Comments (6)
Should I file a separate issue on the unclear failure if used with a GFF file without embedded FASTA sequences? Looking at the code it seems to try to give a warning, https://github.com/sanger-pathogens/SnpEffWrapper/blob/v0.2.5/snpEffWrapper/wrapper.py#L297 - but wouldn't it be better to actually abort without calling snpEff build?
from snpeffwrapper.
hey peterjc,
Might I ask how you merged your fasta and GFF in the end? I used cat .gff .fasta > .fasta.gff and I am getting the following error (which may be unrelated to how I've combined the files, but just want to check!)
[2018-10-19 15:45:10,601] INFO: Checking that the VCF and GFF contigs are consistent
[2018-10-19 15:45:11,724] INFO: Building snpeff database
Traceback (most recent call last):
File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/site-packages/snpEffWrapper/wrapper.py", line 222, in _snpeff_build_database
subprocess.check_call(command, stdout=stdout, stderr=stderr)
File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/subprocess.py", line 291, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/usr/bin/java', '-Xmx4g', '-jar', '/media/sf_SharedDrive/Download/snpEff/snpEff.jar', 'build', '-gff3', '-verbose', 'data', '-c', '/home/manager/WGS/WGS analysis/snpeff_data_dir_hrk9sc02/config']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/manager/miniconda3/envs/ddocent_env/bin/snpEffBuildAndRun", line 45, in
annotate_vcf(args)
File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/site-packages/snpEffWrapper/wrapper.py", line 343, in annotate_vcf
args.vcf_file, config_filename, args.debug)
File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/site-packages/snpEffWrapper/wrapper.py", line 275, in run_snpeff
build_stderr)
File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/site-packages/snpEffWrapper/wrapper.py", line 224, in _snpeff_build_database
raise BuildDatabaseError("Problem building the database from your GFF")
snpEffWrapper.wrapper.BuildDatabaseError: Problem building the database from your GFF
from snpeffwrapper.
What you are likely missing is the special line ##FASTA\n
before the FASTA file starts with ">"...
Luckily I had documented this locally, I did it once by hand and then came up with the following as a reproducible alternative:
bash -c "cat annotation_only.gff; echo '##FASTA' ; cat reference.fasta" > annotation_with_fasta.gff
You could make a dummy file with the magic line, and then concatenate the three files (in order) to make your combined files, but I used the echo command here instead.
from snpeffwrapper.
Hey peter!
Thanks for that, unfortunately the same error message appears after using your cat command to put in that extra line, so I'm back at square one I feel!
Thanks again,
Gordon
from snpeffwrapper.
I suspect there is something else "wrong" with your GFF file then - I would suggest opening a new issue, and offering to share the files directly with the tool authors (or if you can, posting them online, e.g. via https://gist.github.com).
from snpeffwrapper.
Yes I will open another issue as now it seems it's unrelated to how the fasta and GFF are merged.
Thanks,
G
from snpeffwrapper.
Related Issues (3)
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 snpeffwrapper.