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PAiewsakun / GRAViTy

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Several error messages output in a failing run #6

Open terrycojones opened 4 years ago

terrycojones commented 4 years ago

Below is the complete output of a run I did last night. There are several errors in the output:

Input for ReadGenomeDescTable:
====================================================================================================

Main input
--------------------------------------------------
GenomeDescTableFile_UcfVirus: seqs_gravity.txt
ShelveDir_UcfVirus: /home/terry/s/net/GRAViTy1.1/terry/shelve
Database: None
Database_Header: None
====================================================================================================
################################################################################
#Read the GenomeDesc table                                                     #
################################################################################
- Define dir/file paths
    to program output shelve
- Read the GenomeDesc table
Genetic code is not specified. GRAViTy will use the standard code for HQ189459
Genetic code is not specified. GRAViTy will use the standard code for NC_040768
Genetic code is not specified. GRAViTy will use the standard code for MG887758
Genetic code is not specified. GRAViTy will use the standard code for NC_028498
Genetic code is not specified. GRAViTy will use the standard code for NC_021222
Genetic code is not specified. GRAViTy will use the standard code for KX380787
Genetic code is not specified. GRAViTy will use the standard code for NC_013470
Genetic code is not specified. GRAViTy will use the standard code for NC_030888
Genetic code is not specified. GRAViTy will use the standard code for MG596785
Genetic code is not specified. GRAViTy will use the standard code for NC_010985
Genetic code is not specified. GRAViTy will use the standard code for JX976612
Genetic code is not specified. GRAViTy will use the standard code for NC_026954
Genetic code is not specified. GRAViTy will use the standard code for MK492914
- Save variables to ReadGenomeDescTable.AllGenomes.shelve
    BaltimoreList
    OrderList
    FamilyList
    SubFamList
    GenusList
    VirusNameList
    SeqIDLists
    SeqStatusList
    TaxoGroupingList
    TranslTableList
    DatabaseList
- Save variables to ReadGenomeDescTable.CompleteGenomes.shelve
    BaltimoreList
    OrderList
    FamilyList
    SubFamList
    GenusList
    VirusNameList
    SeqIDLists
    SeqStatusList
    TaxoGroupingList
    TranslTableList
    DatabaseList
Input for UcfVirusAnnotator:
====================================================================================================
Main input
--------------------------------------------------
GenomeSeqFile_UcfVirus: seqs_gravity.gb
ShelveDir_UcfVirus: /home/terry/s/net/GRAViTy1.1/terry/shelve
ShelveDirs_RefVirus: ../RefViruses/DBD

Unclassified virus annotation options
--------------------------------------------------
AnnotateIncompleteGenomes_UcfVirus: True
UsingDatabaseIncludingIncompleteRefViruses: False
HMMER_N_CPUs: 12
HMMER_C_EValue_Cutoff: 0.001
HMMER_HitScore_Cutoff: 0
====================================================================================================
################################################################################
#Generate PPHMM signature table, PPHMM location table, and GOM signature table #
#for unclassified viruses, using PPHMM databases of reference viruses          #
################################################################################
- Define dir/file paths
    to program output shelve
- Retrieve variables
    from ReadGenomeDescTable.AllGenomes.shelve
        SeqIDLists
        TranslTableList
- Annotate unclassified viruses using the PPHMM and GOM databases of the reference viruses: DBD (1/1)
    Define dir/file paths
        to HMMER PPHMM database of the reference virus group
    Retrieve variables related to the reference viruses
        from RefVirusAnnotator.CompleteGenomes.shelve
            GOMIDList
            GOMDB_coo
    Generate PPHMMSignatureTable, PPHMMLocationTable, and GOMSignatureTable for unclassified viruses using the reference PPHMM and GOM database
/home/terry/.virtualenvs/gravity/local/lib/python2.7/site-packages/Bio/Seq.py:2859: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.
  BiopythonWarning,
- Save variables to UcfVirusAnnotator.AllUcfGenomes.CompleteRefGenomes.shelve
    PPHMMSignatureTable_Dict_coo
    PPHMMLocationTable_Dict_coo
    GOMSignatureTable_Dict
Input for VirusClassificationAndEvaluation:

====================================================================================================
Main input
--------------------------------------------------
ShelveDir_UcfVirus: /home/terry/s/net/GRAViTy1.1/terry/shelve
ShelveDirs_RefVirus: ../RefViruses/DBD
AnnotateIncompleteGenomes_UcfVirus: True
UsingDatabaseIncludingIncompleteRefViruses: False

Virus annotation (with PPHMM database derived from unclassified viruses) options
--------------------------------------------------
UseUcfVirusPPHMMs: False
GenomeSeqFile_UcfVirus: seqs_gravity.gb
GenomeSeqFiles_RefVirus: ../RefViruses/DBD/GenomeSeqs.gb
HMMER_N_CPUs: 12
HMMER_C_EValue_Cutoff: 0.001
HMMER_HitScore_Cutoff: 0

Virus (dis)similarity measurement options
--------------------------------------------------
SimilarityMeasurementScheme: PG
p: 1

