camillescott
commented
7 years ago Issue addressed on eel pond repo, closing.
Closed taylorreiter closed 7 years ago
camillescott
commented
7 years ago Issue addressed on eel pond repo, closing.
seboles
commented
5 years ago Hello! I am having a similar issue to the one described here. This is my command dammit annotate redabalonefemale_trinity_out.Trinity.fasta --busco-group metazoa --user-databases halruf_proteins.fasta --n_threads 4 and here is my output ```## a tool for easy de novo transcriptome annotation
by Camille Scott
v1.0.rc0, 2018
Traceback (most recent call last):
File "/home/seboles/anaconda2/envs/py3.dammit/bin/dammit", line 9, in
I am not sure how to proceed at this time, any help would be greatly appreciated.
bluegenes
commented
5 years ago Hi @seboles! Did you have any errors when installing the databases? What output did you get while running dammit databases --install --busco-group metazoa?
seboles
commented
5 years ago Hi Tessa, Thanks for the quick reply, I really appreciate it.I didn’t notice any errors when I installed the data bases a while back, but I just tried to re/install them, and I got the same error message (below) that I received earlier. Let me know if you have any suggestions.
Thanks,
Sara
by Camille Scott
v1.0.rc0, 2018
Traceback (most recent call last):
File "/home/seboles/anaconda2/envs/py3.dammit/bin/dammit", line 9, in
On 20 Jun 2019, at 11:49 am, Tessa Pierce notifications@github.com wrote:
Hi @seboles https://github.com/seboles! Did you have any errors when installing the databases? What output did you get while running dammit databases --install --busco-group metazoa?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dib-lab/dammit/issues/91?email_source=notifications&email_token=AEHDXABK4CLWJNXUSV6KZWLP3PGMTA5CNFSM4DCOPDX2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYGJFDY#issuecomment-504140431, or mute the thread https://github.com/notifications/unsubscribe-auth/AEHDXAE4WJW5B5S7Y3WVDGDP3PGMTANCNFSM4DCOPDXQ.
seboles
commented
5 years ago Hi Tessa, I didn’t notice any errors when I installed the data bases a while back, but I just tried to re/install them, and I got the same error message.
by Camille Scott
v1.0.rc0, 2018
Traceback (most recent call last): File "/home/seboles/anaconda2/envs/py3.dammit/bin/dammit", line 9, in
bluegenes
commented
5 years ago Hmm, ok. Might I recommend that you update the version of dammit you're using? The conda install version is slightly out of date compared with the github master branch.
In the same conda environment you're using, you should be able to do this by executing pip install git+https://github.com/dib-lab/dammit
If that doesn't work, you can create a new dammit environment. I've written one into our elvers workflow that is currently working. You can download and create that environment as follows:
wget https://raw.githubusercontent.com/dib-lab/elvers/master/elvers/rules/dammit/environment.yml
conda env create -f environment.yml -n dammit-envHi Tessa,
The pip install didn't work, so I tried the second option, which has now yielded a new error message. Let me know if you have any suggestions. Thank you so much.
Sara seboles@farm:~$ conda env create -f environment.yml -n dammit-env
Fetching package metadata .................
Solving package specifications: .
UnsatisfiableError: The following specifications were found to be in conflict:
python 2.7*
shmlast -> python >=3.6,<3.7.0a0
Use "conda info
On Thu, Jun 20, 2019 at 12:04 PM Tessa Pierce notifications@github.com wrote:
Hmm, ok. Might I recommend that you update the version of dammit you're using? The conda install version is slightly out of date compared with the github master branch.
In the same conda environment you're using, you should be able to do this by executing pip install git+https://github.com/dib-lab/dammit
If that doesn't work, you can create a new dammit environment. I've written one into our elvers workflow that is currently working. You can download and create that environment as follows:
wget https://raw.githubusercontent.com/dib-lab/elvers/master/elvers/rules/dammit/environment.yml conda env create -f environment.yml -n dammit-env
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dib-lab/dammit/issues/91?email_source=notifications&email_token=AEHDXACKK355R35GLVJ4LKTP3PIDDA5CNFSM4DCOPDX2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYGKKVY#issuecomment-504145239, or mute the thread https://github.com/notifications/unsubscribe-auth/AEHDXAEMTJBF5GI3HFSZVL3P3PIDDANCNFSM4DCOPDXQ .
-- Sara E. Boles, MS PhD Candidate | Whitehead Lab Pharmacology and Toxicology Graduate Group Department of Environmental Toxicology University of California, Davis, CA 95616 http://whiteheadresearch.wordpress.com/ https://sites.google.com/a/ucdavis.edu/sara-e-boles/
bluegenes
commented
5 years ago Ah, it's currently trying to use python 2.7, which must be your default. In the environment.yml file, can you change python to python=3.6 and try again?
seboles
commented
5 years ago Hi Tessa,
I tried changing python=3.6 and I received a new error message :) Here are my commands:
source ~/.bashrc
source activate py3.dammit
python=3.6
pip install dammit
metazoa --user-databases halruf_proteins.fasta --n_threads 4```
And here is the output message.
