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dib-lab / dammit

just annotate it, dammit!
http://dib-lab.github.io/dammit/
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TypeError: lastal_task() got an unexpected keyword argument 'pbs' #203

Open AntonioBaeza opened 3 years ago

AntonioBaeza commented 3 years ago

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$

lucapandolfini commented 3 years ago

In dammit-env/lib/python3.6/site-packages/dammit/annotate.py

remove pbs keyword

https://github.com/dib-lab/dammit/blob/dd5420ac05f0be7905ad3cb96402a5b2264c1983/dammit/annotate.py#L378

commenting out this line.

This solved the issue for me.

AntonioBaeza commented 3 years ago

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

https://github.com/dib-lab/dammit/blob/dd5420ac05f0be7905ad3cb96402a5b2264c1983/dammit/annotate.py#L378

commenting out this line.

This solved the issue for me.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/dib-lab/dammit/issues/203#issuecomment-754280446, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALIJRA4HGFEP55FDZTKF2ATSYJEH3ANCNFSM4U3TDEBA .

-- 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

camillescott commented 3 years ago

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.

Werner0 commented 3 years ago

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.

xiekunwhy commented 3 years ago

Hi,

Same error occured when I use dammit 1.2.

Best, Kun

dpgrape commented 2 years ago

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 keyword

https://github.com/dib-lab/dammit/blob/dd5420ac05f0be7905ad3cb96402a5b2264c1983/dammit/annotate.py#L378

commenting out this line.

This solved the issue for me.