!!! Python version: 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] !!! numpy version: 1.12.1 !!! pandas version: 0.20.1 !!! pickle version: $Revision: 72223 $ ################################################################################ ~~~~~PARAMETERS~~~~~~ @@@ FASTA file input: /project/projectdirs/metatlas/projects/magi_tasks/2017/10/0ae82b08-b2a3-40d8-bb9a-e64b567cacd2/fasta_0ae82b08.faa @@@ compound input: /project/projectdirs/metatlas/projects/magi_tasks/2017/10/0ae82b08-b2a3-40d8-bb9a-e64b567cacd2/metabolite_0ae82b08.csv @@@ BLAST filter: 0.85 @@@ Using precomputed compound results: True @@@ Chemnet search to level 2 @@@ Reciprocal closeness: 0.75 @@@ chemnet base penalty: 4.0 @@@ MAGI score weights: [1.0, 1.0, 1.0, 1.0] @@@ Using 64 CPUs !!! Warnings are muted !!! loading refseq and reaction tables... !!! Reference sequences in this file: /global/homes/p/pasteur/repos/magi/workflow/database/mrs_reaction_filtered_refseq_db_newrxns_actinofixed.pkl !!! 135905 reference sequences !!! MRS-Reaction: /global/homes/p/pasteur/repos/magi/workflow/database/mrs_reaction_newrxns_added_actinofix.pkl !!! 16966 reactions !!! 10368 reactions with a refseq !!! 9363 reactions with an EC !!! loading compound table !!! loading chemnet files !!! All databases loaded into memory !!! Saving all results here: /project/projectdirs/metatlas/projects/magi_tasks/2017/10/0ae82b08-b2a3-40d8-bb9a-e64b567cacd2 !!! LOADING GENOME !@# FASTA file loaded with 8210 genes !!! saved gene_sequence table here: /global/homes/p/pasteur/repos/magi/outputs/gene_fastas/fasta_0ae82b08_sequences.pkl !!! blast database stored here: /global/homes/p/pasteur/repos/magi/outputs/BLAST_dbs/fasta_0ae82b08.db Building a new DB, current time: 10/05/2017 16:19:01 New DB name: /global/homes/p/pasteur/repos/magi/outputs/BLAST_dbs/fasta_0ae82b08.db New DB title: /project/projectdirs/metatlas/projects/magi_tasks/2017/10/0ae82b08-b2a3-40d8-bb9a-e64b567cacd2/fasta_0ae82b08.faa Sequence type: Protein Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 8210 sequences in 1.41605 seconds. !!! LOADING COMPOUNDS !!! Scrubbing compounds WARNING: some input compounds were not found in the metabolite database or chemical network; please report these compounds! (see log_unsearched_compounds.csv) !@# 1771 Compounds not being searched; see log_unsearched_compounds.csv !@# 4833 total input compounds to search !@# Conducting gene to reaction search | TLOG 1507245545.3 !!! blast script: /global/homes/p/pasteur/repos/magi/workflow/blastbin/recip_blaster.sh !!! # processes to open: 64 !!! database path: /global/homes/p/pasteur/repos/magi/workflow/database/mrs_reaction_filtered_refseq_db_fasta_blastdb_actinofix !!! results stored: /project/projectdirs/metatlas/projects/magi_tasks/2017/10/0ae82b08-b2a3-40d8-bb9a-e64b567cacd2/intermediate_files/multi_blast_files !@# Homology searching done in 7.07801863352 minutes !!! g2r blast results saved to /project/projectdirs/metatlas/projects/magi_tasks/2017/10/0ae82b08-b2a3-40d8-bb9a-e64b567cacd2/intermediate_files/g2r_blast.pkl !@# gene_to_reaction table completed in 0.0654355843862 minutes !!! gene to reaction results saved to /project/projectdirs/metatlas/projects/magi_tasks/2017/10/0ae82b08-b2a3-40d8-bb9a-e64b567cacd2/intermediate_files/gene_to_reaction.pkl !@# Conducting compound to reaction search | TLOG 1507245974.21 !@# compound_to_reaction table done in 0.214873099327 minutes !!! compound_reaction table saved to /project/projectdirs/metatlas/projects/magi_tasks/2017/10/0ae82b08-b2a3-40d8-bb9a-e64b567cacd2/intermediate_files/compound_to_reaction.pkl !@# Conducting reaction to gene search | TLOG 1507245995.23 !!! 96365 reference sequences to search bee77a1895c34c60b815c525fd9ed3db not in sequence database! 9c61d8a55cbf4549a004745c414c0792 not in sequence database! 3fvu not in sequence database! 3fvx not in sequence database! 764d2de86b6d4a4088da459153fedf99 not in sequence database! 6fcc8193c8554b3f80ec54e254222144 not in sequence database! e870490c41e74662881e2afb5b733c15 not in sequence database! 2f5i not in sequence database! a1bdb74dbec6489d80ffde2b5321d3b7 not in sequence database! ad01ee854cf4464e8e972205a52fa0fc not in sequence database! 1pya not in sequence database! bcdaedb5105d4e86bac330407dc51e22 not in sequence database! a22ce7289fa44701a3d3cc7b08205030 not in sequence database! 3fvs not in sequence database! 1nx4 not in sequence database! 1ofg not in sequence database! 427af085ea824ab5aa971ba3b608bcb2 not in sequence database! 3179ac5e12e243a8b949a7d840e8f8a2 not in sequence database! 9ba815b83efc46f6a96da8e3c8f17311 not in sequence database! 0dde0a584dd54ab3813ef6675b1d7bb9 not in sequence database! 2fxf not in sequence database! 7482fbc98cf34387b57b956e3c6d0526 not in sequence database! 1ord not in sequence database! Q8KTD8 not in sequence database! e113e79021464359a57710681c5a2ece not in sequence database! 