ariahahn
commented
7 years ago Hi,
The tRNA skip is because this is set on your params file. You should be able to set this. metapathways annotates orgs not contigs...I think it might actually be an orf (and contigs is simply the name). It's seems the orfs were annotated with other databases, correct? Also try 2.52 (the newest version).
Aria
On Oct 31, 2016 10:09 AM, "BVG" notifications@github.com wrote:
I am running metapathways2 command line and finding this error.
When executing
python MetaPathways.py -i /home/blanca/Contigs_same.fasta -o /home/blanca/metapa_commandLine -c config/template_config.txt -v -p config/template_param.txt
It skips tRNA search and can't annotate a contig, apparently.
COMMAND : MetaPathways.py -i /home/blanca/Contigs_same.fasta -o /home/blanca/metapa_commandLine -c config/template_config.txt -v -p config/template_param.txt WARNING sequence for db /home/database/blastdb/ MetaPathways_DBs///functional/formatted/metacyc-v5-2011-10-21 not formatted WARNING Trying to format database 'metacyc-v5-2011-10-21' for algorithm 'LAST' INFO Formatted database 'metacyc-v5-2011-10-21' successfully for 'LAST' WARNING Does not have map file '/home/database/blastdb/ MetaPathways_DBs///functional/formatted/metacyc-v5-2011-10-21-names.txt' for 'metacyc-v5-2011-10-21' INFO Successfully created map file '/home/database/blastdb/ MetaPathways_DBs///functional/formatted/metacyc-v5-2011-10-21-names.txt' for 'metacyc-v5-2011-10-21' WARNING sequence for db /home/database/blastdb/ MetaPathways_DBs///functional/formatted/COG_2013-12-27 not formatted WARNING Trying to format database 'COG_2013-12-27' for algorithm 'LAST' INFO Formatted database 'COG_2013-12-27' successfully for 'LAST' WARNING Does not have map file '/home/database/blastdb/ MetaPathways_DBs///functional/formatted/COG_2013-12-27-names.txt' for 'COG_2013-12-27' INFO Successfully created map file '/home/database/blastdb/ MetaPathways_DBs///functional/formatted/COG_2013-12-27-names.txt' for 'COG_2013-12-27' RUNNING MetaPathways version 2.5.1 ============== RUNNING STEPS IN BLOCK 0 ================
################################################
PROCESSING INPUT /home/blanca/Contigs_same.fasta [STEPS BLOCK 0]
EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1/libs/python_scripts/MetaPathways_filter_input.py --min_length 180 --log_file /home/blanca/metapa_commandLine/Contigssame/run statistics//Contigs_same.nuc.stats -i /home/blanca/Contigs_same.fasta -o /home/blanca/metapa_commandLine/Contigs_same/preprocessed//Contigs_same.fasta -M /home/blanca/metapa_commandLine/Contigs_same/ preprocessed//Contigs_same.mapping.txt -t nucleotide -L /home/blanca/metapa_commandLine/Contigs_same/run_statistics//Contigs_same. contig.lengths.txt PREPROCESSING THE INPUT ..... Success!
EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1/libs/python_scripts/MetaPathways_orf_prediction.py --prod_exec /home/programas/metapathways2-2.5.1//executables/ubuntu/prodigal --prod_m --prod_p meta --prod_f gff --prod_g 11 --prodinput /home/blanca/metapa commandLine/Contigs_same/preprocessed//Contigs_same.fasta --prod_output /home/blanca/metapa_commandLine/Contigssame/orf prediction/Contigs_same.gff ORF PREDICTION ..... Success!
EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1/libs/python_scripts/MetaPathways_create_amino_sequences.py -g /home/blanca/metapa_commandLine/Contigs_same/orf_prediction/Contigs_same.gff -n /home/blanca/metapa_commandLine/Contigs_same/ preprocessed//Contigs_same.fasta --outputnuc /home/blanca/metapa commandLine/Contigs_same/orf_prediction//Contigs_same.fna --output_amino /home/blanca/metapa_commandLine/Contigs_same/orf_prediction//Contigs_same.faa --output_gff /home/blanca/metapa_commandLine/Contigssame/orf prediction//Contigs_same.unannot.gff CREATING AMINO ACID SEQS FROM GFF FILE ..... Success!
EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1/libs/python_scripts/MetaPathways_filter_input.py --min_length 60 --log_file /home/blanca/metapa_commandLine/Contigssame/run statistics//Contigssame.amino.stats -i /home/blanca/metapa commandLine/Contigs_same/orf_prediction//Contigs_same.faa -o /home/blanca/metapa_commandLine/Contigssame/orf prediction//Contigssame.qced.faa -L /home/blanca/metapa commandLine/Contigs_same/run_statistics//Contigs_same.orf.lengths.txt -t amino FILTER AMINO ACID SEQS ..... Success!
################################################ PROCESSING INPUT /home/blanca/Contigs_same.fasta [STEPS BLOCK 1] EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1//libs/python_scripts/MetaPathways_func_search.py --algorithm LAST --last_executable /home/programas/metapathways2-2.5.1//executables/ubuntu/lastal --last_o /home/blanca/metapa_commandLine/Contigs_same/ blast_results//Contigs_same.metacyc-v5-2011-10-21.LASTout --last_f 2 --last_db /home/database/blastdb/MetaPathways_DBs///functional/ formatted/metacyc-v5-2011-10-21 --lastquery /home/blanca/metapa commandLine/Contigs_same/orf_prediction//Contigs_same.qced.faa LASTING AMINO SEQS AGAINST metacyc-v5-2011-10-21 ..... Success!
EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1//libs/python_scripts/MetaPathways_func_search.py --algorithm LAST --last_executable /home/programas/metapathways2-2.5.1//executables/ubuntu/lastal --last_o /home/blanca/metapa_commandLine/Contigs_same/ blast_results//Contigs_same.COG_2013-12-27.LASTout --last_f 2 --last_db /home/database/blastdb/MetaPathways_DBs///functional/formatted/COG_2013-12-27 --last_query /home/blanca/metapa_commandLine/Contigssame/orf prediction//Contigs_same.qced.faa LASTING AMINO SEQS AGAINST COG_2013-12-27 ..... Success!
################################################
PROCESSING INPUT /home/blanca/Contigs_same.fasta [STEPS BLOCK 2]
EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1//libs/python_scripts/MetaPathways_refscore.py -o /home/blanca/metapa_commandLine/Contigs_same/blast_results//Contigs_same.refscores.LAST -i /home/blanca/metapa_commandLine/Contigssame/orf prediction//Contigs_same.qced.faa -a LAST COMPUTING REFSCORES FOR BITSCORE ..... Redo Success!
EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1/libs/python_scripts/MetaPathways_parse_blast.py -d metacyc-v5-2011-10-21 -b /home/blanca/metapa_commandLine/Contigs_same/ blast_results//Contigs_same.metacyc-v5-2011-10-21.LASTout -m /home/database/blastdb/MetaPathwaysDBs///functional/ formatted/metacyc-v5-2011-10-21-names.txt -r /home/blanca/metapa commandLine/Contigs_same/blast_results//Contigs_same.refscores.LAST --min_bsr 0.4 --min_score 20 --min_length 60 --max_evalue 0.000001 --algorithm LAST PARSING LAST OUTPUT FOR metacyc-v5-2011-10-21 ..... Redo Success!
EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1/libs/python_scripts/MetaPathways_parse_blast.py -d COG_2013-12-27 -b /home/blanca/metapa_commandLine/Contigs_same/ blast_results//Contigs_same.COG_2013-12-27.LASTout -m /home/database/blastdb/MetaPathways_DBs///functional/ formatted/COG2013-12-27-names.txt -r /home/blanca/metapa commandLine/Contigs_same/blast_results//Contigs_same.refscores.LAST --min_bsr 0.4 --min_score 20 --min_length 60 --max_evalue 0.000001 --algorithm LAST PARSING LAST OUTPUT FOR COG_2013-12-27 ..... Redo Success!
EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1//libs/python_scripts/MetaPathways_tRNA_scan.py --executable /home/programas/metapathways2-2.5.1//executables/ubuntu/trnascan-1.4 -o /home/blanca/metapa_commandLine/Contigs_same/results//tRNA//Contigs_same.tRNA.stats.txt -F /home/blanca/metapa_commandLine/Contigs_same/ results//tRNA//Contigssame.tRNA.fasta -i /home/blanca/metapa commandLine/Contigs_same/preprocessed//Contigs_same.fasta -T /home/programas/metapathways2-2.5.1/resources//TPCsignal -D /home/programas/metapathways2-2.5.1/resources//Dsignal SCANNING FOR tRNA USING tRNA-Scan ..... Skipping!
EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1/libs/python_scripts/MetaPathways_annotate_fast.py --input_gff /home/blanca/metapa_commandLine/Contigs_same/orf_prediction//Contigs_same.unannot.gff -o /home/blanca/metapa_commandLine/Contigs_same/ genbank//Contigs_same.annot.gff --output-comparative-annotation /home/blanca/metapa_commandLine/Contigs_same/results//annotation_table//Contigs_same --algorithm LAST -m /home/blanca/metapa_commandLine/Contigs_same/ preprocessed//Contigssame.mapping.txt -D /home/blanca/metapa commandLine/Contigs_same/blast_results/ -s Contigs_same ANNOTATE ORFS Processing database : COG_2013-12-27
Processing database : metacyc-v5-2011-10-21 ERROR : Failure to annotate in contig Contigs_same_38354 Traceback (most recent call last): File "/home/programas/metapathways2-2.5.1/libs/ python_scripts/MetaPathways_annotate_fast.py", line 291, in write_annotation_for_orf attributes += ";" + "partial="+orf_dictionary[contig][candidate_orf_pos][' partial'] KeyError: 'partial' None ..... Redo Success!
EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1/libs/python_scripts/MetaPathways_create_genbank_ptinput_sequin.py -g /home/blanca/metapa_commandLine/Contigs_same/ genbank//Contigssame.annot.gff -n /home/blanca/metapa commandLine/Contigs_same/preprocessed//Contigs_same.fasta -p /home/blanca/metapa_commandLine/Contigssame/orf prediction//Contigssame.qced.faa --out-ptinput /home/blanca/metapa commandLine/Contigs_same/ptools/ PATHOLOGIC INPUT ..... Skipping [NO INPUT]! MISSING INPUT LIST: /home/blanca/metapa_commandLine/Contigs_same/genbank//Contigs_same.annot. gff
EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1/libs/python_scripts/MetaPathways_create_reports_fast.py --input-annotated-gff /home/blanca/metapa_commandLine/Contigs_same/ genbank//Contigs_same.annot.gff --input-kegg-maps /home/database/blastdb/ MetaPathways_DBs///functional_categories/KO_classification.txt --input-cog-maps /home/database/blastdb/MetaPathways_DBs///functional_categories/COG_categories.txt --input-seed-maps /home/database/blastdb/MetaPathways_DBs///functional_categories/SEED_subsystems.txt --input-cazy-maps /home/database/blastdb/MetaPathways_DBs///functional_categories/CAZY_hierarchy.txt --output-dir /home/blanca/metapa_commandLine/Contigs_same/results//annotation_table/ --ncbi-taxonomy-map /home/database/blastdb/MetaPathways_DBs///ncbi_tree/ncbi_taxonomy_tree.txt --ncbi-megan-map /home/database/blastdb/MetaPathways_DBs///ncbi_tree/ncbi.map -D /home/blanca/metapa_commandLine/Contigs_same/blast_results/ -s Contigs_same -a LAST CREATING REPORT FILE FOR ORF ANNOTATION ..... Skipping [NO INPUT]! MISSING INPUT LIST: /home/blanca/metapa_commandLine/Contigs_same/genbank//Contigs_same.annot. gff
EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1//libs/python_scripts/MetaPathways_run_pathologic.py --reactions /home/blanca/metapa_commandLine/Contigs_same/results//annotation_table// Contigssame.metacyc.orf.annots.txt --ptoolsExec /home/programas/pathway-tools/pathway-tools -i /home/blanca/metapa commandLine/Contigs_same/ptools// -p /home/programas/ptools_config/ ptools-local/pgdbs/user/contigs_samecyc -s Contigs_same --wtd --annotation-table /home/blanca/metapa_commandLine/Contigs_same/ results//annotation_table//functional_and_taxonomic_table.txt --ncbi-tree /home/database/blastdb/MetaPathways_DBs///ncbi_tree/ncbi_taxonomy_tree.txt --ncbi-megan-map /home/database/blastdb/MetaPathways_DBs///ncbi_tree/ncbi.map --output-pwy-table /home/blanca/metapa_commandLine/Contigs_same/ results//pgdb//contigs_same.pwy.txt RUNNING PATHOLOGIC ..... Skipping!