Virus classification options
--------------------------------------------------
Dendrogram_LinkageMethod: average
Bootstrap: True
N_Bootstrap: 10
Bootstrap_method: booster
Bootstrap_N_CPUs: 12
DatabaseAssignmentSimilarityScore_Cutoff: 0.01
N_PairwiseSimilarityScores: 10000

Heatmap construction options
--------------------------------------------------
Heatmap_WithDendrogram: True
Heatmap_DendrogramSupport_Cutoff: 0.75

Virus grouping options
--------------------------------------------------
VirusGrouping: True
====================================================================================================
################################################################################
#Classify virus and evaluate the results                                       #
################################################################################
- Define dir/file paths
    to program output shelve
        to virus classification result file
- Retrieve variables related to unclassified viruses
    from ReadGenomeDescTable.AllGenomes.shelve
        SeqIDLists
        VirusNameList
        TranslTableList
    from UcfVirusAnnotator.AllUcfGenomes.CompleteRefGenomes.shelve
        PPHMMSignatureTable_Dict_coo
        PPHMMLocationTable_Dict_coo
        GOMSignatureTable_Dict
- Classify viruses using DBD as reference (1/1)
    Define dir/file paths
        to program output shelve of the reference virus group
    Retrieve variables related to the reference virus group
        from ReadGenomeDescTable.CompleteGenomes.shelve
            SeqIDLists
            FamilyList
            GenusList
            VirusNameList
            TaxoGroupingList
            TranslTableList
        from RefVirusAnnotator.shelve
        from RefVirusAnnotator.CompleteGenomes.shelve
            PPHMMSignatureTable_coo
            PPHMMLocationTable_coo
            GOMSignatureTable
            GOMIDList
    Build the dendrogram, including all sequences
/home/terry/s/net/GRAViTy1.1/GRAViTy/Utilities/SimilarityMat_Constructor.py:28: RuntimeWarning: invalid value encountered in double_scalars
  PPHMMSignature_GJMat[i,j] = np.sum(np.minimum(PPHMMSignature_i, PPHMMSignature_j))/np.sum(np.maximum(PPHMMSignature_i, PPHMMSignature_j))
/home/terry/s/net/GRAViTy1.1/GRAViTy/Utilities/SimilarityMat_Constructor.py:34: RuntimeWarning: invalid value encountered in double_scalars
  GOMSignature_GJMat[i,j]       = np.sum(np.minimum(GOMSignature_i, GOMSignature_j))/np.sum(np.maximum(GOMSignature_i, GOMSignature_j))
    Compute similarity cut off for each taxonomic class
    Propose a taxonomic class to each unclassified virus and evaluate the taxonomic assignments
        Propose a taxonomic class to each unclassified viruses, using the 1-nearest neighbour algorithm
        Evaluate the taxonomic assignments
    Virus grouping
    Construct result distributions by using the bootstrapping technique
        Round 1
            Bootstrap the data
            Construct a dendrogram from the bootstrapped data
            Compute similarity cut off for each taxonomic class based on the bootstrapped data
/home/terry/s/net/GRAViTy1.1/GRAViTy/VirusClassificationAndEvaluation.py:114: RuntimeWarning: divide by zero encountered in double_scalars
  PairwiseSimilarityScore_Cutoff_Dict[TaxoGrouping]["CutOff"] = -clf.intercept_[0]/clf.coef_[0][0]
            Propose a taxonomic class to each unclassified virus and evaluate the taxonomic assignments based on the bootstrapped data
        Propose a taxonomic class to each unclassified viruses, using the 1-nearest neighbour algorithm
        Evaluate the taxonomic assignments
        Round 2
            Bootstrap the data
            Construct a dendrogram from the bootstrapped data
            Compute similarity cut off for each taxonomic class based on the bootstrapped data
            Propose a taxonomic class to each unclassified virus and evaluate the taxonomic assignments based on the bootstrapped data
        Propose a taxonomic class to each unclassified viruses, using the 1-nearest neighbour algorithm
        Evaluate the taxonomic assignments
        Round 3
            Bootstrap the data
            Construct a dendrogram from the bootstrapped data
            Compute similarity cut off for each taxonomic class based on the bootstrapped data
            Propose a taxonomic class to each unclassified virus and evaluate the taxonomic assignments based on the bootstrapped data
        Propose a taxonomic class to each unclassified viruses, using the 1-nearest neighbour algorithm
        Evaluate the taxonomic assignments
        Round 4
            Bootstrap the data
            Construct a dendrogram from the bootstrapped data
            Compute similarity cut off for each taxonomic class based on the bootstrapped data
            Propose a taxonomic class to each unclassified virus and evaluate the taxonomic assignments based on the bootstrapped data
        Propose a taxonomic class to each unclassified viruses, using the 1-nearest neighbour algorithm
        Evaluate the taxonomic assignments
        Round 5
            Bootstrap the data
            Construct a dendrogram from the bootstrapped data
            Compute similarity cut off for each taxonomic class based on the bootstrapped data
            Propose a taxonomic class to each unclassified virus and evaluate the taxonomic assignments based on the bootstrapped data
        Propose a taxonomic class to each unclassified viruses, using the 1-nearest neighbour algorithm
        Evaluate the taxonomic assignments
        Round 6
            Bootstrap the data
            Construct a dendrogram from the bootstrapped data
            Compute similarity cut off for each taxonomic class based on the bootstrapped data
            Propose a taxonomic class to each unclassified virus and evaluate the taxonomic assignments based on the bootstrapped data
        Propose a taxonomic class to each unclassified viruses, using the 1-nearest neighbour algorithm
        Evaluate the taxonomic assignments
        Round 7
            Bootstrap the data
            Construct a dendrogram from the bootstrapped data
            Compute similarity cut off for each taxonomic class based on the bootstrapped data
            Propose a taxonomic class to each unclassified virus and evaluate the taxonomic assignments based on the bootstrapped data
        Propose a taxonomic class to each unclassified viruses, using the 1-nearest neighbour algorithm
        Evaluate the taxonomic assignments
        Round 8
            Bootstrap the data
            Construct a dendrogram from the bootstrapped data
            Compute similarity cut off for each taxonomic class based on the bootstrapped data
            Propose a taxonomic class to each unclassified virus and evaluate the taxonomic assignments based on the bootstrapped data
        Propose a taxonomic class to each unclassified viruses, using the 1-nearest neighbour algorithm
        Evaluate the taxonomic assignments
        Round 9
            Bootstrap the data
            Construct a dendrogram from the bootstrapped data
            Compute similarity cut off for each taxonomic class based on the bootstrapped data
            Propose a taxonomic class to each unclassified virus and evaluate the taxonomic assignments based on the bootstrapped data
        Propose a taxonomic class to each unclassified viruses, using the 1-nearest neighbour algorithm
        Evaluate the taxonomic assignments
        Round 10
            Bootstrap the data
            Construct a dendrogram from the bootstrapped data
            Compute similarity cut off for each taxonomic class based on the bootstrapped data
            Propose a taxonomic class to each unclassified virus and evaluate the taxonomic assignments based on the bootstrapped data
        Propose a taxonomic class to each unclassified viruses, using the 1-nearest neighbour algorithm
        Evaluate the taxonomic assignments
        Creat a bootstrapped dendrogram
    Construct GRAViTy heat map with dendrogram
Traceback (most recent call last):
  File "../bin/GRAViTy_Pipeline_II", line 851, in <module>
    main()
  File "../bin/GRAViTy_Pipeline_II", line 847, in main
    VirusGrouping = str2bool(options.VirusGrouping),
  File "/home/terry/s/net/GRAViTy1.1/GRAViTy/VirusClassificationAndEvaluation.py", line 764, in VirusClassificationAndEvaluation
    VirusDendrogram     = Phylo.read(BootstrappedVirusDendrogramFile, "newick")
  File "/home/terry/.virtualenvs/gravity/local/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 62, in read
    tree = next(tree_gen)
  File "/home/terry/.virtualenvs/gravity/local/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 49, in parse
    with File.as_handle(file, "r") as fp:
  File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "/home/terry/.virtualenvs/gravity/local/lib/python2.7/site-packages/Bio/File.py", line 120, in as_handle
    with open(handleish, mode, **kwargs) as fp:
IOError: [Errno 2] No such file or directory: '/home/terry/s/net/GRAViTy1.1/terry/shelve/Shelves/BootstrappedDendrogram.RefVirusGroup=DBD.IncompleteUcfRefGenomes=10.Scheme=PG.Method=average.p=1.0.nwk'
Command exited with non-zero status 1
Changhai996 commented 2 years ago