2g3t not in sequence database! adfc99d4724d4c88825705e6934f3bb1 not in sequence database! 1gq6 not in sequence database! 43d9f48b8861433a9eadaa94f247c718 not in sequence database! 1q15 not in sequence database! 458beca5295143c0923bf482babd9d7b not in sequence database! 2a7k not in sequence database! 1hq6 not in sequence database! 1xuz not in sequence database! 1xuu not in sequence database! 02622b52df7343d0befa8128493a71c9 not in sequence database! 0059d7cf35b247868d726e697794638a not in sequence database! 2f402d0a12a9429780c593c8d94eeffe not in sequence database! d8631de6037b48e0b799f820b84b305b not in sequence database! c61ffce5db734212948207dfcf8fb8d8 not in sequence database! 6b319a8aa1db4eef804a996b0f027746 not in sequence database! 6f785ef2b5054f17848d54bdcecc6098 not in sequence database! 5505c3d953f34851bcbb55317548274b not in sequence database! 6a1042947dc142b1addb2d102ad76aab not in sequence database! 9c0f59b0d2e9482284e5cc680f14cbae not in sequence database! 1zz6 not in sequence database! b5540bbebc2f4291812649aed5c20f14 not in sequence database! 6fd7254902e04f81a1354083e13e44dc not in sequence database! de3f4dc45d594b67986c180bd07e53c5 not in sequence database! 227c433e04f54074b73a575ebd489fc8 not in sequence database! a750d0d758834be194215c7097452a9c not in sequence database! 1t6k not in sequence database! 1b9h not in sequence database! 2ihv not in sequence database! 1gz6 not in sequence database! b42a00d9ffb24919ab6f339125e78389 not in sequence database! 1b9i not in sequence database! 2b5g not in sequence database! e993c31e2cbb4c58a45b2ab61543220e not in sequence database! f67a2c26aae94bf0b03d24cb264590a8 not in sequence database! 3236afbd0e1f404c9ca30e7507bf6f19 not in sequence database! D3RNJ4 not in sequence database! !!! blast script: /global/homes/p/pasteur/repos/magi/workflow/blastbin/recip_blaster.sh !!! # processes to open: 64 !!! database path: /global/homes/p/pasteur/repos/magi/outputs/BLAST_dbs/fasta_0ae82b08.db !!! results stored: /project/projectdirs/metatlas/projects/magi_tasks/2017/10/0ae82b08-b2a3-40d8-bb9a-e64b567cacd2/intermediate_files/multi_blast_files !@# WARNING: BLAST script error message: Warning: [blastp] lcl|Query_13 Q8TS73: Warning: One or more O characters replaced by X for alignment score calculations at positions 333 Warning: [blastp] lcl|Query_287 P58974: Warning: One or more O characters replaced by X for alignment score calculations at positions 333 Warning: [blastp] lcl|Query_288 P58973: Warning: One or more O characters replaced by X for alignment score calculations at positions 333 Warning: [blastp] lcl|Query_284 Q12TR2: Warning: One or more O characters replaced by X for alignment score calculations at positions 334 Warning: [blastp] lcl|Query_425 Q24MI3: Warning: One or more O characters replaced by X for alignment score calculations at positions 330 Warning: [blastp] lcl|Query_454 Q8TTA9: Warning: One or more O characters replaced by X for alignment score calculations at positions 333 Warning: [blastp] lcl|Query_845 P0C0W7: Warning: One or more O characters replaced by X for alignment score calculations at positions 333 Warning: [blastp] lcl|Query_893 Q18TV3: Warning: One or more O characters replaced by X for alignment score calculations at positions 330 Warning: [blastp] lcl|Query_1116 O93658: Warning: One or more O characters replaced by X for alignment score calculations at positions 333 Warning: [blastp] lcl|Query_1171 Q9P995: Warning: One or more O characters replaced by X for alignment score calculations at positions 333 -------------------------------------------------------------------------------- !!! r2g blast results saved to /project/projectdirs/metatlas/projects/magi_tasks/2017/10/0ae82b08-b2a3-40d8-bb9a-e64b567cacd2/intermediate_files/r2g_blast.pkl !@# reaction_to_gene table done in 6.99852526585 minutes !!! reaction_to_gene table saved to /project/projectdirs/metatlas/projects/magi_tasks/2017/10/0ae82b08-b2a3-40d8-bb9a-e64b567cacd2/intermediate_files/reaction_to_gene.pkl !@# Merging final table | TLOG 1507246415.14 !@# Final Merged table done in 6.85887984832 minutes !!! Final Merged table saved to /project/projectdirs/metatlas/projects/magi_tasks/2017/10/0ae82b08-b2a3-40d8-bb9a-e64b567cacd2/intermediate_files/merged_before_score.h5 !@# Calculating final scores | TLOG 1507246826.67 !@# Scoring done in 1.85051608483 minutes !@# Formatting final table | TLOG 1507246937.7 !@# Saving Tables | TLOG 1507246989.32 full results saved to /project/projectdirs/metatlas/projects/magi_tasks/2017/10/0ae82b08-b2a3-40d8-bb9a-e64b567cacd2/magi_results.csv !@# MAGI Scoring done in 0.882065117359 minutes !@# MAGI analysis complete in 25.0148272157 minutes !!! final results stored to /project/projectdirs/metatlas/projects/magi_tasks/2017/10/0ae82b08-b2a3-40d8-bb9a-e64b567cacd2/magi_results.csv