search

baliga-lab / cmonkey2

Python port of cMonkey, a machine-learning based method for clustering
GNU Lesser General Public License v3.0
26 stars 16 forks source link

MEME parallel environment fail #58

Closed adelomana closed 8 years ago

adelomana commented 8 years ago

I'm running cmonkey2 single thread, but it seems that the parallel version of MEME is failing? I'm not sure, just guessing. Any advice?

Thanks!!!

Gates 2016-08-17 11:24:29 ~/gDrive2/projects/TREES-C/PfuEGRIN/src/cmonkeyRuns : cmonkey2 --organism pfu --verbose --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 2016-08-17 11:24:40 INFO checking MEME... 2016-08-17 11:24:40 INFO Input matrix has # rows: 2040, # columns: 39 2016-08-17 11:24:40 INFO # clusters/row: 2 2016-08-17 11:24:40 INFO # clusters/column: 136 2016-08-17 11:24:40 INFO # CLUSTERS: 204 2016-08-17 11:24:40 INFO use operons: 1 2016-08-17 11:24:40 INFO using MEME version 4.11.1 2016-08-17 11:24:40 DEBUG creating aux directories 2016-08-17 11:24:40 DEBUG created output database schema 2016-08-17 11:24:40 DEBUG added row and column names to output database 2016-08-17 11:24:41 DEBUG creating aux directories 2016-08-17 11:24:41 INFO attempting automatic download of operons from Microbes Online 2016-08-17 11:24:41 INFO NCBI CODE IS: 186497 2016-08-17 11:24:41 INFO Automatically using STRING file in 'cache/186497.gz' (URL: http://networks.systemsbiology.net/string9/186497.gz) 2016-08-17 11:24:41 DEBUG adding operon network factory 2016-08-17 11:24:41 DEBUG Creating Microbe object for 'pfu' 2016-08-17 11:24:41 DEBUG RSAT - get_directory() 2016-08-17 11:24:54 WARNING can't find the correct RSAT mapping ! 2016-08-17 11:24:54 INFO KEGG = 'Pyrococcus furiosus DSM 3638' -> RSAT = 'Pyrococcus_furiosus' 2016-08-17 11:24:54 INFO Creating networks... 2016-08-17 11:24:54 INFO stringdb.read_edges2() 2016-08-17 11:24:55 INFO Finished loading cache/186497.gz 2016-08-17 11:24:56 WARNING 36 (out of 375528) nodes not found in synonyms 2016-08-17 11:24:56 WARNING 23 (out of 375528) nodes not found in canonical gene names 2016-08-17 11:24:56 INFO stringdb.read_edges2(), 185414 edges read, 2350 edges ignored 2016-08-17 11:24:56 DEBUG Network.create() called with 185414 edges 2016-08-17 11:24:56 DEBUG # nodes in network 'STRING': 1998 (of 1998) 2016-08-17 11:24:57 DEBUG Created network 'STRING' with 92471 edges 2016-08-17 11:24:57 INFO MicrobesOnline - make_network() 2016-08-17 11:24:57 INFO MicrobesOnline.get_operon_predictions_for(186497) 2016-08-17 11:24:57 INFO 852 prediction pairs read 2016-08-17 11:24:57 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:24:57 INFO 440 operons created 2016-08-17 11:24:57 INFO 2105 edges computed 2016-08-17 11:24:57 DEBUG Network.create() called with 2105 edges 2016-08-17 11:24:57 DEBUG # nodes in network 'operons': 1231 (of 1292) 2016-08-17 11:24:57 DEBUG Created network 'operons' with 2023 edges 2016-08-17 11:24:57 INFO Finished creating networks. 2016-08-17 11:24:57 DEBUG creating and seeding memberships 2016-08-17 11:24:58 DEBUG seed column members in 11.000000 s. 2016-08-17 11:24:58 INFO MicrobesOnline.get_operon_predictions_for(186497) 2016-08-17 11:24:58 INFO 852 prediction pairs read 2016-08-17 11:24:58 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:24:58 INFO 440 operons created 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s003' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0033' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_t001' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_t002' not found in RSAT features 2016-08-17 11:24:58 WARNING Operon did not contain any available genes 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s004' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0222.1n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s007' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0298.1n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s008' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s009' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0328' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0355.1n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s011' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0551' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s014' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0706.1n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0720' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0732.2n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0776.1n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_t015' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_t016' not found in RSAT features 2016-08-17 11:24:58 WARNING Operon did not contain any available genes 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0841.1n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s017' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0855.1n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0879' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0882' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF0897.1n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF1015.1n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s020' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF1093.1n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF1112.1n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF1162' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF1226' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF1255' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF1309' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF1319' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s026' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF1357.1n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_t026' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_t027' not