Comments (6)
I have the same issue.
When I tried to install enrichm at personal pc, this uniref100.dmnd is not present:
[2019-08-20 09:31:42 AM] INFO: Decompressing new database
x enrichm_database_v10/
x enrichm_database_v10/databases/
x enrichm_database_v10/databases/cazy.hmm
x enrichm_database_v10/databases/pfam.hmm
x enrichm_database_v10/databases/tigrfam.hmm
x enrichm_database_v10/databases/uniref100.EC.dmnd
x enrichm_database_v10/databases/uniref100.KO.dmnd
x enrichm_database_v10/databases/ko.hmm
x enrichm_database_v10/gtdb/
x enrichm_database_v10/gtdb/gtdb_cazy.tsv
x enrichm_database_v10/gtdb/gtdb_ec.tsv
x enrichm_database_v10/gtdb/gtdb_ko.tsv
x enrichm_database_v10/gtdb/gtdb_pfam.tsv
x enrichm_database_v10/gtdb/gtdb_tigrfam.tsv
x enrichm_database_v10/ids/
x enrichm_database_v10/ids/CAZY_IDS.txt
x enrichm_database_v10/ids/EC_IDS.txt
x enrichm_database_v10/ids/KO_IDS.txt
x enrichm_database_v10/ids/PFAM_CLANS.txt
x enrichm_database_v10/ids/PFAM_IDS.txt
x enrichm_database_v10/ids/TIGRFAM_IDS.txt
x enrichm_database_v10/README
x enrichm_database_v10/VERSION
x enrichm_database_v10/br08001.26-11-2018.pickle
x enrichm_database_v10/clan_to_name.26-11-2018.pickle
x enrichm_database_v10/clan_to_pfam.26-11-2018.pickle
x enrichm_database_v10/compound_descriptions.26-11-2018.pickle
x enrichm_database_v10/compound_to_reaction.26-11-2018.pickle
x enrichm_database_v10/ko00000.tsv
x enrichm_database_v10/ko_descriptions.26-11-2018.pickle
x enrichm_database_v10/module_descriptions.26-11-2018.pickle
x enrichm_database_v10/module_to_cpd.26-11-2018.pickle
x enrichm_database_v10/module_to_reaction.26-11-2018.pickle
x enrichm_database_v10/pathway_descriptions.26-11-2018.pickle
x enrichm_database_v10/pathway_to_reaction.26-11-2018.pickle
x enrichm_database_v10/pfam_to_clan.26-11-2018.pickle
x enrichm_database_v10/pfam_to_description.26-11-2018.pickle
x enrichm_database_v10/pfam_to_name.26-11-2018.pickle
x enrichm_database_v10/reaction_descriptions.26-11-2018.pickle
x enrichm_database_v10/reaction_to_compound.26-11-2018.pickle
x enrichm_database_v10/reaction_to_module.26-11-2018.pickle
x enrichm_database_v10/reaction_to_orthology.26-11-2018.pickle
x enrichm_database_v10/reaction_to_pathway.26-11-2018.pickle
x enrichm_database_v10/taxonomy_gtdb.tsv
x enrichm_database_v10/tigrfam_descriptions.26-11-2018.pickle
x enrichm_database_v10/ec_to_description.26-11-2018.pickle
x enrichm_database_v10/module_to_definition.26-11-2018.pickle
x enrichm_database_v10/ko_cutoffs.tsv
[2019-08-20 09:32:43 AM] INFO: Cleaning up
[2019-08-20 09:32:44 AM] INFO: Finished running EnrichM
from enrichm.
Hey @geronimp
I'm having the same issue as the above two. The uniref100.dmnd
database is missing from the databases folder where the installation occurred.
