# Kneaddata-Trimmomatic Permission Error

**URL:** <https://forum.biobakery.org/t/kneaddata-trimmomatic-permission-error/3677>\
**Category:** KneadData\
**Created:** [June 2, 2022, 10:05pm UTC](https://forum.biobakery.org/t/kneaddata-trimmomatic-permission-error/3677 "2022-06-02T22:05:01Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![fsaravia](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fsaravia/32/716_2.png) [@fsaravia](https://forum.biobakery.org/u/fsaravia)\
**Post date:** [June 2, 2022, 10:05pm UTC](https://forum.biobakery.org/t/kneaddata-trimmomatic-permission-error/3677/1 "2022-06-02T22:05:01Z")

</div>

I am running kneaddata and trimmomatic and get the following error. Any input would be appreciated.

Decontaminating …

Traceback (most recent call last):

File “/opt/miniconda3/bin/kneaddata”, line 33, in

sys.exit(load\_entry\_point(‘kneaddata==0.11.0’, ‘console\_scripts’, ‘kneaddata’)())

File “/opt/miniconda3/lib/python3.9/site-packages/kneaddata/knead\_data.py”, line 541, in main

final\_output\_files=run.decontaminate(args, full\_path\_output\_prefix, trf\_output\_files)

File “/opt/miniconda3/lib/python3.9/site-packages/kneaddata/run.py”, line 561, in decontaminate

alignment\_output\_files = align([files\_to\_align[0][0],files\_to\_align[0][1]]+utilities.resolve\_sublists(files\_to\_align[1:]),

File “/opt/miniconda3/lib/python3.9/site-packages/kneaddata/run.py”, line 164, in align

utilities.start\_processes(commands,processors,verbose)

File “/opt/miniconda3/lib/python3.9/site-packages/kneaddata/utilities.py”, line 151, in start\_processes

pool = multiprocessing.Pool(processes)

File “/opt/miniconda3/lib/python3.9/multiprocessing/context.py”, line 119, in Pool

return Pool(processes, initializer, initargs, maxtasksperchild,

File “/opt/miniconda3/lib/python3.9/multiprocessing/pool.py”, line 212, in **init**

self.\_repopulate\_pool()

File “/opt/miniconda3/lib/python3.9/multiprocessing/pool.py”, line 303, in \_repopulate\_pool

return self.\_repopulate\_pool\_static(self.\_ctx, self.Process,

File “/opt/miniconda3/lib/python3.9/multiprocessing/pool.py”, line 326, in \_repopulate\_pool\_static

w.start()

File “/opt/miniconda3/lib/python3.9/multiprocessing/process.py”, line 121, in start

self.\_popen = self.\_Popen(self)

File “/opt/miniconda3/lib/python3.9/multiprocessing/context.py”, line 284, in \_Popen

return Popen(process\_obj)

File “/opt/miniconda3/lib/python3.9/multiprocessing/popen\_spawn\_posix.py”, line 32, in **init**

super(). **init** (process\_obj)

File “/opt/miniconda3/lib/python3.9/multiprocessing/popen\_fork.py”, line 19, in **init**

self.\_launch(process\_obj)

File “/opt/miniconda3/lib/python3.9/multiprocessing/popen\_spawn\_posix.py”, line 42, in \_launch

prep\_data = spawn.get\_preparation\_data(process\_obj.\_name)

File “/opt/miniconda3/lib/python3.9/multiprocessing/spawn.py”, line 176, in get\_preparation\_data

dir=os.getcwd(),

PermissionError: [Errno 1] Operation not permitted

Traceback (most recent call last):

File “”, line 1, in

File “”, line 1007, in \_find\_and\_load

File “”, line 982, in \_find\_and\_load\_unlocked

File “”, line 925, in \_find\_spec

File “”, line 1414, in find\_spec

File “”, line 1383, in \_get\_spec

File “”, line 1347, in \_path\_importer\_cache

PermissionError: [Errno 1] Operation not permitted