found in RSAT features 2016-08-17 11:24:58 WARNING Operon did not contain any available genes 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s030' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_t036' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_t037' not found in RSAT features 2016-08-17 11:24:58 WARNING Operon did not contain any available genes 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s035' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF1633' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_t039' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_t042' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s039' not found in RSAT features 2016-08-17 11:24:58 WARNING Operon did not contain any available genes 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s041' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s044' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF1940.1n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s045' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s046' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s049' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s050' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF2048.1n' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF_s053' not found in RSAT features 2016-08-17 11:24:58 WARNING Microbes Online operon gene 'PF2054.1n' not found in RSAT features 2016-08-17 11:24:58 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:24:58 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:24:58 DEBUG Computing global background file on seqtype 'upstream' (2001 sequences) 2016-08-17 11:25:02 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:02 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:02 DEBUG building reverse map... 2016-08-17 11:25:02 WARNING 39 genes not found in synonyms. 2016-08-17 11:25:02 DEBUG reverse map built in 4 ms. 2016-08-17 11:25:02 INFO cmonkey_run config_params: 2016-08-17 11:25:02 INFO memb.prob_col_change=1.0 2016-08-17 11:25:02 INFO use_string=True 2016-08-17 11:25:02 INFO Columns={'schedule': 1,5} 2016-08-17 11:25:02 INFO memb.max_changes_per_row=1 2016-08-17 11:25:02 INFO rsat_base_url=http://rsat01.biologie.ens.fr/rsat/ 2016-08-17 11:25:02 INFO start_iteration=1 2016-08-17 11:25:02 INFO multiprocessing=True 2016-08-17 11:25:02 INFO Weeder={'top': '50', 'orgcode': '', 'schedule': 1,100, 'analysis': 'small', 'freqfile_dir': '', 'nmotifs_rvec': 'c(rep(1, num_iterations/3), rep(2, num_iterations/3))', 'global_background': 'True'} 2016-08-17 11:25:02 INFO random_seed=431981325 2016-08-17 11:25:02 INFO interactive=False 2016-08-17 11:25:02 INFO ratios_file=/Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/expression/ratios/ratios.39samplesx2045genes.2016aug.txt 2016-08-17 11:25:02 INFO quantile_normalize=False 2016-08-17 11:25:02 INFO dbfile_name=cmonkey_run.db 2016-08-17 11:25:02 INFO debug=set() 2016-08-17 11:25:02 INFO num_clusters=204 2016-08-17 11:25:02 INFO nomotifs=False 2016-08-17 11:25:02 INFO operon_file=None 2016-08-17 11:25:02 INFO checkratios=False 2016-08-17 11:25:02 INFO new_data_file=False 2016-08-17 11:25:02 INFO result_freq=10 2016-08-17 11:25:02 INFO Rows={'scaling': ('scaling_const', 0.3), 'schedule': 1,2} 2016-08-17 11:25:02 INFO string_file=cache/186497.gz 2016-08-17 11:25:02 INFO memb.min_cluster_rows_allowed=3 2016-08-17 11:25:02 INFO logfile=None 2016-08-17 11:25:02 INFO rsat_organism=None 2016-08-17 11:25:02 INFO log_subresults=True 2016-08-17 11:25:02 INFO SequenceType-upstream={'scan_distance': '-30,250', 'search_distance': '-20,150'} 2016-08-17 11:25:02 INFO sequence_types=['upstream'] 2016-08-17 11:25:02 INFO memb.clusters_per_col=136 2016-08-17 11:25:02 INFO synonym_file=None 2016-08-17 11:25:02 INFO rsat_dir=None 2016-08-17 11:25:02 INFO Postprocessing={'run_tomtom': 'False'} 2016-08-17 11:25:02 INFO normalize_ratios=True 2016-08-17 11:25:02 INFO stats_freq=10 2016-08-17 11:25:02 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} 2016-08-17 11:25:02 INFO tmp_dir= 2016-08-17 11:25:02 INFO memb.clusters_per_row=2 2016-08-17 11:25:02 INFO search_distances={'upstream': (-20, 150)} 2016-08-17 11:25:02 INFO nonetworks=False 2016-08-17 11:25:02 INFO organism_code=pfu 2016-08-17 11:25:02 INFO num_cores=None 2016-08-17 11:25:02 INFO memb.max_changes_per_col=5 2016-08-17 11:25:02 INFO MEME={'use_revcomp': 'True', 'schedule': 1,100, 'background_order': '3', 'version': '4.11.1', 'arg_mod': 'zoops', 'max_width': '24', 'nmotifs_rvec': 'c(rep(1, num_iterations/3), rep(2, num_iterations/3))', 'global_background': 'True'} 2016-08-17 11:25:02 INFO fasta_file=None 2016-08-17 11:25:02 INFO pipeline={'column-scoring': {'id': 'Columns', 'function': {'class': 'ColumnScoringFunction', 'module': 'cmonkey.scoring'}}, 'row-scoring': {'id': 'combiner', 'function': {'class': 'ScoringFunctionCombiner', 'module': 'cmonkey.scoring'}, 'args': {'functions': [{'id': 