EXECUTED COMMAND : /home/programas/metapathways2- 2.5.1/libs/python_scripts/MetaPathwaysrpkm.py -c /home/blanca/metapa commandLine/Contigs_same/preprocessed//Contigs_same.fasta --rpkmExec /home/programas/metapathways2-2.5.1//executables/ubuntu/rpkm --rpkmdir /home/blanca/reads -O /home/blanca/metapa_commandLine/Contigssame/orf prediction//Contigssame.unannot.gff -o /home/blanca/metapa commandLine/Contigs_same/results//rpkm/Contigs_same.orf_rpkm.txt --sample_name Contigssame --stats /home/blanca/metapa commandLine/Contigs_same/results//rpkm/Contigs_same.orf_rpkm_stats.txt --bwaFolder /home/blanca/metapa_commandLine/Contigs_same/bwa/ --bwaExec /home/programas/metapathways2-2.5.1//executables/ubuntu/bwa RUNNING RPKM_CALCULATION ..... Skipping!
INFO : FINISHED PROCESSING THE SAMPLES THE END
Content of errors_warnings_log.txt
STEP ORF_PREDICTION
STEP FUNC_SEARCH
STEP FUNC_SEARCH
STEP COMPUTE_REFSCORE
STEP PARSE_BLAST
STEP PARSE_BLAST
STEP ANNOTATE_ORFS
STEP PATHOLOGIC_INPUT
ERROR Missing input /home/blanca/metapa_commandLine/Contigs_same/ genbank//Contigs_same.annot.gff ERROR Missing input /home/blanca/metapa_commandLine/Contigs_same/ genbank//Contigs_same.annot.gff
STEP CREATE_ANNOT_REPORTS
ERROR Missing input /home/blanca/metapa_commandLine/Contigs_same/ genbank//Contigs_same.annot.gff ERROR Missing input /home/blanca/metapa_commandLine/Contigs_same/ genbank//Contigs_same.annot.gff
Content of metapathways_steps_log.txt ============== BEGIN RUN Contigs_same BLOCK0 ================ PREPROCESS_INPUT RUNNING PREPROCESS_INPUT SUCCESS ORF_PREDICTION RUNNING ORF_PREDICTION SUCCESS ORF_TO_AMINO RUNNING ORF_TO_AMINO SUCCESS FILTER_AMINOS RUNNING FILTER_AMINOS SUCCESS
============== BEGIN RUN Contigs_same BLOCK1 ================ FUNC_SEARCH:metacyc-v5-2011-10-21 RUNNING FUNC_SEARCH:metacyc-v5-2011-10-21 SUCCESS FUNC_SEARCH:COG_2013-12-27 RUNNING FUNC_SEARCH:COG_2013-12-27 SUCCESS
============== BEGIN RUN Contigs_same BLOCK2 ================ COMPUTE_REFSCORES RUNNING COMPUTE_REFSCORES SUCCESS PARSE_FUNC_SEARCH:metacyc-v5-2011-10-21 RUNNING PARSE_FUNC_SEARCH:metacyc-v5-2011-10-21 SUCCESS PARSE_FUNC_SEARCH:COG_2013-12-27 RUNNING PARSE_FUNC_SEARCH:COG_2013-12-27 SUCCESS SCAN_tRNA SKIPPED ANNOTATE_ORFS RUNNING ANNOTATE_ORFS SUCCESS PATHOLOGIC_INPUT MISSING_INPUT CREATE_ANNOT_REPORTS MISSING_INPUT BUILD_PGDB SKIPPED COMPUTE_RPKM SKIPPED
And here it is the contig it failes to annotate:
Contigs_same_38354 ATTTGGGAAGACGTGCTtgATCGTTTcGATGAGCATGAAAATATAGAGCTGGCCTACCCA ACcATGCGCATCTATCGCTAGTTAAGCTTATTAATTATTATCTTAAGTCATACCTTTCCT ATGCTTAACTGTTATTTTTGATCGCCTGATCAACAATGAACAATAaTTTTATTGCTTGGA TgGTACTTTTGGGCGTCCAAAAGTACCGAAAAAaCGCCGGACAAGgATTTGCGCGGCgGG GCACCGGTGccccTTGACGGGGTtAAAACAATGATCCTTCCcACTCAGAGATTACTTTCG GGATCTCATCGGTGTgTTTTTACCaTCACCCGCCTGCGCGTCCCCcTCGCAACCACCTGC CTCACAACTCCAAGgCCGTGGAgAAAATTTtCAtcAGATAGATAAAACgGcTGCGAATTT tATAAGGAAATAATCgGGGgTTTGGGGggTATTGCGGGAAAgTCGAGCGCAAAaGCGCTG GGTGTGGAAGAGCAGGGTTTAACGTACGCCTTTAGTCAGAACAATATCTCAAtACCCccg AtGGcTTTTCctGAAGGgATGCcTTtGgCaTtGGTtCTTTTttGGCCatCCAaAAAatGA aCACcTtCAGACTAAgTAACAGCaGCTTTCTGgATTTgTGCTTCTTAgAAAaGCAGCCGA tCCTATTTAACCTGAGTTcgatataaaTaATaataGAGATAtttcagaaagtc
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blancaverag
hallamlab
I am running metapathways2 command line and finding this error.
