urllib.error.HTTPError: HTTP Error 404: Not Found

[AminaLEM]

Hello @adbailey4

I get the following error when I run the minimal example with the docker image:

Running SignalAlign Traceback (most recent call last): File "/opt/venv/bin/inference_pipeline.py", line 232, in ret, time = (time_it(main)) File "/opt/venv/lib/python3.7/site-packages/py3helpers/utils.py", line 169, in time_it something = func(args) File "/opt/venv/bin/inference_pipeline.py", line 218, in main threads=args.threads) File "/opt/venv/bin/inference_pipeline.py", line 143, in create_config urllib.request.urlretrieve(os.path.join(head_node, x), os.path.join(outpath, x)) File "/usr/lib/python3.7/urllib/request.py", line 247, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: File "/usr/lib/python3.7/urllib/request.py", line 222, in urlopen return opener.open(url, data, timeout) File "/usr/lib/python3.7/urllib/request.py", line 531, in open response = meth(req, response) File "/usr/lib/python3.7/urllib/request.py", line 641, in http_response 'http', request, response, code, msg, hdrs) File "/usr/lib/python3.7/urllib/request.py", line 569, in error return self._call_chain(args) File "/usr/lib/python3.7/urllib/request.py", line 503, in _call_chain result = func(*args) File "/usr/lib/python3.7/urllib/request.py", line 649, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp) urllib.error.HTTPError: HTTP Error 404: Not Found

It seems that the trained model ("https://bailey-k8s.s3-us-west-2.amazonaws.com/yeast_models") is not accessible.

Thanks,

Amina

[adbailey4]

Ah, ok this is a good catch. I think I migrated those models elsewhere after I graduated but forgot to update the Docker file. I will fix it sometime next week.

[adbailey4]

@AminaLEM Ok, I updated the Docker image. Can you try pulling the new image and running the same command?

[AminaLEM]

Thank you very much @adbailey4 , I used docker again. The problem of the training model is fixed but another problem is raising something related to multithread package:

Traceback (most recent call last): File "/opt/venv/bin/runSignalAlign.py", line 12, in from signalalign.filter_reads import filter_reads, filter_reads_to_string_wrapper File "/opt/venv/lib/python3.7/site-packages/signalalign/filter_reads.py", line 20, in from signalalign.utils import multithread File "/opt/venv/lib/python3.7/site-packages/signalalign/utils/multithread.py", line 4, in from pathos.multiprocessing import ProcessingPool as Pool File "/opt/venv/lib/python3.7/site-packages/pathos/init.py", line 48, in from . import pools File "/opt/venv/lib/python3.7/site-packages/pathos/pools.py", line 12, in from pathos.helpers import ProcessPool as _ProcessPool File "/opt/venv/lib/python3.7/site-packages/pathos/helpers/init.py", line 10, in from . import pp_helper File "/opt/venv/lib/python3.7/site-packages/pathos/helpers/pp_helper.py", line 30, in from pp import _Task ImportError: cannot import name '_Task' from 'pp' (/opt/venv/lib/python3.7/site-packages/pp/init.py) Traceback (most recent call last): File "/opt/venv/bin/inference_pipeline.py", line 232, in ret, time = (time_it(main)) File "/opt/venv/lib/python3.7/site-packages/py3helpers/utils.py", line 169, in time_it something = func(*args) File "/opt/venv/bin/inference_pipeline.py", line 222, in main check_call(f"runSignalAlign.py run --config {config_path}".split()) File "/usr/lib/python3.7/subprocess.py", line 363, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['runSignalAlign.py', 'run', '--config', '/data/signalalign_output/sa_run_config.json']' returned non-zero exit status 1.

[adbailey4]

Alright, I just updated some stuff to fix that issue. Try pulling the latest docker image and let me know what happens!

[adbailey4]

I just re-ran the commands from here and everything finished as expected. Closing issue for now