'Rows', 'function': {'class': 'RowScoringFunction', 'module': 'cmonkey.microarray'}}, {'id': 'Networks', 'function': {'class': 'ScoringFunction', 'module': 'cmonkey.network'}}, {'id': 'Motifs', 'function': {'class': 'MemeScoringFunction', 'module': 'cmonkey.motif'}}]}}} 2016-08-17 11:25:02 INFO command_line=/Users/alomana/anaconda/bin/cmonkey2 --organism pfu --verbose --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 2016-08-17 11:25:02 INFO remap_network_nodes=False 2016-08-17 11:25:02 INFO use_operons=True 2016-08-17 11:25:02 INFO resume=False 2016-08-17 11:25:02 INFO output_dir=/Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/cmonkeyRuns/39samplesx2045genesRun1 2016-08-17 11:25:02 INFO postadjust=True 2016-08-17 11:25:02 INFO ncbi_code=186497 2016-08-17 11:25:02 INFO debug_freq=50 2016-08-17 11:25:02 INFO cache_dir=cache 2016-08-17 11:25:02 INFO use_chi2=False 2016-08-17 11:25:02 INFO rsat_features=feature 2016-08-17 11:25:02 INFO memb.prob_row_change=0.5 2016-08-17 11:25:02 INFO add_fuzz=rows 2016-08-17 11:25:02 INFO pipeline_file= 2016-08-17 11:25:02 INFO memb.max_cluster_rows_allowed=70 2016-08-17 11:25:02 INFO minimize_io=False 2016-08-17 11:25:02 INFO scan_distances={'upstream': (-30, 250)} 2016-08-17 11:25:02 INFO Networks={'scaling': ('scaling_rvec', 'seq(1e-5, 0.5, length=num_iterations_3/4)'), 'schedule': 1,7} 2016-08-17 11:25:02 INFO use_BSCM=False 2016-08-17 11:25:02 INFO case_sensitive=False 2016-08-17 11:25:02 INFO out_database=/Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/cmonkeyRuns/39samplesx2045genesRun1/cmonkey_run.db 2016-08-17 11:25:02 INFO num_iterations=2000 2016-08-17 11:25:02 INFO Iteration # 1 2016-08-17 11:25:02 DEBUG running 'Rows' in iteration 1 with scaling: 0.300000 2016-08-17 11:25:03 DEBUG **compute_row_scores_for_clusters() in 0.334000 s. 2016-08-17 11:25:03 DEBUG made result matrix in 0.006000 s. 2016-08-17 11:25:03 DEBUG function 'Rows', trim mean score: -1.696937 2016-08-17 11:25:03 DEBUG running 'Networks' in iteration 1 with scaling: 0.000010 2016-08-17 11:25:03 DEBUG Compute scores for network 'STRING', WEIGHT: 0.500000 2016-08-17 11:25:03 DEBUG NETWORK 'STRING' SCORING TIME: 0.572000 s. 2016-08-17 11:25:03 DEBUG Compute scores for network 'operons', WEIGHT: 0.500000 2016-08-17 11:25:04 DEBUG NETWORK 'operons' SCORING TIME: 0.154000 s. 2016-08-17 11:25:04 DEBUG function 'Networks', trim mean score: -1.477909 2016-08-17 11:25:04 DEBUG Running Motifing for sequence type 'upstream'... 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:04 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:04 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:05 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:06 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:07 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:08 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:09 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:10 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:10 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:10 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:10 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:10 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:10 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:10 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:10 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:10 DEBUG RSAT - get_features(Pyrococcus_furiosus) 2016-08-17 11:25:10 DEBUG RSAT - get_contig_sequence(Pyrococcus_furiosus, NC_003413.1) 2016-08-17 11:25:10 DEBUG prepared sequences in 6075 ms. 2016-08-17 11:25:10 DEBUG prepared MEME parameters in 0 ms. 2016-08-17 11:25:10 INFO running meme/mast on cluster 1, # sequences: 14 2016-08-17 11:25:10 INFO running meme/mast on cluster 14, # sequences: 10 2016-08-17 11:25:10 INFO running meme/mast on cluster 27, # sequences: 7 2016-08-17 11:25:10 INFO running meme/mast on cluster 40, # sequences: 6 2016-08-17 11:25:10 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out.tj8ryjsv /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqsju5b_x3o -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutydp74u_u 2016-08-17 11:25:10 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out.gud373sd /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqs8daowty9 -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutaluap_3s 2016-08-17 11:25:10 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutydp74u_u... 2016-08-17 11:25:10 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutaluap_3s... 2016-08-17 11:25:10 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out.2iivh9ay /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqstcwv1f9u -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutf_az069w 2016-08-17 11:25:10 INFO running meme/mast on cluster 53, # sequences: 9 2016-08-17 11:25:11 INFO running meme/mast on cluster 66, # sequences: 4 2016-08-17 11:25:11 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutf_az069w... 2016-08-17 11:25:11 INFO running meme/mast on cluster 79, # sequences: 5 2016-08-17 11:25:11 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out._89sq8zc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqss54psxfd -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutmfzg_eff 2016-08-17 11:25:11 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out.ppoo6r5c /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqs713ziy8x -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastout5fwwr1u2 2016-08-17 11:25:11 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out.dyza2a44 /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqsj96nai5q -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastouttyoi99kf 2016-08-17 11:25:11 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutmfzg_eff... 2016-08-17 11:25:11 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out.4dt7g4n1 /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqsj79gh_4n -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutkyf0j7zp 2016-08-17 11:25:11 INFO running meme/mast on cluster 92, # sequences: 4 2016-08-17 11:25:11 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastout5fwwr1u2... 