same problem in running the Test file: Traceback (most recent call last): File "/Users/opt/anaconda3/envs/py2.7/bin/GRAViTy_Pipeline_I", line 956, in main() File "/Users/opt/anaconda3/envs/py2.7/bin/GRAViTy_Pipeline_I", line 922, in main VirusGrouping = str2bool(options.VirusGrouping), File "/Users/opt/anaconda3/envs/py2.7/lib/python2.7/site-packages/GRAViTy/GRAViTyDendrogramAndHeatmapConstruction.py", line 345, in GRAViTyDendrogramAndHeatmapConstruction VirusDendrogram = Phylo.read(Heatmap_DendrogramFile, "newick") File "/Users/opt/anaconda3/envs/py2.7/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 62, in read tree = next(tree_gen) File "/Users/opt/anaconda3/envs/py2.7/lib/python2.7/site-packages/Bio/Phylo/_io.py", line 49, in parse with File.as_handle(file, "r") as fp: File "/Users/opt/anaconda3/envs/py2.7/lib/python2.7/contextlib.py", line 17, in enter return self.gen.next() File "/Users/opt/anaconda3/envs/py2.7/lib/python2.7/site-packages/Bio/File.py", line 120, in as_handle with open(handleish, mode, **kwargs) as fp: IOError: [Errno 2] No such file or directory: 'Test/Analysis/Ref/VI/Shelves/BootstrappedDendrogram.IncompleteGenomes=0.Scheme=PG.Method=average.p=1.nwk'