When executing
It skips tRNA search and can't annotate a contig, apparently.
COMMAND : MetaPathways.py -i /home/blanca/Contigs_same.fasta -o /home/blanca/metapa_commandLine -c config/template_config.txt -v -p config/template_param.txt WARNING sequence for db /home/database/blastdb/MetaPathways_DBs///functional/formatted/metacyc-v5-2011-10-21 not formatted WARNING Trying to format database 'metacyc-v5-2011-10-21' for algorithm 'LAST' INFO Formatted database 'metacyc-v5-2011-10-21' successfully for 'LAST' WARNING Does not have map file '/home/database/blastdb/MetaPathways_DBs///functional/formatted/metacyc-v5-2011-10-21-names.txt' for 'metacyc-v5-2011-10-21' INFO Successfully created map file '/home/database/blastdb/MetaPathways_DBs///functional/formatted/metacyc-v5-2011-10-21-names.txt' for 'metacyc-v5-2011-10-21' WARNING sequence for db /home/database/blastdb/MetaPathways_DBs///functional/formatted/COG_2013-12-27 not formatted WARNING Trying to format database 'COG_2013-12-27' for algorithm 'LAST' INFO Formatted database 'COG_2013-12-27' successfully for 'LAST' WARNING Does not have map file '/home/database/blastdb/MetaPathways_DBs///functional/formatted/COG_2013-12-27-names.txt' for 'COG_2013-12-27' INFO Successfully created map file '/home/database/blastdb/MetaPathways_DBs///functional/formatted/COG_2013-12-27-names.txt' for 'COG_2013-12-27' RUNNING MetaPathways version 2.5.1 ============== RUNNING STEPS IN BLOCK 0 ================
################################################
PROCESSING INPUT /home/blanca/Contigs_same.fasta [STEPS BLOCK 0]
EXECUTED COMMAND : /home/programas/metapathways2-2.5.1/libs/python_scripts/MetaPathways_filter_input.py --min_length 180 --log_file /home/blanca/metapa_commandLine/Contigs_same/run_statistics//Contigs_same.nuc.stats -i /home/blanca/Contigs_same.fasta -o /home/blanca/metapa_commandLine/Contigs_same/preprocessed//Contigs_same.fasta -M /home/blanca/metapa_commandLine/Contigs_same/preprocessed//Contigs_same.mapping.txt -t nucleotide -L /home/blanca/metapa_commandLine/Contigs_same/run_statistics//Contigs_same.contig.lengths.txt PREPROCESSING THE INPUT ..... Success!
EXECUTED COMMAND : /home/programas/metapathways2-2.5.1/libs/python_scripts/MetaPathways_orf_prediction.py --prod_exec /home/programas/metapathways2-2.5.1//executables/ubuntu/prodigal --prod_m --prod_p meta --prod_f gff --prod_g 11 --prod_input /home/blanca/metapa_commandLine/Contigs_same/preprocessed//Contigs_same.fasta --prod_output /home/blanca/metapa_commandLine/Contigs_same/orf_prediction/Contigs_same.gff ORF PREDICTION ..... Success!
EXECUTED COMMAND : /home/programas/metapathways2-2.5.1/libs/python_scripts/MetaPathways_create_amino_sequences.py -g /home/blanca/metapa_commandLine/Contigs_same/orf_prediction/Contigs_same.gff -n /home/blanca/metapa_commandLine/Contigs_same/preprocessed//Contigs_same.fasta --output_nuc /home/blanca/metapa_commandLine/Contigs_same/orf_prediction//Contigs_same.fna --output_amino /home/blanca/metapa_commandLine/Contigs_same/orf_prediction//Contigs_same.faa --output_gff /home/blanca/metapa_commandLine/Contigs_same/orf_prediction//Contigs_same.unannot.gff CREATING AMINO ACID SEQS FROM GFF FILE ..... Success!