2016-08-17 11:25:11 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastouttyoi99kf... 2016-08-17 11:25:11 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out.w5k86tfo /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqs4or2u4mk -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutsvxheimo 2016-08-17 11:25:11 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutsvxheimo... 2016-08-17 11:25:11 INFO running meme/mast on cluster 105, # sequences: 7 2016-08-17 11:25:11 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutkyf0j7zp... 2016-08-17 11:25:11 INFO running meme/mast on cluster 118, # sequences: 5 2016-08-17 11:25:12 INFO running meme/mast on cluster 131, # sequences: 3 2016-08-17 11:25:12 INFO running meme/mast on cluster 144, # sequences: 6 2016-08-17 11:25:12 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out.3e4lr77l /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqs_4n92n_v -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutphna1r9w 2016-08-17 11:25:12 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out.z2lksah2 /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqsdotyn558 -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutl5ymxiyy 2016-08-17 11:25:12 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out.wn6hd_uq /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqsvx7f3d6p -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastout7_2pfva7 2016-08-17 11:25:12 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out.43nyhp18 /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqsfllv9_zs -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutns82jm35 2016-08-17 11:25:12 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutl5ymxiyy... 2016-08-17 11:25:12 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutphna1r9w... 2016-08-17 11:25:12 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutns82jm35... 2016-08-17 11:25:12 INFO running meme/mast on cluster 157, # sequences: 14 2016-08-17 11:25:12 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastout7_2pfva7... 2016-08-17 11:25:12 INFO running meme/mast on cluster 170, # sequences: 6 2016-08-17 11:25:12 INFO running meme/mast on cluster 183, # sequences: 11 2016-08-17 11:25:12 INFO running meme/mast on cluster 196, # sequences: 3 2016-08-17 11:25:12 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out.raji6q4h /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqsuzk8hgzo -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutm23i6eac 2016-08-17 11:25:12 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out.rdga5ydx /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqswhw622fj -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutb0o5ew5d 2016-08-17 11:25:13 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutb0o5ew5d... 2016-08-17 11:25:13 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutm23i6eac... 2016-08-17 11:25:13 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out._nw6t61e /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqskf3jdccb -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastout4b3q_a6n 2016-08-17 11:25:13 DEBUG running: mast /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/meme.out.5b4yw_pc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memeseqs1h92oere -bfile /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/memebg_dhmq340 -nostatus -ev 1500 -mev 99999 -mt 0.99 -nohtml -notext -seqp -remcorr -oc /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutmr167abl 2016-08-17 11:25:13 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastout4b3q_a6n... 2016-08-17 11:25:13 DEBUG removing /var/folders/mx/mt8hncrj171dk_tgll33hcm8lpl922/T/mastoutmr167abl... multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/Users/alomana/anaconda/lib/python3.5/multiprocessing/pool.py", line 119, in worker result = (True, func(_args, _kwds)) File "/Users/alomana/anaconda/lib/python3.5/multiprocessing/pool.py", line 44, in mapstar return list(map(args)) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/motif.py", line 461, in compute_cluster_score run_result = params.meme_runner(params) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/meme.py", line 168, in __call** input_seqs.keys()) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/meme.py", line 372, in read_mast_output return read_mast_output_xml(mast_output, genes) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/meme.py", line 530, in read_mast_outputxml motifnum = int(hit.get('motif').replace('motif', '')) AttributeError: 'NoneType' object has no attribute 'replace' """

