Open AntonioBaeza opened 3 years ago
In dammit-env/lib/python3.6/site-packages/dammit/annotate.py
remove pbs
keyword
commenting out this line.
This solved the issue for me.
Thanks! I will give it a try!
On Mon, Jan 4, 2021 at 6:19 PM Luca Pandolfini notifications@github.com wrote:
In dammit-env/lib/python3.6/site-packages/dammit/annotate.py
remove pbs keyword
commenting out this line.
This solved the issue for me.
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-- J. Antonio Baeza
Associate Professor Department of Biological Sciences, Clemson University South Carolina, USA & Research Associate Smithsonian Marine Station at Fort Pierce, Florida, USA & Adjunct Faculty Universidad Catolica del Norte, Coquimbo, Chile
Email: baeza.antonio@google.com & jbaezam@clemson.edu Website: http://baezaantonio.wix.com/baezalabclemson Website (CI-team): https://baezaantonio.wixsite.com/clemsonmitogenomics Website ResearchGate: https://www.researchgate.net/profile/J_Baeza/ Website SemanticScholar: https://www.semanticscholar.org/author/Juan-Antonio-Baeza/144723920
Hey folks, sorry for this! I pushed a new shmlast
version and forgot to update the dammit 1.2 recipe to pin to the old version :grimacing: Lemme see about pushing out a fix.
Hey folks, sorry for this! I pushed a new
shmlast
version and forgot to update the dammit 1.2 recipe to pin to the old version 😬 Lemme see about pushing out a fix.
We bypassed the problem by removing the pbs keyword where it was placed as an argument somewhere in the script. We will report the results in a scientific manuscript. We only need the associations between annotated genes and phenotypes of interest to be correct in order for the results to be valid.
Hi,
Same error occured when I use dammit 1.2.
Best, Kun
Hi all,
I had the same error as well. Is this the right solution? Thank you!
Best, Diana
In dammit-env/lib/python3.6/site-packages/dammit/annotate.py
remove
pbs
keywordcommenting out this line.
This solved the issue for me.
Hi Camille. I installed dammit with bioconda, followed instructions, downloaded databases. When running dammit with the command below I am getting the error above (and below). I will continue trying to figure out what it means. Thanks
(base) antonio@jock:/fastdrive/antonio/annotation$ ll total 147368 drwxrwxr-x 2 antonio antonio 4096 Dec 15 09:03 ./ drwxrwxr-x 4 antonio users 4096 Dec 15 09:00 ../ -rw-r--r-- 1 antonio antonio 150896113 Dec 15 09:04 brain_trinity.clean_filtered6.fasta (base) antonio@jock:/fastdrive/antonio/annotation$ (base) antonio@jock:/fastdrive/antonio/annotation$ conda activate dammit (dammit) antonio@jock:/fastdrive/antonio/annotation$ (dammit) antonio@jock:/fastdrive/antonio/annotation$ dammit annotate brain_trinity.clean_filtered6.fasta --busco-group arthropoda --n_threads 10
dammit
a tool for easy de novo transcriptome annotation
by Camille Scott
v1.2, 2018
submodule: annotate
Database Check
Info
All database tasks up-to-date.
Traceback (most recent call last): File "/home/antonio/miniconda3/envs/dammit/bin/dammit", line 9, in
sys.exit(app.DammitApp(arg_src=sys.argv[1:]).run())
File "/home/antonio/miniconda3/envs/dammit/lib/python3.8/site-packages/dammit/app.py", line 45, in run
return self.args.func()
File "/home/antonio/miniconda3/envs/dammit/lib/python3.8/site-packages/dammit/app.py", line 333, in handle_annotate
build_default_pipeline(annotate_handler,
File "/home/antonio/miniconda3/envs/dammit/lib/python3.8/site-packages/dammit/annotate.py", line 136, in build_default_pipeline
register_lastal_tasks(handler, config, databases,
File "/home/antonio/miniconda3/envs/dammit/lib/python3.8/site-packages/dammit/annotate.py", line 371, in register_lastal_tasks
LastalTask().task(input_fn,
File "/home/antonio/miniconda3/envs/dammit/lib/python3.8/site-packages/dammit/tasks/last.py", line 69, in task
return last.lastal_task(*args, kwargs)
File "/home/antonio/miniconda3/envs/dammit/lib/python3.8/site-packages/shmlast/util.py", line 35, in d_to_t
ret_dict = task_dict_func(*args, *kwargs)
File "/home/antonio/miniconda3/envs/dammit/lib/python3.8/site-packages/shmlast/profile.py", line 156, in func
task = task_func(args, kwargs)
TypeError: lastal_task() got an unexpected keyword argument 'pbs'
(dammit) antonio@jock:/fastdrive/antonio/annotation$