EXECUTED COMMAND : /home/programas/metapathways2-2.5.1/libs/python_scripts/MetaPathways_filter_input.py --min_length 60 --log_file /home/blanca/metapa_commandLine/Contigs_same/run_statistics//Contigs_same.amino.stats -i /home/blanca/metapa_commandLine/Contigs_same/orf_prediction//Contigs_same.faa -o /home/blanca/metapa_commandLine/Contigs_same/orf_prediction//Contigs_same.qced.faa -L /home/blanca/metapa_commandLine/Contigs_same/run_statistics//Contigs_same.orf.lengths.txt -t amino FILTER AMINO ACID SEQS ..... Success!
################################################ PROCESSING INPUT /home/blanca/Contigs_same.fasta [STEPS BLOCK 1] EXECUTED COMMAND : /home/programas/metapathways2-2.5.1//libs/python_scripts/MetaPathways_func_search.py --algorithm LAST --last_executable /home/programas/metapathways2-2.5.1//executables/ubuntu/lastal --last_o /home/blanca/metapa_commandLine/Contigs_same/blast_results//Contigs_same.metacyc-v5-2011-10-21.LASTout --last_f 2 --last_db /home/database/blastdb/MetaPathways_DBs///functional/formatted/metacyc-v5-2011-10-21 --last_query /home/blanca/metapa_commandLine/Contigs_same/orf_prediction//Contigs_same.qced.faa LASTING AMINO SEQS AGAINST metacyc-v5-2011-10-21 ..... Success!
EXECUTED COMMAND : /home/programas/metapathways2-2.5.1//libs/python_scripts/MetaPathways_func_search.py --algorithm LAST --last_executable /home/programas/metapathways2-2.5.1//executables/ubuntu/lastal --last_o /home/blanca/metapa_commandLine/Contigs_same/blast_results//Contigs_same.COG_2013-12-27.LASTout --last_f 2 --last_db /home/database/blastdb/MetaPathways_DBs///functional/formatted/COG_2013-12-27 --last_query /home/blanca/metapa_commandLine/Contigs_same/orf_prediction//Contigs_same.qced.faa LASTING AMINO SEQS AGAINST COG_2013-12-27 ..... Success!
################################################
PROCESSING INPUT /home/blanca/Contigs_same.fasta [STEPS BLOCK 2]
EXECUTED COMMAND : /home/programas/metapathways2-2.5.1//libs/python_scripts/MetaPathways_refscore.py -o /home/blanca/metapa_commandLine/Contigs_same/blast_results//Contigs_same.refscores.LAST -i /home/blanca/metapa_commandLine/Contigs_same/orf_prediction//Contigs_same.qced.faa -a LAST COMPUTING REFSCORES FOR BITSCORE ..... Redo Success!
EXECUTED COMMAND : /home/programas/metapathways2-2.5.1/libs/python_scripts/MetaPathways_parse_blast.py -d metacyc-v5-2011-10-21 -b /home/blanca/metapa_commandLine/Contigs_same/blast_results//Contigs_same.metacyc-v5-2011-10-21.LASTout -m /home/database/blastdb/MetaPathways_DBs///functional/formatted/metacyc-v5-2011-10-21-names.txt -r /home/blanca/metapa_commandLine/Contigs_same/blast_results//Contigs_same.refscores.LAST --min_bsr 0.4 --min_score 20 --min_length 60 --max_evalue 0.000001 --algorithm LAST PARSING LAST OUTPUT FOR metacyc-v5-2011-10-21 ..... Redo Success!
EXECUTED COMMAND : /home/programas/metapathways2-2.5.1/libs/python_scripts/MetaPathways_parse_blast.py -d COG_2013-12-27 -b /home/blanca/metapa_commandLine/Contigs_same/blast_results//Contigs_same.COG_2013-12-27.LASTout -m /home/database/blastdb/MetaPathways_DBs///functional/formatted/COG_2013-12-27-names.txt -r /home/blanca/metapa_commandLine/Contigs_same/blast_results//Contigs_same.refscores.LAST --min_bsr 0.4 --min_score 20 --min_length 60 --max_evalue 0.000001 --algorithm LAST PARSING LAST OUTPUT FOR COG_2013-12-27 ..... Redo Success!