The above exception was the direct cause of the following exception:

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 513, in run self.run_iterations() File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/cmonkey_run.py", line 771, in run_iterations self.run_iteration(iteration, force=force) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/cmonkey_run.py", line 701, in run_iteration rscores = self.row_scoring.compute(iteration_result) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/scoring.py", line 480, in compute matrix = scoring_function.compute(iteration_result, reference_matrix) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/motif.py", line 224, in compute return self.compute(iteration_result, False, ref_matrix) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/motif.py", line 252, in compute num_motifs, force) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/motif.py", line 373, in compute_pvalues results = pool.map(compute_cluster_score, params.values()) File "/Users/alomana/anaconda/lib/python3.5/multiprocessing/pool.py", line 260, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/Users/alomana/anaconda/lib/python3.5/multiprocessing/pool.py", line 608, in get raise self._value AttributeError: 'NoneType' object has no attribute 'replace' Gates 2016-08-17 11:25:13 ~/gDrive2/projects/TREES-C/PfuEGRIN/src/cmonkeyRuns :

weiju commented 8 years ago

could you please do me a favor, set multiprocessing to "False" ? You can do this, e.g. by creating a configuration file config.ini with the contents

----- config.ini --------- [General] use_multiprocessing = False

------ config.ini end ----

and use it with the switch --config config.ini on the command line. I feel that for some reasons your setup retrieves empty or non-existing sequences.

