It is stopped in scikit-learn

[okapick]

Ok. It is worked. The script continued to the next stop. It look like that import scikit-learn should add it to FeatureValueTableConstruction. What more do you see? Thanks

sudo python3 ./Pipeline_ConstructingGRAViTYClfs_v2.py

Define dir/file paths

Running scripts: main pipeline

Read the GenomeDesc Table

• Specify dir/file paths
• Read the GenomeDesc table
• Clean the host annotations
• Save variables

Build a database of virus protein HMMs

• Define dir/file paths, import local functions, and set BLAST parameter values Define dir/file paths Import local functions Set Blastp parameters
• Retrieve variables from GenomeDesc.shelve
• Read the GenBank file
• Extract protein sequences from virus genomes, and write them to fasta files [====================] 541/541 viruses
• ALL-VERSUS-ALL BLASTp Re-build BLAST and HMM prof dirs if exist Make BLAST db Performing ALL-VERSUS-ALL BLASTp [====================] 2738/2738 protein sequences Save the BitScores
• Cluster protein sequences based on BLASTp BitScores, using the MCL algorithm
• Add 'singleton' protein sequences to the cluster list
• Make HMMs [====================] 836/836 HMMs
• Make a HMM DB
• Make a HMMDBSummary file
• Save variables File "/home/postdoc/Documents/Work/Programs-linux/METAgenomic/GRAVITy_VIRUS/GRAViTy-master/Scripts/FeatureValueTableConstruction.py", line 4 import scikit-learn ^ SyntaxError: invalid syntax

Running scripts: data analyses and summary CGJ similarity heatmap

• Define dir/file paths, and import local functions Define dir/file paths Import local functions
• Retrieve variables from GenomeDesc.shelve from FeatuerValueTableConstruction.shelve Traceback (most recent call last): File "/home/postdoc/Documents/Work/Programs-linux/METAgenomic/GRAVITy_VIRUS/GRAViTy-master/Scripts/DataSum_CGJHeatmap.py", line 43, in globals()[key] = Parameters[key] File "/usr/lib/python2.7/shelve.py", line 121, in getitem f = StringIO(self.dict[key]) File "/usr/lib/python2.7/bsddb/init.py", line 270, in getitem return _DeadlockWrap(lambda: self.db[key]) # self.db[key] File "/usr/lib/python2.7/bsddb/dbutils.py", line 68, in DeadlockWrap return function(*_args, **_kwargs) File "/usr/lib/python2.7/bsddb/init.py", line 270, in return _DeadlockWrap(lambda: self.db[key]) # self.db[key] KeyError: 'UniqueClassList'

Mutual information calculator: Overall

• Define dir/file paths, and import local functions Define dir/file paths
• Retrieve variables from GenomeDesc.shelve from FeatuerValueTableConstruction.shelve Traceback (most recent call last): File "/home/postdoc/Documents/Work/Programs-linux/METAgenomic/GRAVITy_VIRUS/GRAViTy-master/Scripts/DataSum_MICalculator.Overall.WithResampling.py", line 36, in globals()[key] = Parameters[key] File "/usr/lib/python2.7/shelve.py", line 121, in getitem f = StringIO(self.dict[key]) File "/usr/lib/python2.7/bsddb/init.py", line 270, in getitem return _DeadlockWrap(lambda: self.db[key]) # self.db[key] File "/usr/lib/python2.7/bsddb/dbutils.py", line 68, in DeadlockWrap return function(_args, _kwargs) File "/usr/lib/python2.7/bsddb/init.py", line 270, in return _DeadlockWrap(lambda: self.db[key]) # self.db[key] KeyError: 'FeatureValueTable' Estimate a (bootstrapped) dendrogram based on CGJ similarity***
• Define dir/file paths, and import local functions Define dir/file paths Import local functions
• Retrieve variables from GenomeDesc.shelve from FeatuerValueTableConstruction.shelve Traceback (most recent call last): File "/home/postdoc/Documents/Work/Programs-linux/METAgenomic/GRAVITy_VIRUS/GRAViTy-master/Scripts/DataSum_TreeBoostrapping.py", line 44, in globals()[key] = Parameters[key] File "/usr/lib/python2.7/shelve.py", line 121, in getitem f = StringIO(self.dict[key]) File "/usr/lib/python2.7/bsddb/init.py", line 270, in getitem return _DeadlockWrap(lambda: self.db[key]) # self.db[key] File "/usr/lib/python2.7/bsddb/dbutils.py", line 68, in DeadlockWrap return function(*_args, **_kwargs) File "/usr/lib/python2.7/bsddb/init.py", line 270, in return _DeadlockWrap(lambda: self.db[key]) # self.db[key] KeyError: 'UniqueClassList'

`

[okapick]

I saw error. I had a import scikit-learn in Feature script.