TypeError: lastal_task() got an unexpected keyword argument 'pbs'

[AntonioBaeza]

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

• Database Directory: /home/antonio/.dammit/databases
• Doit Database: /home/antonio/.dammit/databases/databases.doit.db

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]

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

remove pbs keyword

dammit/dammit/annotate.py

Line 378 in dd5420a

pbs=config['sshloginfile'],

commenting out this line.

This solved the issue for me.

[AntonioBaeza]

Thanks! I will give it a try!

…

On Mon, Jan 4, 2021 at 6:19 PM Luca Pandolfini ***@***.***> 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 <#203 (comment)>, 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]

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.

[Werner0]

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]

Hi,

Same error occured when I use dammit 1.2.

Best,
Kun

[dpgrape]

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

dammit/dammit/annotate.py

Line 378 in dd5420a

pbs=config['sshloginfile'],

commenting out this line.

This solved the issue for me.