Wei-ju

weiju commented 8 years ago

if possible, you can also provide me with your input files in our shared /proj/omics4tb folder

adelomana commented 8 years ago

Same error. I think meme.py has some bug?

Gates 2016-08-18 15:20:09 ~/gDrive2/projects/TREES-C/PfuEGRIN/src/cmonkeyRuns : cmonkey2 --organism pfu --config config.ini --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 15:20:26 INFO checking MEME... 2016-08-18 15:20:26 INFO Input matrix has # rows: 2040, # columns: 39 2016-08-18 15:20:26 INFO # clusters/row: 2 2016-08-18 15:20:26 INFO # clusters/column: 136 2016-08-18 15:20:26 INFO # CLUSTERS: 204 2016-08-18 15:20:26 INFO use operons: 1 2016-08-18 15:20:26 INFO using MEME version 4.11.1 2016-08-18 15:20:27 INFO attempting automatic download of operons from Microbes Online 2016-08-18 15:20:27 INFO NCBI CODE IS: 186497 2016-08-18 15:20:27 INFO Automatically using STRING file in 'cache/186497.gz' (URL: http://networks.systemsbiology.net/string9/186497.gz) 2016-08-18 15:20:39 WARNING can't find the correct RSAT mapping ! 2016-08-18 15:20:39 INFO KEGG = 'Pyrococcus furiosus DSM 3638' -> RSAT = 'Pyrococcus_furiosus' 2016-08-18 15:20:39 INFO Creating networks... 2016-08-18 15:20:39 INFO stringdb.read_edges2() 2016-08-18 15:20:40 INFO Finished loading cache/186497.gz 2016-08-18 15:20:41 WARNING 36 (out of 375528) nodes not found in synonyms 2016-08-18 15:20:41 WARNING 23 (out of 375528) nodes not found in canonical gene names 2016-08-18 15:20:41 INFO stringdb.read_edges2(), 185414 edges read, 2350 edges ignored 2016-08-18 15:20:41 INFO MicrobesOnline - make_network() 2016-08-18 15:20:41 INFO MicrobesOnline.get_operon_predictions_for(186497) 2016-08-18 15:20:41 INFO 852 prediction pairs read 2016-08-18 15:20:41 INFO 440 operons created 2016-08-18 15:20:41 INFO 2105 edges computed 2016-08-18 15:20:41 INFO Finished creating networks. 2016-08-18 15:20:42 INFO MicrobesOnline.get_operon_predictions_for(186497) 2016-08-18 15:20:42 INFO 852 prediction pairs read 2016-08-18 15:20:42 INFO 440 operons created 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s003' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0033' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_t001' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_t002' not found in RSAT features 2016-08-18 15:20:42 WARNING Operon did not contain any available genes 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s004' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0222.1n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s007' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0298.1n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s008' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s009' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0328' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0355.1n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s011' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0551' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s014' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0706.1n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0720' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0732.2n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0776.1n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_t015' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_t016' not found in RSAT features 2016-08-18 15:20:42 WARNING Operon did not contain any available genes 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0841.1n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s017' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0855.1n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0879' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0882' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF0897.1n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF1015.1n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s020' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF1093.1n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF1112.1n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF1162' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF1226' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF1255' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF1309' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF1319' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s026' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF1357.1n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_t026' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_t027' not