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License: MIT License
Assign environment ontology (EnvO) terms to DNA sequences
License: MIT License
Running sequences through the upui normalisation gives error:
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.
It appears that the seq_to_names.tsv
output file does not have the envo ids correctly mapped to the names and is therefore identical to seq_to_concepts.tsv
.
If output_dir
is not specified program throws error:
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/'
This seems to be because it attempts to create a directory with exactly the same name as the input file.
Running 'pip install seqenv' places the seqenv program in /usr/local/bin. However, an error message occurs in the first run:
Traceback (most recent call last):
File "/usr/local/bin/seqenv", line 18, in
doc_params = re.findall('^### All parameters(.+?)###', readme_contents, flags=re.M|re.DOTALL)[0]
IndexError: list index out of range
I think this is an issue with the placement of the README.md file. Line 13 of /usr/local/bin/seqenv sets the README.md path as:
readme_path = current_dir + '../README.md'
This implies that the README.md file should be in /usr/local. In the case of my server, another README.md file was already there. I downloaded the seqenv README.md file from Github and copied it to /usr/local, and this seems to have resolved the issue. Seqenv now works.
Could this be avoided in the install, for example by placing the README.md file somewhere else, giving the README.md file a more unique name, or having a specific action to take when another README.md file is already in /usr/local?
Hi Lucas,
Rather than defaulting to using the 1000 most abundant sequences, could we just default to using all of them? The --N option can remain as is otherwise as a way for people to speed up analyses.
Thanks,
Chris
Hi-
I've been trying for a few days now to get seqenv working without success, so I figured it's time to reach out.
I'm attempting to run seqenv using your test.fasta file (here). Against the nt database.
I can use local blastn, i.e.:
blastn -db /fdb/blastdb/nt -query test.fasta >> test.out.txt
And I get results for each OTU given, but when I run seqenv using the same input/db parameters:
seqenv test.fasta --search_db /fdb/blastdb/nt
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.
I get nothing back. Is this an issue with the seqenv installation/configuration?
blastn is in my path. When I installed seqenv I had to manually add a pygraphviz and orange from conda, but other than that things went smoothly.
I'm pretty new to python and unix is general, so if you need something more to help diagnose, please let me know.
Thanks for any help you can offer.
-Ben
Do you have a source for a pre-September 2016 version of the nt database that I can use for seqenv?
Thank you,
Dan.
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