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Failure to annotate (KeyError: 'partial') #95

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jessieluolab opened this issue Sep 20, 2016 · 4 comments
Closed

Failure to annotate (KeyError: 'partial') #95

jessieluolab opened this issue Sep 20, 2016 · 4 comments

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

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@kishori82 @jessieluolab