found in RSAT features 2016-08-18 15:20:42 WARNING Operon did not contain any available genes 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s030' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_t036' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_t037' not found in RSAT features 2016-08-18 15:20:42 WARNING Operon did not contain any available genes 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s035' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF1633' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_t039' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_t042' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s039' not found in RSAT features 2016-08-18 15:20:42 WARNING Operon did not contain any available genes 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s041' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s044' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF1940.1n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s045' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s046' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s049' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s050' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF2048.1n' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF_s053' not found in RSAT features 2016-08-18 15:20:42 WARNING Microbes Online operon gene 'PF2054.1n' not found in RSAT features 2016-08-18 15:20:46 WARNING 39 genes not found in synonyms. 2016-08-18 15:20:46 INFO cmonkey_run config_params: 2016-08-18 15:20:46 INFO rsat_features=feature 2016-08-18 15:20:46 INFO log_subresults=True 2016-08-18 15:20:46 INFO fasta_file=None 2016-08-18 15:20:46 INFO command_line=/Users/alomana/anaconda/bin/cmonkey2 --organism pfu --config config.ini --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 15:20:46 INFO scan_distances={'upstream': (-30, 250)} 2016-08-18 15:20:46 INFO Motifs={'schedule': 2,10, 'sequence_types': 'upstream', 'scaling': ('scaling_rvec', 'c(rep(1e-5, 100), seq(1e-5, 1, length=num_iterations_3/4))')} 2016-08-18 15:20:46 INFO memb.prob_col_change=1.0 2016-08-18 15:20:46 INFO Columns={'schedule': 1,5} 2016-08-18 15:20:46 INFO use_BSCM=False 2016-08-18 15:20:46 INFO normalize_ratios=True 2016-08-18 15:20:46 INFO num_iterations=2000 2016-08-18 15:20:46 INFO num_clusters=204 2016-08-18 15:20:46 INFO operon_file=None 2016-08-18 15:20:46 INFO use_chi2=False 2016-08-18 15:20:46 INFO search_distances={'upstream': (-20, 150)} 2016-08-18 15:20:46 INFO rsat_base_url=http://rsat01.biologie.ens.fr/rsat/ 2016-08-18 15:20:46 INFO out_database=/Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/cmonkeyRuns/39samplesx2045genesRun1/cmonkey_run.db 2016-08-18 15:20:46 INFO memb.max_cluster_rows_allowed=70 2016-08-18 15:20:46 INFO debug=set() 2016-08-18 15:20:46 INFO checkratios=False 2016-08-18 15:20:46 INFO memb.max_changes_per_row=1 2016-08-18 15:20:46 INFO result_freq=10 2016-08-18 15:20:46 INFO nomotifs=False 2016-08-18 15:20:46 INFO postadjust=True 2016-08-18 15:20:46 INFO Rows={'schedule': 1,2, 'scaling': ('scaling_const', 0.3)} 2016-08-18 15:20:46 INFO organism_code=pfu 2016-08-18 15:20:46 INFO pipeline={'column-scoring': {'id': 'Columns', 'function': {'class': 'ColumnScoringFunction', 'module': 'cmonkey.scoring'}}, 'row-scoring': {'id': 'combiner', 'args': {'functions': [{'id': 'Rows', 'function': {'class': 'RowScoringFunction', 'module': 'cmonkey.microarray'}}, {'id': 'Networks', 'function': {'class': 'ScoringFunction', 'module': 'cmonkey.network'}}, {'id': 'Motifs', 'function': {'class': 'MemeScoringFunction', 'module': 'cmonkey.motif'}}]}, 'function': {'class': 'ScoringFunctionCombiner', 'module': 'cmonkey.scoring'}}} 2016-08-18 15:20:46 INFO random_seed=532527178 2016-08-18 15:20:46 INFO rsat_dir=None 2016-08-18 15:20:46 INFO ncbi_code=186497 2016-08-18 15:20:46 INFO logfile=None 2016-08-18 15:20:46 INFO MEME={'version': '4.11.1', 'nmotifs_rvec': 