Traceback (most recent call last):
File "/home/seboles/anaconda2/envs/py3.dammit/bin/dammit", line 4, in
<module>
import dammit
File
"/home/seboles/anaconda2/envs/py3.dammit/lib/python3.6/site-packages/dammit/__init__.py",
line 4, in <module>
import log
ModuleNotFoundError: No module named 'log'
Let me know if you have any suggestions.
Sara
On Thu, Jun 20, 2019 at 1:00 PM Tessa Pierce <notifications@github.com>
wrote:
> Ah, it's currently trying to use python 2.7, which must be your default.
> In the environment.yml file, can you change python to python=3.6 and try
> again?
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <https://github.com/dib-lab/dammit/issues/91?email_source=notifications&email_token=AEHDXAHFODIGQC6NHRNS6JLP3POVZA5CNFSM4DCOPDX2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYGOPEI#issuecomment-504162193>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AEHDXACEPSOMD5AFGL7F6E3P3POVZANCNFSM4DCOPDXQ>
> .
>
--
Sara E. Boles, MS
PhD Candidate | Whitehead Lab
Pharmacology and Toxicology Graduate Group
Department of Environmental Toxicology
University of California, Davis, CA 95616
http://whiteheadresearch.wordpress.com/
https://sites.google.com/a/ucdavis.edu/sara-e-boles/Hi @seboles,
Using pip that way, you're installing the pip uploaded version of dammit, not the github master version. The environment.yml file should read:
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- python=3.6
- numpy
- pandas
- numexpr>=2.3.1
- khmer>=2.1
- sphinx_rtd_theme>=0.1.9
- pytest
- pytest-runner
- doit>=0.29.0
- matplotlib
- shmlast
- infernal
- hmmer
- transdecoder=3.0.1
- last
- busco=3.0.2
- parallel
- bioconductor-seqlogo
- pip:
- git+https://github.com/dib-lab/dammitThen, you can create an environment from this file with:
conda env create -f environment.yml -n dammit-envThen, enter this environment with source activate dammit-env, and try to run dammit dammit -h
seboles
commented
5 years ago It worked! Thank you for your help. Happy Monday!
On Thu, Jun 20, 2019 at 3:06 PM Tessa Pierce notifications@github.com wrote:
Hi @seboles https://github.com/seboles,
Using pip that way, you're installing the pip uploaded version of dammit, not the github master version. The environment.yml file should read:
channels:
- bioconda
- conda-forge
- defaults dependencies:
- python=3.6
- numpy
- pandas
- numexpr>=2.3.1
- khmer>=2.1
- sphinx_rtd_theme>=0.1.9
- pytest
- pytest-runner
- doit>=0.29.0
- matplotlib
- shmlast
- infernal
- hmmer
- transdecoder=3.0.1
- last
- busco=3.0.2
- parallel
- bioconductor-seqlogo
- pip:
Then, you can create an environment from this file with:
conda env create -f environment.yml -n dammit-env
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dib-lab/dammit/issues/91?email_source=notifications&email_token=AEHDXAEQ4ZY25QRZOZYWUK3P3P5NTA5CNFSM4DCOPDX2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYG32XY#issuecomment-504216927, or mute the thread https://github.com/notifications/unsubscribe-auth/AEHDXAFCIWSWM53DFYJEIWTP3P5NTANCNFSM4DCOPDXQ .
-- Sara E. Boles, MS PhD Candidate | Whitehead Lab Pharmacology and Toxicology Graduate Group Department of Environmental Toxicology University of California, Davis, CA 95616 http://whiteheadresearch.wordpress.com/ https://sites.google.com/a/ucdavis.edu/sara-e-boles/
When running dammit in the eel pond protocol (https://github.com/dib-lab/eel-pond/blob/master/5-annotating.rst), I received the following error message:
(dammit) ubuntu@ip:~$ dammit databases --install --busco-group eukaryotaor(dammit) ubuntu@ip:~$ dammit databases --installproduce the following error message:# dammit## a tool for easy de novo transcriptome annotationby Camille Scott**v1.0.dev0**, 2016## submodule: databasesTraceback (most recent call last): File "/home/ubuntu/miniconda3/envs/dammit/bin/dammit", line 9, in <module> app.DammitApp(arg_src=sys.argv[1:]).run() File "/home/ubuntu/miniconda3/envs/dammit/lib/python3.5/site-packages/dammit/app.py", line 41, in runself.args.func()File "/home/ubuntu/miniconda3/envs/dammit/lib/python3.5/site-packages/dammit/app.py", line 253, in handle_databases with_uniref=self.args.full)File "/home/ubuntu/miniconda3/envs/dammit/lib/python3.5/site-packages/dammit/databases.py", line 133, in build_default_pipeline register_orthodb_tasks(handler, config['last']['lastdb'], databases)File "/home/ubuntu/miniconda3/envs/dammit/lib/python3.5/site-packages/dammit/databases.py", line 201, in register_orthodb_tasks params=params))File "/home/ubuntu/miniconda3/envs/dammit/lib/python3.5/site-packages/dammit/tasks/last.py", line 46, in task exc = self.deps()File "/home/ubuntu/miniconda3/envs/dammit/lib/python3.5/site-packages/dammit/tasks/last.py", line 35, in deps raise InstallationError('lastdb not found.') dammit.tasks.utils.InstallationError: lastdb not found.I have insured that busco, hmmer, last, infernal, TransDecoder, blast+, and crb-blast are installed.