Error in rule operon_mapping

[ombystoma-young]

Error in rule operon_mapping during the first launch of the tool

[Mon Sep 25 14:09:08 2023]
rule operon_mapping:
    input: ecolihs/ecoli_hs.no_transposone.fna
    output: ecolihs/operonmapper_output/predicted_protein_sequences, ecolihs/operonmapper_output/list_of_operons
    jobid: 5
    reason: Missing output files: ecolihs/operonmapper_output/predicted_protein_sequences, ecolihs/operonmapper_output/list_of_operons; Input files updated by another job: ecolihs/ecoli_hs.no_transposone.fna
    resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/46d1fab59678c938bcc038d9eb72a332_
Reuse not availabe: no reuse file found at ecolihs/operonmapper_output/.reuse.

Collecting httpx (from -r scripts/operonmapper.requirements.txt (line 1))
  Obtaining dependency information for httpx from https://files.pythonhosted.org/packages/33/0d/d9ce469af019741c8999711d36b270ff992ceb1a0293f73f9f34fdf131e9/httpx-0.25.0-py3-none-any.whl.metadata
  Downloading httpx-0.25.0-py3-none-any.whl.metadata (7.6 kB)
Collecting certifi (from httpx->-r scripts/operonmapper.requirements.txt (line 1))
  Obtaining dependency information for certifi from https://files.pythonhosted.org/packages/4c/dd/2234eab22353ffc7d94e8d13177aaa050113286e93e7b40eae01fbf7c3d9/certifi-2023.7.22-py3-none-any.whl.metadata
  Downloading certifi-2023.7.22-py3-none-any.whl.metadata (2.2 kB)
Collecting httpcore<0.19.0,>=0.18.0 (from httpx->-r scripts/operonmapper.requirements.txt (line 1))
  Obtaining dependency information for httpcore<0.19.0,>=0.18.0 from https://files.pythonhosted.org/packages/ac/97/724afbb7925339f6214bf1fdb5714d1a462690466832bf8fb3fd497649f1/httpcore-0.18.0-py3-none-any.whl.metadata
  Downloading httpcore-0.18.0-py3-none-any.whl.metadata (18 kB)
Collecting idna (from httpx->-r scripts/operonmapper.requirements.txt (line 1))
  Using cached idna-3.4-py3-none-any.whl (61 kB)
Collecting sniffio (from httpx->-r scripts/operonmapper.requirements.txt (line 1))
  Using cached sniffio-1.3.0-py3-none-any.whl (10 kB)
Collecting anyio<5.0,>=3.0 (from httpcore<0.19.0,>=0.18.0->httpx->-r scripts/operonmapper.requirements.txt (line 1))
  Obtaining dependency information for anyio<5.0,>=3.0 from https://files.pythonhosted.org/packages/36/55/ad4de788d84a630656ece71059665e01ca793c04294c463fd84132f40fe6/anyio-4.0.0-py3-none-any.whl.metadata
  Downloading anyio-4.0.0-py3-none-any.whl.metadata (4.5 kB)
Collecting h11<0.15,>=0.13 (from httpcore<0.19.0,>=0.18.0->httpx->-r scripts/operonmapper.requirements.txt (line 1))
  Using cached h11-0.14.0-py3-none-any.whl (58 kB)
Downloading httpx-0.25.0-py3-none-any.whl (75 kB)
   ━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━ 41.0/75.7 kB 622.4 kB/s eta 0:00:01done!
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 75.7/75.7 kB 832.1 kB/s eta 0:00:00
Downloading httpcore-0.18.0-py3-none-any.whl (76 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 76.0/76.0 kB 624.0 kB/s eta 0:00:00
Using cached certifi-2023.7.22-py3-none-any.whl (158 kB)
Downloading anyio-4.0.0-py3-none-any.whl (83 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 83.1/83.1 kB 1.3 MB/s eta 0:00:00
done!
Examining upstream regions and training starts...Installing collected packages: sniffio, idna, h11, certifi, anyio, httpcore, httpx
Successfully installed anyio-4.0.0 certifi-2023.7.22 h11-0.14.0 httpcore-0.18.0 httpx-0.25.0 idna-3.4 sniffio-1.3.0
done!


Traceback (most recent call last):
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpcore/_exceptions.py", line 10, in map_exceptions
    yield
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpcore/_backends/sync.py", line 136, in write
    n = self._sock.send(buffer)
        ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/ssl.py", line 1210, in send
    return self._sslobj.write(data)
           ^^^^^^^^^^^^^^^^^^^^^^^^
TimeoutError: The write operation timed out

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpx/_transports/default.py", line 66, in map_httpcore_exceptions
    yield
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpx/_transports/default.py", line 228, in handle_request
    resp = self._pool.handle_request(req)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpcore/_sync/connection_pool.py", line 262, in handle_request
    raise exc
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpcore/_sync/connection_pool.py", line 245, in handle_request
    response = connection.handle_request(request)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpcore/_sync/connection.py", line 103, in handle_request
    return self._connection.handle_request(request)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpcore/_sync/http11.py", line 133, in handle_request
    raise exc
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpcore/_sync/http11.py", line 94, in handle_request
    self._send_request_body(**kwargs)
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpcore/_sync/http11.py", line 156, in _send_request_body
    self._send_event(event, timeout=timeout)
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpcore/_sync/http11.py", line 165, in _send_event
    self._network_stream.write(bytes_to_send, timeout=timeout)
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpcore/_backends/sync.py", line 133, in write
    with map_exceptions(exc_map):
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/contextlib.py", line 155, in __exit__
    self.gen.throw(typ, value, traceback)
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpcore/_exceptions.py", line 14, in map_exceptions
    raise to_exc(exc) from exc
httpcore.WriteTimeout: The write operation timed out