'c(rep(1, num_iterations/3), rep(2, num_iterations/3))', 'background_order': '3', 'global_background': 'True', 'schedule': 1,100, 'arg_mod': 'zoops', 'use_revcomp': 'True', 'max_width': '24'} 2016-08-18 15:20:46 INFO nonetworks=False 2016-08-18 15:20:46 INFO memb.clusters_per_col=136 2016-08-18 15:20:46 INFO remap_network_nodes=False 2016-08-18 15:20:46 INFO Postprocessing={'run_tomtom': 'False'} 2016-08-18 15:20:46 INFO rsat_organism=None 2016-08-18 15:20:46 INFO quantile_normalize=False 2016-08-18 15:20:46 INFO pipeline_file= 2016-08-18 15:20:46 INFO dbfile_name=cmonkey_run.db 2016-08-18 15:20:46 INFO tmp_dir= 2016-08-18 15:20:46 INFO string_file=cache/186497.gz 2016-08-18 15:20:46 INFO start_iteration=1 2016-08-18 15:20:46 INFO output_dir=/Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/cmonkeyRuns/39samplesx2045genesRun1 2016-08-18 15:20:46 INFO memb.clusters_per_row=2 2016-08-18 15:20:46 INFO case_sensitive=False 2016-08-18 15:20:46 INFO use_string=True 2016-08-18 15:20:46 INFO Weeder={'nmotifs_rvec': 'c(rep(1, num_iterations/3), rep(2, num_iterations/3))', 'analysis': 'small', 'global_background': 'True', 'freqfile_dir': '', 'schedule': 1,100, 'orgcode': '', 'top': '50'} 2016-08-18 15:20:46 INFO synonym_file=None 2016-08-18 15:20:46 INFO num_cores=None 2016-08-18 15:20:46 INFO use_operons=True 2016-08-18 15:20:46 INFO multiprocessing=False 2016-08-18 15:20:46 INFO minimize_io=False 2016-08-18 15:20:46 INFO add_fuzz=rows 2016-08-18 15:20:46 INFO memb.max_changes_per_col=5 2016-08-18 15:20:46 INFO resume=False 2016-08-18 15:20:46 INFO stats_freq=10 2016-08-18 15:20:46 INFO interactive=False 2016-08-18 15:20:46 INFO Networks={'schedule': 1,7, 'scaling': ('scaling_rvec', 'seq(1e-5, 0.5, length=num_iterations_3/4)')} 2016-08-18 15:20:46 INFO SequenceType-upstream={'search_distance': '-20,150', 'scan_distance': '-30,250'} 2016-08-18 15:20:46 INFO cache_dir=cache 2016-08-18 15:20:46 INFO debug_freq=50 2016-08-18 15:20:46 INFO new_data_file=False 2016-08-18 15:20:46 INFO memb.min_cluster_rows_allowed=3 2016-08-18 15:20:46 INFO sequence_types=['upstream'] 2016-08-18 15:20:46 INFO memb.prob_row_change=0.5 2016-08-18 15:20:46 INFO ratios_file=/Users/alomana/gDrive2/projects/TREES-C/PfuEGRIN/data/expression/ratios/ratios.39samplesx2045genes.2016aug.txt 2016-08-18 15:20:46 INFO Iteration # 1 2016-08-18 15:21:01 INFO running meme/mast on cluster 1, # sequences: 5 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 513, in run self.run_iterations() File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/cmonkey_run.py", line 771, in run_iterations self.run_iteration(iteration, force=force) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/cmonkey_run.py", line 701, in run_iteration rscores = self.row_scoring.compute(iteration_result) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/scoring.py", line 480, in compute matrix = scoring_function.compute(iteration_result, reference_matrix) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/motif.py", line 224, in compute return self.compute(iteration_result, False, ref_matrix) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/motif.py", line 252, in compute num_motifs, force) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/motif.py", line 392, in computepvalues , pvalues, run_result = compute_cluster_score(params[cluster]) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/motif.py", line 461, in compute_cluster_score run_result = params.meme_runner(params) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/meme.py", line 168, in call input_seqs.keys()) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/meme.py", line 372, in read_mast_output return read_mast_output_xml(mast_output, genes) File "/Users/alomana/anaconda/lib/python3.5/site-packages/cmonkey/meme.py", line 530, in read_mast_outputxml motifnum = int(hit.get('motif').replace('motif', '')) AttributeError: 'NoneType' object has no attribute 'replace' Gates 2016-08-18 15:21:02 ~/gDrive2/projects/TREES-C/PfuEGRIN/src/cmonkeyRuns : cat config.ini [General] use_multiprocessing = FalseGates 2016-08-18 15:21:09 ~/gDrive2/projects/TREES-C/PfuEGRIN/src/cmonkeyRuns :

adelomana commented 8 years ago

ah, the solution was to use the patched version of MEME 4.10, thanks Wei-Ju!