Below is the error that I got:
[2019-09-24 10:51:30 AM] INFO: - Annotating genomes with ko ids
[2019-09-24 10:51:30 AM] INFO: - BLASTing genomes
[2019-09-24 10:51:30 AM] DEBUG: bash /tmp/tmp67x35qbn | diamond blastp --quiet --outfmt 6 --max-target-seqs 1 --query /dev/stdin --out enrichm_B4_dastoolbins/annotations_ko/DIAMOND_search.tsv --db /home/users/sbusi/databases/enrichm_database_v10/databases/uniref100.dmnd --threads 24 --evalue 1e-05 --id 30.0 --query-c
over 70.0 --subject-cover 70.0
diamond v0.9.26.127 | by Benjamin Buchfink <[email protected]>
Licensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>
Check http://github.com/bbuchfink/diamond for updates.
No such file or directory
Error: Error opening file /home/users/sbusi/databases/enrichm_database_v10/databases/uniref100.dmnd
[2019-09-24 10:51:30 AM] DEBUG: Finished
Traceback (most recent call last):
File "/home/users/sbusi/apps/miniconda3/envs/enrichm/bin/enrichm", line 357, in <module>
r.main(args, sys.argv)
File "/home/users/sbusi/apps/miniconda3/envs/enrichm/lib/python3.7/site-packages/enrichm/run.py", line 323, in main
args.protein_files)
File "/home/users/sbusi/apps/miniconda3/envs/enrichm/lib/python3.7/site-packages/enrichm/annotate.py", line 661, in do
self.annotate_ko(genomes_list)
File "/home/users/sbusi/apps/miniconda3/envs/enrichm/lib/python3.7/site-packages/enrichm/annotate.py", line 230, in annotate_ko
for genome_name, batch in self.get_batches(output_annotation_path):
File "/home/users/sbusi/apps/miniconda3/envs/enrichm/lib/python3.7/site-packages/enrichm/annotate.py", line 242, in get_batches
input_file_io = open(input_file)
FileNotFoundError: [Errno 2] No such file or directory: 'enrichm_B4_dastoolbins/annotations_ko/DIAMOND_search.tsv'
Also, like @liangjinsong, I checked my database folder and only have the following:
(enrichm) [sbusi@iris-004 enrichm]$ ls /home/users/sbusi/databases/enrichm_database_v10/databases/
cazy.hmm ko.hmm pfam.hmm tigrfam.hmm uniref100.EC.dmnd uniref100.KO.dmnd
Thanks for your urgent help with this one!
-Susheel
from enrichm.
@liangjinsong I encountered the same issue. I might be super incorrect since I'm pretty new to bioinformatics but I made a copy of the uniref100.KO.dmnd file and renamed it uniref100.dmnd (since I was only interested in KO annotation for now). It ran fine after this.
from enrichm.
@ashley-isaac Thank you for this tip. I did the same, but wanted to verify that the ".KO" and the other were the same database or otherwise different. It'll be nice to get confirmation from the authors. ;)
from enrichm.
hi all, yes @ashley-isaac 's solution is correct. This error was due to a misnaming error of mine, apologies for that mishap! I will correct asap
from enrichm.
Also sorry for the delays guys, I've been away away since the start of october. Will be working through these issues now
from enrichm.
Related Issues (20)
- Custom Database
- "xargs: illegal option -- -" leading to "No files found with .faa suffix in input directory"
- bioconda package
- There is probably a wrong version of urlib in the conda package.
- 0.5.1 run error HOT 2
- cannot open help pages/wiki HOT 1
- ERROR while classifying using custom module HOT 2
- download the database separately HOT 2
- enrichm error
- Index out of range error during enrichm annotate HOT 2
- enrichm annotate KO frequency table but all zeros HOT 3
- fuzzywuzzi missing from conda env HOT 1
- enrichM database HOT 5
- AttributeError: 'Databases' object has no attribute 'M2DEF' HOT 1
- issues with help page/wiki
- Missing KO in my ko_frequency_table.tsv
- Error receiving while generating database
- K00362 cannot assign to model M00530
- Issues with Conda installation HOT 4
- keyERROR HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from enrichm.