xapple / seqenv Goto Github PK

seqenv AllSites_C05.fa --min_identity 0.95 --num_threads 32 --out_dir All_95_upui --min_coverage 0.95 --max_targets 100 --normalization upui            
seqenv version 1.1.4 (pid 60382)
The exact version of the code is: 4e407e1
Start at: 2016-05-03 13:34:45.570319
--> STEP 1: Parse the input FASTA file.
Elapsed time: 0:00:00.046785
Using: All_95_upui/renamed.fasta
--> STEP 2: Similarity search against the 'nt' database with 32 processes
Elapsed time: 0:01:33.193498
--> STEP 3: Filter out bad hits from the search results
Elapsed time: 0:00:00.017426
--> STEP 4: Parsing the search results
Elapsed time: 0:00:00.027052
--> STEP 5: Setting up the SQLite3 database connection.
Elapsed time: 0:00:00.000913
Got 4114 GI hits and 3851 of them had one or more EnvO terms associated.
--> STEP 6: Computing EnvO term frequencies.
Traceback (most recent call last):
  File "/home/chris/repos/seqenv/seqenv/seqenv", line 68, in <module>
    seqenv.Analysis(input_path, **kwargs).run()
  File "/home/chris/repos/seqenv/seqenv/analysis.py", line 151, in run
    self.outputs.make_all()
  File "/home/chris/repos/seqenv/seqenv/outputs.py", line 40, in make_all
    self.tsv_seq_to_concepts()
  File "/home/chris/repos/seqenv/seqenv/outputs.py", line 93, in tsv_seq_to_concepts
    content = self.df_seqs_concepts.to_csv(None, sep=self.sep, float_format=self.float_format)
  File "/home/chris/repos/seqenv/seqenv/common/cache.py", line 35, in retrieve_from_cache
    else: result = f(self)
  File "/home/chris/repos/seqenv/seqenv/outputs.py", line 53, in df_seqs_concepts
    df = pandas.DataFrame(self.a.seq_to_counts)
  File "/home/chris/repos/seqenv/seqenv/common/cache.py", line 35, in retrieve_from_cache
    else: result = f(self)
  File "/home/chris/repos/seqenv/seqenv/analysis.py", line 396, in seq_to_counts
    if not results: raise Exception("We found no isolation sources with your input. Sorry.")
Exception: We found no isolation sources with your input. Sorry.

Traceback (most recent call last):
  File "/home/chris/repos/seqenv/seqenv/seqenv", line 59, in <module>
    seqenv.Analysis(input_path, **kwargs).run()
  File "/home/chris/repos/seqenv/seqenv/analysis.py", line 128, in __init__
    if not os.path.exists(self.out_dir): os.makedirs(self.out_dir)
  File "/usr/lib64/python2.7/os.py", line 157, in makedirs
    mkdir(name, mode)
OSError: [Errno 17] File exists: 'AllSites_C05.fa/'

Start at: 2017-10-30 12:31:20.710219
Got 0 GI hits and 0 of them had one or more EnvO terms associated.
--> STEP 6: Computing EnvO term frequencies.
Traceback (most recent call last):
  File "/home/krajacichbj/.conda/envs/krajpy/bin/seqenv", line 64, in <module>
    seqenv.Analysis(input_path, **kwargs).run()
  File "/home/krajacichbj/.conda/envs/krajpy/lib/python2.7/site-packages/seqenv/analysis.py", line 151, in run
    self.outputs.make_all()
  File "/home/krajacichbj/.conda/envs/krajpy/lib/python2.7/site-packages/seqenv/outputs.py", line 41, in make_all
    self.tsv_seq_to_concepts()
  File "/home/krajacichbj/.conda/envs/krajpy/lib/python2.7/site-packages/seqenv/outputs.py", line 108, in tsv_seq_to_concepts
    content = self.df_seqs_concepts.to_csv(None, sep=self.sep, float_format=self.float_format)
  File "/home/krajacichbj/.conda/envs/krajpy/lib/python2.7/site-packages/seqenv/common/cache.py", line 35, in retrieve_from_cache
    else: result = f(self)
  File "/home/krajacichbj/.conda/envs/krajpy/lib/python2.7/site-packages/seqenv/outputs.py", line 55, in df_seqs_concepts
    df = pandas.DataFrame(self.a.seq_to_counts)
  File "/home/krajacichbj/.conda/envs/krajpy/lib/python2.7/site-packages/seqenv/common/cache.py", line 35, in retrieve_from_cache
    else: result = f(self)
  File "/home/krajacichbj/.conda/envs/krajpy/lib/python2.7/site-packages/seqenv/analysis.py", line 398, in seq_to_counts
    if not results: raise Exception("We found no isolation sources with your input. Sorry.")
Exception: We found no isolation sources with your input. Sorry.