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loosolab / UROPA

Universal RObust Peak Annotator
https://uropa-manual.readthedocs.io/
MIT License
15 stars 6 forks source link

Errno 32 Broken Pipe #7

Closed jjp55 closed 2 years ago

jjp55 commented 3 years ago

Hello,

I recently installed UROPA using:

conda install -c bioconda uropa

And the package was able to install and I can see the options when I use: uropa -h.

I tried to run the code:

uropa -b Arabidopsis_w50_g2_PE.bed -g /Users/jjp/Desktop/TAIR10_GFF3_genes.gff --feature protein_coding -o Arabidopsis-UROPA

Afterwards, I received the following message:

2021-06-14 13:46:56 (34865) [INFO] Started UROPA 4.0.1 2021-06-14 13:46:56 (34865) [INFO] Working directory: /Users/jjp/Desktop/new_HOMER 2021-06-14 13:46:56 (34865) [INFO] Command-line call: /Users/jjp/opt/anaconda3/envs/epic/bin/uropa -b NPR1-SA-SICER_w50_g2_PE.bed -g /Users/jjp/Desktop/TAIR10_GFF3_genes.gff --feature protein_coding -o NPR1-SA-SICER-UROPA 2021-06-14 13:46:56 (34865) [INFO] Reading configuration from commandline/input config 2021-06-14 13:46:56 (34865) [INFO] Preparing .gtf-file for fast access 2021-06-14 13:46:58 (34865) [INFO] Config key show_attributes was set to 'all'.

Followed by was appears to be all the genes in the Arabidopsis genome. (example 'Parent=ATMG01410.1')

After the gene list prints I received the following message: Traceback (most recent call last): File "/Users/jjp/opt/anaconda3/envs/epic/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/Users/jjp/opt/anaconda3/envs/epic/lib/python3.6/multiprocessing/process.py", line 93, in run self._target(*self._args, **self._kwargs) File "/Users/jjp/opt/anaconda3/envs/epic/lib/python3.6/site-packages/uropa/utils.py", line 88, in main_logger_process record = self.q.get() File "", line 2, in get File "/Users/jjp/opt/anaconda3/envs/epic/lib/python3.6/multiprocessing/managers.py", line 756, in _callmethod conn.send((self._id, methodname, args, kwds)) File "/Users/jjp/opt/anaconda3/envs/epic/lib/python3.6/multiprocessing/connection.py", line 206, in send self._send_bytes(_ForkingPickler.dumps(obj)) File "/Users/jjp/opt/anaconda3/envs/epic/lib/python3.6/multiprocessing/connection.py", line 404, in _send_bytes self._send(header + buf) File "/Users/jjp/opt/anaconda3/envs/epic/lib/python3.6/multiprocessing/connection.py", line 368, in _send n = write(self._handle, buf) BrokenPipeError: [Errno 32] Broken pipe

Do you have any way to solve this or know what may have caused the error?

msbentsen commented 3 years ago

Hi jjp55,

UROPA unfortunately only reads .gtf files, and not .gff, so that might be part of the issue here. This is also why it prints all the genes, as it thinks these are all different features from a .gtf-file. I don't know if this is the reason for the BrokenPipe (which seems to be the same error as #6).

For the error, can you give me some more information on the system you are on? And at exactly which point the pipeline fails? E.g. by the last written print before the error. Thank you!

jjp55 commented 3 years ago

That was a complete oversight on my part. Using a .gtf-gile completely fixed the problem.

I am running on a Mac with Big Sur.

msbentsen commented 3 years ago

Great! I saw you wrote another comment - was that solved in the meantime?