hallamlab
commented
7 years ago A new version of MP will be available shortly and address this issue
Closed ademenez closed 7 years ago
hallamlab
commented
7 years ago A new version of MP will be available shortly and address this issue
Hi metapathway developers,
I am trying to run metapathways but having a few final hurdles to get through. When I run one sample, most tasks were completed successfully, but the final annotation against the database failed. Would you be able to offer me any advice to fix this? I copied the error message below.
Thanks in advance,
Alex
Error message:
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 '/dem056/metacyc_BLASTDB/BLASTDB///functional/formatted/COG_2013-12-27-names.txt' for 'COG_2013-12-27' INFO Successfully created map file '/dem056/metacyc_BLASTDB/BLASTDB///functional/formatted/COG_2013-12-27-names.txt' for 'COG_2013-12-27' RUNNING MetaPathways version 2.5.2 ============== RUNNING STEPS IN BLOCK 0 ================
PROCESSING INPUT /dem056/EBI_files/processed_reads/ProcessedReads/ERR911340_ProcessedReads.fasta [STEPS BLOCK 0] PREPROCESSING THE INPUT ..... Already Computed! ORF PREDICTION ..... Already Computed! CREATING AMINO ACID SEQS FROM GFF FILE ..... Already Computed! FILTER AMINO ACID SEQS ..... Already Computed!
PROCESSING INPUT /dem056/EBI_files/processed_reads/ProcessedReads/ERR911340_ProcessedReads.fasta [STEPS BLOCK 1] LASTING AMINO SEQS AGAINST COG_2013-12-27 ..... Success!
PROCESSING INPUT /dem056/EBI_files/processed_reads/ProcessedReads/ERR911340_ProcessedReads.fasta [STEPS BLOCK 2] COMPUTING REFSCORES FOR BITSCORE ..... Already Computed! PARSING LAST OUTPUT FOR COG_2013-12-27 ..... Success! SCANNING FOR tRNA USING tRNA-Scan ..... Already Computed! ANNOTATE ORFS Processing database : COG_2013-12-27 ERROR : Failure to annotate in contig ERR911340_ProcessedReads_23959 Traceback (most recent call last): File "/dem056/metapathways2-master/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 ..... Success! GENBANK FILE ..... Skipping [NO INPUT]! PATHOLOGIC INPUT ..... Skipping [NO INPUT]! CREATING REPORT FILE FOR ORF ANNOTATION ..... Skipping [NO INPUT]! RUNNING PATHOLOGIC ..... Skipping [NO INPUT]! RUNNING RPKM_CALCULATION ..... Skipping [NO INPUT]!
INFO : FINISHED PROCESSING THE SAMPLES THE END