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hallamlab / metapathways2

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds
http://hallam.microbiology.ubc.ca/MetaPathways/
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Failure to annotate (KeyError: 'partial') #95

Closed jessieluolab closed 7 years ago

jessieluolab commented 7 years ago

Dear Admin, Could you please help me out? It seems the *.gff file couldn't be generated due to the annotation error (KeyError: 'partial').

Thanks!

PROCESSING INPUT myproject/input//test_sample2.fasta [STEPS BLOCK 2] COMPUTING REFSCORES FOR BITSCORE ..... Redo Success! PARSING LAST OUTPUT FOR metacyc-v5-2011-10-21 ..... Redo Success! PARSING LAST OUTPUT FOR CAZY_2014_09_04 ..... Redo Success! PARSING LAST OUTPUT FOR COG_2013-12-27 ..... Redo Success! SCANNING FOR tRNA USING tRNA-Scan ..... Already Computed! ANNOTATE ORFS Processing database : metacyc-v5-2011-10-21

Processing database : CAZY_2014_09_04

Processing database : COG_2013-12-27 ERROR : Failure to annotate in contig test_sample2_54 Traceback (most recent call last): File "/home/yhuang/software/MetaPathway/metapathways2-2.5.2/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! 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

kishori82 commented 7 years ago

Hi

I seem that the lasting stage did not complete or one of the stages did not complete fully, possibly because of unexpected interrupt. Could you please reprocess this samples and let me know?

Thanks Kishori

On Tue, Sep 20, 2016 at 6:29 AM, jessieluolab notifications@github.com wrote:

Dear Admin, Could you please help me out? It seems the *.gff file couldn't be generated due to the annotation error (KeyError: 'partial').

Thanks!

####################################################

PROCESSING INPUT myproject/input//test_sample2.fasta [STEPS BLOCK 2] COMPUTING REFSCORES FOR BITSCORE ..... Redo Success! PARSING LAST OUTPUT FOR metacyc-v5-2011-10-21 ..... Redo Success! PARSING LAST OUTPUT FOR CAZY_2014_09_04 ..... Redo Success! PARSING LAST OUTPUT FOR COG_2013-12-27 ..... Redo Success! SCANNING FOR tRNA USING tRNA-Scan ..... Already Computed! ANNOTATE ORFS Processing database : metacyc-v5-2011-10-21

Processing database : CAZY_2014_09_04

Processing database : COG_2013-12-27 ERROR : Failure to annotate in contig test_sample2_54 Traceback (most recent call last): File "/home/yhuang/software/MetaPathway/metapathways2-2.5. 2/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! 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

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jessieluolab commented 7 years ago

HI Kishori,

Thanks for your quick response. Please kindly find the test case input and output from the attached. It was created by following the guide line in the metapathways wiki page, "Question 11: I usually connect to my Linux/Unix machine through a ssh shell. How do I run MetaPathways from a command line?"

Please note that the metapathways was installed in our Fedora22 linux system via command line, so as the PathwayTools. We run metapathway from the terminals using SSH (PuTTY and Xming). The keyerror:'partial' occurs when running metapathways for test_sample2.

Thanks again for your help!

Best, Yongjie

On Tue, Sep 20, 2016 at 9:30 PM, kishori82 notifications@github.com wrote:

Hi

I seem that the lasting stage did not complete or one of the stages did not complete fully, possibly because of unexpected interrupt. Could you please reprocess this samples and let me know?

Thanks Kishori

On Tue, Sep 20, 2016 at 6:29 AM, jessieluolab notifications@github.com wrote:

Dear Admin, Could you please help me out? It seems the *.gff file couldn't be generated due to the annotation error (KeyError: 'partial').

Thanks!

####################################################

PROCESSING INPUT myproject/input//test_sample2.fasta [STEPS BLOCK 2] COMPUTING REFSCORES FOR BITSCORE ..... Redo Success! PARSING LAST OUTPUT FOR metacyc-v5-2011-10-21 ..... Redo Success! PARSING LAST OUTPUT FOR CAZY_2014_09_04 ..... Redo Success! PARSING LAST OUTPUT FOR COG_2013-12-27 ..... Redo Success! SCANNING FOR tRNA USING tRNA-Scan ..... Already Computed! ANNOTATE ORFS Processing database : metacyc-v5-2011-10-21

Processing database : CAZY_2014_09_04

Processing database : COG_2013-12-27 ERROR : Failure to annotate in contig test_sample2_54 Traceback (most recent call last): File "/home/yhuang/software/MetaPathway/metapathways2-2.5. 2/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! 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

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kishori82 commented 7 years ago

Hi Yongjie,

I did not see any attachment with your email.

Thanks Kishori

On Tue, Sep 20, 2016 at 11:34 AM, jessieluolab notifications@github.com wrote:

HI Kishori,

Thanks for your quick response. Please kindly find the test case input and output from the attached. It was created by following the guide line in the metapathways wiki page, "Question 11: I usually connect to my Linux/Unix machine through a ssh shell. How do I run MetaPathways from a command line?"

Please note that the metapathways was installed in our Fedora22 linux system via command line, so as the PathwayTools. We run metapathway from the terminals using SSH (PuTTY and Xming). The keyerror:'partial' occurs when running metapathways for test_sample2.

Thanks again for your help!

Best, Yongjie

On Tue, Sep 20, 2016 at 9:30 PM, kishori82 notifications@github.com wrote:

Hi

I seem that the lasting stage did not complete or one of the stages did not complete fully, possibly because of unexpected interrupt. Could you please reprocess this samples and let me know?

Thanks Kishori

On Tue, Sep 20, 2016 at 6:29 AM, jessieluolab notifications@github.com wrote:

Dear Admin, Could you please help me out? It seems the *.gff file couldn't be generated due to the annotation error (KeyError: 'partial').

Thanks!

####################################################

PROCESSING INPUT myproject/input//test_sample2.fasta [STEPS BLOCK 2] COMPUTING REFSCORES FOR BITSCORE ..... Redo Success! PARSING LAST OUTPUT FOR metacyc-v5-2011-10-21 ..... Redo Success! PARSING LAST OUTPUT FOR CAZY_2014_09_04 ..... Redo Success! PARSING LAST OUTPUT FOR COG_2013-12-27 ..... Redo Success! SCANNING FOR tRNA USING tRNA-Scan ..... Already Computed! ANNOTATE ORFS Processing database : metacyc-v5-2011-10-21

Processing database : CAZY_2014_09_04

Processing database : COG_2013-12-27 ERROR : Failure to annotate in contig test_sample2_54 Traceback (most recent call last): File "/home/yhuang/software/MetaPathway/metapathways2-2.5. 2/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! 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

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hallamlab commented 7 years ago

A new version of MP will be available shortly and address this issue