EXECUTED COMMAND : /home/programas/metapathways2-2.5.1//libs/python_scripts/MetaPathways_tRNA_scan.py --executable /home/programas/metapathways2-2.5.1//executables/ubuntu/trnascan-1.4 -o /home/blanca/metapa_commandLine/Contigs_same/results//tRNA//Contigs_same.tRNA.stats.txt -F /home/blanca/metapa_commandLine/Contigs_same/results//tRNA//Contigs_same.tRNA.fasta -i /home/blanca/metapa_commandLine/Contigs_same/preprocessed//Contigs_same.fasta -T /home/programas/metapathways2-2.5.1/resources//TPCsignal -D /home/programas/metapathways2-2.5.1/resources//Dsignal SCANNING FOR tRNA USING tRNA-Scan ..... Skipping!
EXECUTED COMMAND : /home/programas/metapathways2-2.5.1/libs/python_scripts/MetaPathways_annotate_fast.py --input_gff /home/blanca/metapa_commandLine/Contigs_same/orf_prediction//Contigs_same.unannot.gff -o /home/blanca/metapa_commandLine/Contigs_same/genbank//Contigs_same.annot.gff --output-comparative-annotation /home/blanca/metapa_commandLine/Contigs_same/results//annotation_table//Contigs_same --algorithm LAST -m /home/blanca/metapa_commandLine/Contigs_same/preprocessed//Contigs_same.mapping.txt -D /home/blanca/metapa_commandLine/Contigs_same/blast_results/ -s Contigs_same ANNOTATE ORFS
Processing database : COG_2013-12-27
Processing database : metacyc-v5-2011-10-21 ERROR : Failure to annotate in contig Contigs_same_38354 Traceback (most recent call last): File "/home/programas/metapathways2-2.5.1/libs/python_scripts/MetaPathways_annotate_fast.py", line 291, in write_annotation_for_orf attributes += ";" + "partial="+orf_dictionary[contig][candidate_orf_pos]['partial'] KeyError: 'partial' None ..... Redo Success!
EXECUTED COMMAND : /home/programas/metapathways2-2.5.1/libs/python_scripts/MetaPathways_create_genbank_ptinput_sequin.py -g /home/blanca/metapa_commandLine/Contigs_same/genbank//Contigs_same.annot.gff -n /home/blanca/metapa_commandLine/Contigs_same/preprocessed//Contigs_same.fasta -p /home/blanca/metapa_commandLine/Contigs_same/orf_prediction//Contigs_same.qced.faa --out-ptinput /home/blanca/metapa_commandLine/Contigs_same/ptools/ PATHOLOGIC INPUT ..... Skipping [NO INPUT]! MISSING INPUT LIST: /home/blanca/metapa_commandLine/Contigs_same/genbank//Contigs_same.annot.gff
EXECUTED COMMAND : /home/programas/metapathways2-2.5.1/libs/python_scripts/MetaPathways_create_reports_fast.py --input-annotated-gff /home/blanca/metapa_commandLine/Contigs_same/genbank//Contigs_same.annot.gff --input-kegg-maps /home/database/blastdb/MetaPathways_DBs///functional_categories/KO_classification.txt --input-cog-maps /home/database/blastdb/MetaPathways_DBs///functional_categories/COG_categories.txt --input-seed-maps /home/database/blastdb/MetaPathways_DBs///functional_categories/SEED_subsystems.txt --input-cazy-maps /home/database/blastdb/MetaPathways_DBs///functional_categories/CAZY_hierarchy.txt --output-dir /home/blanca/metapa_commandLine/Contigs_same/results//annotation_table/ --ncbi-taxonomy-map /home/database/blastdb/MetaPathways_DBs///ncbi_tree/ncbi_taxonomy_tree.txt --ncbi-megan-map /home/database/blastdb/MetaPathways_DBs///ncbi_tree/ncbi.map -D /home/blanca/metapa_commandLine/Contigs_same/blast_results/ -s Contigs_same -a LAST CREATING REPORT FILE FOR ORF ANNOTATION ..... Skipping [NO INPUT]! MISSING INPUT LIST: /home/blanca/metapa_commandLine/Contigs_same/genbank//Contigs_same.annot.gff
EXECUTED COMMAND : /home/programas/metapathways2-2.5.1//libs/python_scripts/MetaPathways_run_pathologic.py --reactions /home/blanca/metapa_commandLine/Contigs_same/results//annotation_table//Contigs_same.metacyc.orf.annots.txt --ptoolsExec /home/programas/pathway-tools/pathway-tools -i /home/blanca/metapa_commandLine/Contigs_same/ptools// -p /home/programas/ptools_config/ptools-local/pgdbs/user/contigs_samecyc -s Contigs_same --wtd --annotation-table /home/blanca/metapa_commandLine/Contigs_same/results//annotation_table//functional_and_taxonomic_table.txt --ncbi-tree /home/database/blastdb/MetaPathways_DBs///ncbi_tree/ncbi_taxonomy_tree.txt --ncbi-megan-map /home/database/blastdb/MetaPathways_DBs///ncbi_tree/ncbi.map --output-pwy-table /home/blanca/metapa_commandLine/Contigs_same/results//pgdb//contigs_same.pwy.txt RUNNING PATHOLOGIC ..... Skipping!