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/oxalotl/OantigenMiner/scripts/operonmapper.py", line 206, in <module>
    main()
  File "/home/oxalotl/OantigenMiner/scripts/operonmapper.py", line 201, in main
    return args.func(args)
           ^^^^^^^^^^^^^^^
  File "/home/oxalotl/OantigenMiner/scripts/operonmapper.py", line 109, in _find_operons
    args.task_id = _submit(fastafile, gfffile, args.description, args.email)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oxalotl/OantigenMiner/scripts/operonmapper.py", line 44, in _submit
    r = httpx.post(url=form_action, headers=headers, data=data)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpx/_api.py", line 304, in post
    return request(
           ^^^^^^^^
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpx/_api.py", line 100, in request
    return client.request(
           ^^^^^^^^^^^^^^^
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpx/_client.py", line 814, in request
    return self.send(request, auth=auth, follow_redirects=follow_redirects)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpx/_client.py", line 901, in send
    response = self._send_handling_auth(
               ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpx/_client.py", line 929, in _send_handling_auth
    response = self._send_handling_redirects(
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpx/_client.py", line 966, in _send_handling_redirects
    response = self._send_single_request(request)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpx/_client.py", line 1002, in _send_single_request
    response = transport.handle_request(request)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpx/_transports/default.py", line 227, in handle_request
    with map_httpcore_exceptions():
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/contextlib.py", line 155, in __exit__
    self.gen.throw(typ, value, traceback)
  File "/home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages/httpx/_transports/default.py", line 83, in map_httpcore_exceptions
    raise mapped_exc(message) from exc
httpx.WriteTimeout: The write operation timed out

[Mon Sep 25 14:09:17 2023]
Error in rule operon_mapping:
    jobid: 5
    input: ecolihs/ecoli_hs.no_transposone.fna
    output: ecolihs/operonmapper_output/predicted_protein_sequences, ecolihs/operonmapper_output/list_of_operons
    conda-env: /home/oxalotl/OantigenMiner/.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_
    shell:
        
        pip install -r scripts/operonmapper.requirements.txt
        python scripts/operonmapper.py             start ecolihs/ecoli_hs.no_transposone.fna             --email email@mail.com             --reuse             -o ecolihs/operonmapper_output
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

After the second launch:

[Mon Sep 25 14:22:40 2023]
rule operon_mapping:
    input: ecolihs/ecoli_hs.no_transposone.fna
    output: ecolihs/operonmapper_output/predicted_protein_sequences, ecolihs/operonmapper_output/list_of_operons
    jobid: 5
    reason: Missing output files: ecolihs/operonmapper_output/list_of_operons, ecolihs/operonmapper_output/predicted_protein_sequences
    resources: tmpdir=/tmp

Activating conda environment: .snakemake/conda/46d1fab59678c938bcc038d9eb72a332_


Requirement already satisfied: httpx in ./.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages (from -r scripts/operonmapper.requirements.txt (line 1)) (0.25.0)
Requirement already satisfied: certifi in ./.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages (from httpx->-r scripts/operonmapper.requirements.txt (line 1)) (2023.7.22)
Requirement already satisfied: httpcore<0.19.0,>=0.18.0 in ./.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages (from httpx->-r scripts/operonmapper.requirements.txt (line 1)) (0.18.0)
Requirement already satisfied: idna in ./.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages (from httpx->-r scripts/operonmapper.requirements.txt (line 1)) (3.4)
Requirement already satisfied: sniffio in ./.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages (from httpx->-r scripts/operonmapper.requirements.txt (line 1)) (1.3.0)
Requirement already satisfied: anyio<5.0,>=3.0 in ./.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages (from httpcore<0.19.0,>=0.18.0->httpx->-r scripts/operonmapper.requirements.txt (line 1)) (4.0.0)
Requirement already satisfied: h11<0.15,>=0.13 in ./.snakemake/conda/46d1fab59678c938bcc038d9eb72a332_/lib/python3.11/site-packages (from httpcore<0.19.0,>=0.18.0->httpx->-r scripts/operonmapper.requirements.txt (line 1)) (0.14.0)
Reuse not availabe: no reuse file found at ecolihs/operonmapper_output/.reuse.
Operon finder task submitted
	Task id: 3516577
Visit https://biocomputo.ibt.unam.mx/operon_mapper/out/out_3516577.html to manually check status
Task id was written to reuse file ecolihs/operonmapper_output/.reuse
Results are not ready yet, keep waiting (495.00sec passed)
Result is ready, it took only 494.9999999999893 seconds

Output files are:
	 ecolihs/operonmapper_output/.reuse
	 ecolihs/operonmapper_output/ORFs_coordinates
	 ecolihs/operonmapper_output/functional_descriptions
	 ecolihs/operonmapper_output/list_of_operons
	 ecolihs/operonmapper_output/operonic_gene_pairs
	 ecolihs/operonmapper_output/predicted_COGs
	 ecolihs/operonmapper_output/predicted_orfs
	 ecolihs/operonmapper_output/predicted_protein_sequences

[Mon Sep 25 14:31:33 2023]
Finished job 5.
2 of 11 steps (18%) done