 8 2016-08-18 16:49:29 INFO running meme/mast on cluster 101, # sequences: 7 2016-08-18 16:49:29 INFO running meme/mast on cluster 105, # sequences: 11 2016-08-18 16:49:30 INFO running meme/mast on cluster 102, # sequences: 8 2016-08-18 16:49:31 INFO running meme/mast on cluster 106, # sequences: 7 2016-08-18 16:49:31 INFO running meme/mast on cluster 103, # sequences: 10 2016-08-18 16:49:32 INFO running meme/mast on cluster 91, # sequences: 4 2016-08-18 16:49:32 INFO running meme/mast on cluster 107, # sequences: 10 2016-08-18 16:49:32 INFO running meme/mast on cluster 118, # sequences: 2 2016-08-18 16:49:32 INFO running meme/mast on cluster 119, # sequences: 9 2016-08-18 16:49:33 INFO running meme/mast on cluster 104, # sequences: 9 2016-08-18 16:49:33 INFO running meme/mast on cluster 64, # sequences: 10 2016-08-18 16:49:33 INFO running meme/mast on cluster 108, # sequences: 8 2016-08-18 16:49:34 INFO running meme/mast on cluster 120, # sequences: 6 2016-08-18 16:49:34 INFO running meme/mast on cluster 131, # sequences: 9 2016-08-18 16:49:34 INFO running meme/mast on cluster 109, # sequences: 11 2016-08-18 16:49:34 INFO running meme/mast on cluster 65, # sequences: 3 2016-08-18 16:49:35 INFO running meme/mast on cluster 121, # sequences: 8 2016-08-18 16:49:35 INFO running meme/mast on cluster 144, # sequences: 21 2016-08-18 16:49:35 INFO running meme/mast on cluster 132, # sequences: 8 2016-08-18 16:49:36 INFO running meme/mast on cluster 122, # sequences: 10 2016-08-18 16:49:36 INFO running meme/mast on cluster 110, # sequences: 3 2016-08-18 16:49:36 INFO running meme/mast on cluster 133, # sequences: 2 2016-08-18 16:49:36 INFO running meme/mast on cluster 134, # sequences: 8 2016-08-18 16:49:36 INFO running meme/mast on cluster 111, # sequences: 5 2016-08-18 16:49:37 INFO running meme/mast on cluster 123, # sequences: 12 2016-08-18 16:49:37 INFO running meme/mast on cluster 112, # sequences: 8 2016-08-18 16:49:37 INFO running meme/mast on cluster 135, # sequences: 10 2016-08-18 16:49:38 INFO running meme/mast on cluster 113, # sequences: 11 2016-08-18 16:49:38 INFO running meme/mast on cluster 124, # sequences: 6 2016-08-18 16:49:39 INFO running meme/mast on cluster 136, # sequences: 3 2016-08-18 16:49:39 INFO running meme/mast on cluster 145, # sequences: 6 2016-08-18 16:49:39 INFO running meme/mast on cluster 125, # sequences: 3 2016-08-18 16:49:39 INFO running meme/mast on cluster 137, # sequences: 4 2016-08-18 16:49:40 INFO running meme/mast on cluster 126, # sequences: 12 2016-08-18 16:49:40 INFO running meme/mast on cluster 114, # sequences: 6 2016-08-18 16:49:40 INFO running meme/mast on cluster 146, # sequences: 4 2016-08-18 16:49:40 INFO running meme/mast on cluster 138, # sequences: 4 2016-08-18 16:49:41 INFO running meme/mast on cluster 147, # sequences: 8 2016-08-18 16:49:41 INFO running meme/mast on cluster 115, # sequences: 9 2016-08-18 16:49:41 INFO running meme/mast on cluster 139, # sequences: 9 2016-08-18 16:49:42 INFO running meme/mast on cluster 127, # sequences: 6 2016-08-18 16:49:42 INFO running meme/mast on cluster 148, # sequences: 10