EXECUTED COMMAND : /home/programas/metapathways2-2.5.1/libs/python_scripts/MetaPathways_rpkm.py -c /home/blanca/metapa_commandLine/Contigs_same/preprocessed//Contigs_same.fasta --rpkmExec /home/programas/metapathways2-2.5.1//executables/ubuntu/rpkm --rpkmdir /home/blanca/reads -O /home/blanca/metapa_commandLine/Contigs_same/orf_prediction//Contigs_same.unannot.gff -o /home/blanca/metapa_commandLine/Contigs_same/results//rpkm/Contigs_same.orf_rpkm.txt --sample_name Contigs_same --stats /home/blanca/metapa_commandLine/Contigs_same/results//rpkm/Contigs_same.orf_rpkm_stats.txt --bwaFolder /home/blanca/metapa_commandLine/Contigs_same/bwa/ --bwaExec /home/programas/metapathways2-2.5.1//executables/ubuntu/bwa RUNNING RPKM_CALCULATION ..... Skipping!
INFO : FINISHED PROCESSING THE SAMPLES THE END
Content of errors_warnings_log.txt
STEP ORF_PREDICTION
STEP FUNC_SEARCH
STEP FUNC_SEARCH
STEP COMPUTE_REFSCORE
STEP PARSE_BLAST
STEP PARSE_BLAST
STEP ANNOTATE_ORFS
STEP PATHOLOGIC_INPUT
ERROR Missing input /home/blanca/metapa_commandLine/Contigs_same/genbank//Contigs_same.annot.gff ERROR Missing input /home/blanca/metapa_commandLine/Contigs_same/genbank//Contigs_same.annot.gff
STEP CREATE_ANNOT_REPORTS
ERROR Missing input /home/blanca/metapa_commandLine/Contigs_same/genbank//Contigs_same.annot.gff ERROR Missing input /home/blanca/metapa_commandLine/Contigs_same/genbank//Contigs_same.annot.gff
Content of metapathways_steps_log.txt ============== BEGIN RUN Contigs_same BLOCK0 ================ PREPROCESS_INPUT RUNNING PREPROCESS_INPUT SUCCESS ORF_PREDICTION RUNNING ORF_PREDICTION SUCCESS ORF_TO_AMINO RUNNING ORF_TO_AMINO SUCCESS FILTER_AMINOS RUNNING FILTER_AMINOS SUCCESS
============== BEGIN RUN Contigs_same BLOCK1 ================ FUNC_SEARCH:metacyc-v5-2011-10-21 RUNNING FUNC_SEARCH:metacyc-v5-2011-10-21 SUCCESS FUNC_SEARCH:COG_2013-12-27 RUNNING FUNC_SEARCH:COG_2013-12-27 SUCCESS
============== BEGIN RUN Contigs_same BLOCK2 ================ COMPUTE_REFSCORES RUNNING COMPUTE_REFSCORES SUCCESS PARSE_FUNC_SEARCH:metacyc-v5-2011-10-21 RUNNING PARSE_FUNC_SEARCH:metacyc-v5-2011-10-21 SUCCESS PARSE_FUNC_SEARCH:COG_2013-12-27 RUNNING PARSE_FUNC_SEARCH:COG_2013-12-27 SUCCESS SCAN_tRNA SKIPPED ANNOTATE_ORFS RUNNING ANNOTATE_ORFS SUCCESS PATHOLOGIC_INPUT MISSING_INPUT CREATE_ANNOT_REPORTS MISSING_INPUT BUILD_PGDB SKIPPED COMPUTE_RPKM SKIPPED
And here it is the contig it failes to annotate: