Error: Connection reset by peer

[covavara]

Hi,
I am trying to generate a hal file and I keep encountering the following error in different steps:

[2026-03-27T10:58:17+0100] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker progressive_workflow file:/projects_eg/projects/cova/DENOVO/MAR26_clean/myfavCactus/js kind-progressive_workflow/instance-zooa6r9w.
[2026-03-27T10:58:17+0100] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'progressive_workflow' kind-progressive_workflow/instance-zooa6r9w v1
Exit reason: None
[2026-03-27T10:58:18+0100] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'progressive_workflow' kind-progressive_workflow/instance-zooa6r9w v2
[2026-03-27T10:58:18+0100] [MainThread] [W] [toil.leader] Log from job "kind-progressive_workflow/instance-zooa6r9w" follows:
=========>
[2026-03-27T10:58:13+0100] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2026-03-27T10:58:13+0100] [MainThread] [I] [toil] Running Toil version 9.3.0-b1c1536aaedac21a09dc3b4c094692a929e13b28 on host sydney.
[2026-03-27T10:58:13+0100] [MainThread] [I] [toil.worker] Working on job 'progressive_workflow' kind-progressive_workflow/instance-zooa6r9w v1
[2026-03-27T10:58:17+0100] [MainThread] [C] [toil.worker] Worker crashed with traceback:
Traceback (most recent call last):
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/site-packages/toil/worker.py", line 555, in workerScript
job = Job.loadJob(job_store, jobDesc)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/site-packages/toil/job.py", line 3209, in loadJob
user_module = cls._loadUserModule(user_module_descriptor)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/site-packages/toil/job.py", line 2774, in _loadUserModule
result = userModule.load()
^^^^^^^^^^^^^^^^^
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/site-packages/toil/resource.py", line 662, in load
return importlib.import_module(module.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 1204, in _gcd_import
File "", line 1176, in _find_and_load
File "", line 1147, in _find_and_load_unlocked
File "", line 690, in _load_unlocked
File "", line 940, in exec_module
File "", line 241, in _call_with_frames_removed
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/site-packages/cactus/progressive/cactus_progressive.py", line 20, in
from toil.lib.bioio import getTempFile
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/site-packages/toil/lib/bioio.py", line 18, in
from toil.test import get_temp_file
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/site-packages/toil/test/init.py", line 427, in
_skip_online() or not _aws_s3_avail() or not os.getenv("TOIL_AWS_KEYNAME"),
^^^^^^^^^^^^^^^
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/site-packages/toil/test/init.py", line 404, in _aws_s3_avail
or running_on_ec2()
^^^^^^^^^^^^^^^^
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/site-packages/toil/lib/aws/init.py", line 188, in running_on_ec2
urlopen(
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/urllib/request.py", line 216, in urlopen
return opener.open(url, data, timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/urllib/request.py", line 519, in open
response = self._open(req, data)
^^^^^^^^^^^^^^^^^^^^^
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/urllib/request.py", line 536, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/urllib/request.py", line 496, in _call_chain
result = func(*args)
^^^^^^^^^^^
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/urllib/request.py", line 1377, in http_open
return self.do_open(http.client.HTTPConnection, req)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/urllib/request.py", line 1352, in do_open
r = h.getresponse()
^^^^^^^^^^^^^^^
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/http/client.py", line 1415, in getresponse
response.begin()
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/http/client.py", line 330, in begin
version, status, reason = self._read_status()
^^^^^^^^^^^^^^^^^^^
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/http/client.py", line 291, in _read_status
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/soft/system/software/Miniconda3/202411/envs/cactus/lib/python3.11/socket.py", line 718, in readinto
return self._sock.recv_into(b)
^^^^^^^^^^^^^^^^^^^^^^^
ConnectionResetError: [Errno 104] Connection reset by peer

It seems to be related with an url to one of the libraries?

My cactus command is the following: cactus /pathto/js /pathto/myfavGenomes.txt /pathto/myfavGenomes.hal --binariesMode local

I would appreciate any help on this. Many thanks!

[glennhickey]

Yeah, looks like Cactus isn't well installed. You need to install it in a virtualenv (as per the installation instructions) for it to work, from your logs it looks like you have it in conda. If virtualenv isn't an option, you can try running directly from Docker.