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bioexcel / biobb_pmx

Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.
https://mmb.irbbarcelona.org/biobb/
Apache License 2.0
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PMX_WF env yaml fails #8

Closed bdGut333eee closed 1 year ago

bdGut333eee commented 1 year ago

Hello I have tried to run conda env create -f conda_env/environment.yml from the mutation tutorial. I have tried on several computer: MacBook Pro, Windows 10 WSL2. It just returns "Killed". Am I missing another config?

gbayarri commented 1 year ago

Hi,

We would need more information. Is your anaconda installation running properly? Have you tried to create other environments with this same conda installation?

Which MacBook Pro (macOS) are you using? We have recently tested this WF in macOS 11 (Intel) and macOS 12 (M1) without problems.

Can you provide all the logs the terminal gives you?

bdGut333eee commented 1 year ago

Hi, on the pc (windows 10, WSL2, Ubuntu 20.04.5 LTS-fully updated) out of the box with not additional configuration changes such as memory allocation, etc)) I could load a run all the other environments for the other BioBB_wf tutorials. So, I assume the I believe the anaconda on this set up and running correctly. From the terminal here, following the tutorial at: https://mmb.irbbarcelona.org/biobb/workflows/tutorials/pmx with this command, conda env create -f conda_env/environment.yml, collecting package metadata(repodata.json):done solving environment: killed

bdGut333eee commented 1 year ago

bguthrie@DESKTOP-SURMM5L:~/biobb_wf_pmx_tutorial$ conda env create -f conda_env/environment.yml --debug DEBUG conda.gateways.logging:set_verbosity(236): verbosity set to 2 DEBUG conda.core.solve:solve_final_state(265): solving prefix /home/bguthrie/anaconda3/envs/biobb_wf_pmx_tutorial specs_to_remove: frozenset() specs_to_add: frozenset({MatchSpec("conda"), MatchSpec("jupyter_contrib_nbextensions"), MatchSpec("biobb_analysis==3.8.0"), MatchSpec("ipywidgets==7.6.6"), MatchSpec("biobb_gromacs==3.8.0"), MatchSpec("plotly"), MatchSpec("biobb_pmx==3.8.1"), MatchSpec("nb_conda_kernels")}) prune: False Collecting package metadata (repodata.json): ...working... DEBUG conda.core.package_cache_data:_check_writable(268): package cache directory '/home/bguthrie/anaconda3/pkgs' writable: True DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://conda.anaconda.org/conda-forge/linux-64/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/497deca9.json DEBUG urllib3.connectionpool:_new_conn(813): Starting new HTTPS connection (1): conda.anaconda.org:443 DEBUG urllib3.connectionpool:_make_request(393): https://conda.anaconda.org:443 "GET /conda-forge/linux-64/repodata.json HTTP/1.1" 200 None DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /conda-forge/linux-64/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive If-Modified-Since: Sat, 03 Dec 2022 14:47:56 GMT If-None-Match: W/"88a9a471a83683036f08b299f0c0e19a"

<<HTTPS 200 OK < Age: 1135 < Cache-Control: public, max-age=1200 < CF-Cache-Status: HIT < CF-Ray: 773d6f1728f22a3c-ORD < Content-Encoding: gzip < Content-Type: application/json < Date: Sat, 03 Dec 2022 15:46:14 GMT < ETag: W/"6bbde2b0f2e0ff0e4d3b5cebe8af5c48" < Expires: Sat, 03 Dec 2022 16:06:14 GMT < Last-Modified: Sat, 03 Dec 2022 15:26:48 GMT < Server: cloudflare < Set-Cookie: __cf_bm=Jm.laHnUFe_vfhDNBrinonqCzyikZt8jXvze3DSmGOw-1670082374-0-AUj2AN5MuILzE+7w8nyzkslm/FV08LBEXyq/RxFxp/h7s6yKnwyQCM+vjj8rZeTfDwaZYdaGEPMeb3wQMwLc/kYZjZTz33bVCm9d+1ZIhhVT; path=/; expires=Sat, 03-Dec-22 16:16:14 GMT; domain=.anaconda.org; HttpOnly; Secure; SameSite=None < Transfer-Encoding: chunked < Vary: Accept-Encoding < x-amz-id-2: Oc+VSDhXGU/AEih8sCTb4BlxRuOcURsQN7/N6irU7Kb657wV7qvOp9f0opFjOORLFo/MA+Z1eS0= < x-amz-request-id: 6EGKB91DTGD4Y6A4 < x-amz-version-id: null < Connection: keep-alive < Elapsed: 00:00.414922

{ "info": { "subdir": "linux-64" }, "packages": { "21cmfast-3.0.2-py36h1af98f8_1.tar.bz2": { "build": "py36h1af98f8_1", "build_number": 1, "depends": [ "_openmp_mutex >=4.5", "astropy >=2.0", "cached-

DEBUG conda.core.subdir_data:_pickle_me(317): Saving pickled state for https://conda.anaconda.org/conda-forge/linux-64/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/497deca9.q DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://conda.anaconda.org/conda-forge/noarch/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/09cdf8bf.json DEBUG urllib3.connectionpool:_make_request(393): https://conda.anaconda.org:443 "GET /conda-forge/noarch/repodata.json HTTP/1.1" 200 None DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /conda-forge/noarch/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive Cookie: __cf_bm=Jm.laHnUFe_vfhDNBrinonqCzyikZt8jXvze3DSmGOw-1670082374-0-AUj2AN5MuILzE+7w8nyzkslm/FV08LBEXyq/RxFxp/h7s6yKnwyQCM+vjj8rZeTfDwaZYdaGEPMeb3wQMwLc/kYZjZTz33bVCm9d+1ZIhhVT If-Modified-Since: Sat, 03 Dec 2022 14:36:03 GMT If-None-Match: W/"0f8b68e0460bbab5ff4a25a229c9cab2"

<<HTTPS 200 OK < Age: 2375 < Cache-Control: public, max-age=1200 < CF-Cache-Status: HIT < CF-Ray: 773d70bb4b692a3c-ORD < Content-Encoding: gzip < Content-Type: application/json < Date: Sat, 03 Dec 2022 15:47:21 GMT < ETag: W/"cc18cc539823ecf8d02e285cc83cffbf" < Expires: Sat, 03 Dec 2022 16:07:21 GMT < Last-Modified: Sat, 03 Dec 2022 15:07:04 GMT < Server: cloudflare < Transfer-Encoding: chunked < Vary: Accept-Encoding < x-amz-id-2: MxrhBCeIco23bARSWoqPL7xKQDH734dxSSbWlBsUTLdekl+/BhYaNqCWlm+IhAJHEScaY69IGek= < x-amz-request-id: ANW9WD8EBXSFEYXP < x-amz-version-id: null < Connection: keep-alive < Elapsed: 00:00.060068

{ "info": { "subdir": "noarch" }, "packages": { "_current_repodata_hack_gcc_linux_64_75-0.0.1-0.tar.bz2": { "build": "0", "build_number": 0, "depends": [ "gcc_linux-64 7.5.*" ], "license": "LicenseRef-OTH

DEBUG conda.core.subdir_data:_pickle_me(317): Saving pickled state for https://conda.anaconda.org/conda-forge/noarch/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/09cdf8bf.q DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://conda.anaconda.org/bioconda/linux-64/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/ffeee55f.json DEBUG urllib3.connectionpool:_make_request(393): https://conda.anaconda.org:443 "GET /bioconda/linux-64/repodata.json HTTP/1.1" 304 0 DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /bioconda/linux-64/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive Cookie: __cf_bm=Jm.laHnUFe_vfhDNBrinonqCzyikZt8jXvze3DSmGOw-1670082374-0-AUj2AN5MuILzE+7w8nyzkslm/FV08LBEXyq/RxFxp/h7s6yKnwyQCM+vjj8rZeTfDwaZYdaGEPMeb3wQMwLc/kYZjZTz33bVCm9d+1ZIhhVT If-Modified-Since: Sat, 03 Dec 2022 01:27:36 GMT If-None-Match: W/"b57a947f36d9cb49386297a34639c13e-4"

<<HTTPS 304 Not Modified < Age: 50661 < Cache-Control: public, max-age=1200 < CF-Cache-Status: HIT < CF-Ray: 773d715f0e512a3c-ORD < Date: Sat, 03 Dec 2022 15:47:47 GMT < ETag: "b57a947f36d9cb49386297a34639c13e-4" < Expires: Sat, 03 Dec 2022 16:07:47 GMT < Last-Modified: Sat, 03 Dec 2022 01:27:36 GMT < Server: cloudflare < Vary: Accept-Encoding < x-amz-id-2: vFklTtppYM50YxXyaPO5VqbVCr67t9z9r7K+EkB3NjpNh3+QxLo4nED4TtXtgPnaXL7l70iL/Ms= < x-amz-request-id: AJP664Z7X81S688E < x-amz-version-id: null < Connection: keep-alive < Elapsed: 00:00.062270

DEBUG conda.core.subdir_data:_load(293): 304 NOT MODIFIED for 'https://conda.anaconda.org/bioconda/linux-64/repodata.json'. Updating mtime and loading from disk DEBUG conda.core.subdir_data:_read_pickled(357): found pickle file /home/bguthrie/anaconda3/pkgs/cache/ffeee55f.q DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://conda.anaconda.org/bioconda/noarch/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/2a957770.json DEBUG urllib3.connectionpool:_make_request(393): https://conda.anaconda.org:443 "GET /bioconda/noarch/repodata.json HTTP/1.1" 304 0 DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /bioconda/noarch/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive Cookie: __cf_bm=Jm.laHnUFe_vfhDNBrinonqCzyikZt8jXvze3DSmGOw-1670082374-0-AUj2AN5MuILzE+7w8nyzkslm/FV08LBEXyq/RxFxp/h7s6yKnwyQCM+vjj8rZeTfDwaZYdaGEPMeb3wQMwLc/kYZjZTz33bVCm9d+1ZIhhVT If-Modified-Since: Sat, 03 Dec 2022 14:28:34 GMT If-None-Match: W/"c4aa049a94fef698f7fe61950c684bcb-4"

<<HTTPS 304 Not Modified < Cache-Control: public, max-age=1200 < CF-Cache-Status: HIT < CF-Ray: 773d716afcba2a3c-ORD < Date: Sat, 03 Dec 2022 15:47:49 GMT < ETag: "c4aa049a94fef698f7fe61950c684bcb-4" < Expires: Sat, 03 Dec 2022 16:07:49 GMT < Last-Modified: Sat, 03 Dec 2022 14:28:34 GMT < Server: cloudflare < Vary: Accept-Encoding < x-amz-id-2: oV4U2kepMhmsFZdV3BjEFpVrZqYVjhZ5MZEyg0AM/MpmjwlcKFhfExUzp5L8NNwx81/XwPljOI4= < x-amz-request-id: Y6R8DMMQMX6J836B < x-amz-version-id: null < Connection: keep-alive < Elapsed: 00:00.105419

DEBUG conda.core.subdir_data:_load(293): 304 NOT MODIFIED for 'https://conda.anaconda.org/bioconda/noarch/repodata.json'. Updating mtime and loading from disk DEBUG conda.core.subdir_data:_read_pickled(357): found pickle file /home/bguthrie/anaconda3/pkgs/cache/2a957770.q DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://repo.anaconda.com/pkgs/main/linux-64/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/47929eba.json DEBUG urllib3.connectionpool:_new_conn(813): Starting new HTTPS connection (1): repo.anaconda.com:443 DEBUG urllib3.connectionpool:_make_request(393): https://repo.anaconda.com:443 "GET /pkgs/main/linux-64/repodata.json HTTP/1.1" 304 0 DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /pkgs/main/linux-64/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive If-Modified-Since: Sat, 03 Dec 2022 00:13:30 GMT If-None-Match: W/"2c24fef494030b498e59f430dc68dbfa"

<<HTTPS 304 Not Modified < Age: 56018 < Cache-Control: public, max-age=30 < CF-Cache-Status: HIT < CF-RAY: 773d717b6d322249-ORD < Date: Sat, 03 Dec 2022 15:47:52 GMT < ETag: "2c24fef494030b498e59f430dc68dbfa" < Expires: Sat, 03 Dec 2022 15:48:22 GMT < Last-Modified: Sat, 03 Dec 2022 00:13:30 GMT < Server: cloudflare < Set-Cookie: __cf_bm=1wCPR42wiDLlJ5EhP7WyMoBYvldEZAW7n8j4GoCpPqs-1670082472-0-AVuV7WU1KHlMLcscmexcHsWSI0xi9byEZ6uKRCrRYDv1wFoZdevSm1hi5UJ99OWz4qZCMxOVybfV/AeTDr1bAQk=; path=/; expires=Sat, 03-Dec-22 16:17:52 GMT; domain=.anaconda.com; HttpOnly; Secure; SameSite=None < Vary: Accept-Encoding < x-amz-id-2: sKgWVxpb3hoRBjZy3oJluOD+NKmxzjms68R4IRioEQ9i0jY4B9oD1FiI4/paQHXzovUYR0acio0= < x-amz-request-id: 8D9WAF9BA3PP7DBW < x-amz-version-id: WgCH7Zg_Dv3mM9AYLjSEQMXvjvioTNAL < Connection: keep-alive < Elapsed: 00:00.242708

DEBUG conda.core.subdir_data:_load(293): 304 NOT MODIFIED for 'https://repo.anaconda.com/pkgs/main/linux-64/repodata.json'. Updating mtime and loading from disk DEBUG conda.core.subdir_data:_read_pickled(357): found pickle file /home/bguthrie/anaconda3/pkgs/cache/47929eba.q DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://repo.anaconda.com/pkgs/main/noarch/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/3e39a7aa.json DEBUG urllib3.connectionpool:_make_request(393): https://repo.anaconda.com:443 "GET /pkgs/main/noarch/repodata.json HTTP/1.1" 304 0 DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /pkgs/main/noarch/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive Cookie: __cf_bm=1wCPR42wiDLlJ5EhP7WyMoBYvldEZAW7n8j4GoCpPqs-1670082472-0-AVuV7WU1KHlMLcscmexcHsWSI0xi9byEZ6uKRCrRYDv1wFoZdevSm1hi5UJ99OWz4qZCMxOVybfV/AeTDr1bAQk= If-Modified-Since: Tue, 29 Nov 2022 16:03:07 GMT If-None-Match: W/"6e04ba60f4112b8b66a702155b149789"

<<HTTPS 304 Not Modified < Age: 344657 < Cache-Control: public, max-age=30 < CF-Cache-Status: HIT < CF-RAY: 773d717fcb922249-ORD < Date: Sat, 03 Dec 2022 15:47:52 GMT < ETag: "6e04ba60f4112b8b66a702155b149789" < Expires: Sat, 03 Dec 2022 15:48:22 GMT < Last-Modified: Tue, 29 Nov 2022 16:03:07 GMT < Server: cloudflare < Vary: Accept-Encoding < x-amz-id-2: XOcwXl6k5xoUe4CZu165pl5DxNRL491AX2Bo9oR0kKVB7C17o3jsWbDG9NiZYZJdTx5oBpaxcqA= < x-amz-request-id: GVVB079XW40XCD4Q < x-amz-version-id: Q4_RUh4DCA9G9p4t7FVjTf1kw3tFux.. < Connection: keep-alive < Elapsed: 00:00.044299

DEBUG conda.core.subdir_data:_load(293): 304 NOT MODIFIED for 'https://repo.anaconda.com/pkgs/main/noarch/repodata.json'. Updating mtime and loading from disk DEBUG conda.core.subdir_data:_read_pickled(357): found pickle file /home/bguthrie/anaconda3/pkgs/cache/3e39a7aa.q DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://repo.anaconda.com/pkgs/r/linux-64/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/2ce54b42.json DEBUG urllib3.connectionpool:_make_request(393): https://repo.anaconda.com:443 "GET /pkgs/r/linux-64/repodata.json HTTP/1.1" 304 0 DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /pkgs/r/linux-64/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive Cookie: __cf_bm=1wCPR42wiDLlJ5EhP7WyMoBYvldEZAW7n8j4GoCpPqs-1670082472-0-AVuV7WU1KHlMLcscmexcHsWSI0xi9byEZ6uKRCrRYDv1wFoZdevSm1hi5UJ99OWz4qZCMxOVybfV/AeTDr1bAQk= If-Modified-Since: Fri, 19 Aug 2022 21:27:15 GMT If-None-Match: W/"ba836b3510aff2e8ebc178babf77105f"

<<HTTPS 304 Not Modified < Age: 950613 < Cache-Control: public, max-age=30 < CF-Cache-Status: HIT < CF-RAY: 773d71814ddd2249-ORD < Date: Sat, 03 Dec 2022 15:47:53 GMT < ETag: "ba836b3510aff2e8ebc178babf77105f" < Expires: Sat, 03 Dec 2022 15:48:23 GMT < Last-Modified: Fri, 19 Aug 2022 21:27:15 GMT < Server: cloudflare < Vary: Accept-Encoding < x-amz-id-2: PBJPlzKMi0uZpJ5SqSlg9Dc9z0V5XG2K0ehuJ+Dv3gM00Ug9XYkgdIFXYAWit4G/IbjQl4ULLIo= < x-amz-request-id: KZS85WPAEGKWKJZV < x-amz-version-id: opgyjS.I6OVxKa0A2_7J5ZzdMWds2WBO < Connection: keep-alive < Elapsed: 00:00.047171

DEBUG conda.core.subdir_data:_load(293): 304 NOT MODIFIED for 'https://repo.anaconda.com/pkgs/r/linux-64/repodata.json'. Updating mtime and loading from disk DEBUG conda.core.subdir_data:_read_pickled(357): found pickle file /home/bguthrie/anaconda3/pkgs/cache/2ce54b42.q DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://repo.anaconda.com/pkgs/r/noarch/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/4ea078d6.json DEBUG urllib3.connectionpool:_make_request(393): https://repo.anaconda.com:443 "GET /pkgs/r/noarch/repodata.json HTTP/1.1" 304 0 DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /pkgs/r/noarch/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive Cookie: __cf_bm=1wCPR42wiDLlJ5EhP7WyMoBYvldEZAW7n8j4GoCpPqs-1670082472-0-AVuV7WU1KHlMLcscmexcHsWSI0xi9byEZ6uKRCrRYDv1wFoZdevSm1hi5UJ99OWz4qZCMxOVybfV/AeTDr1bAQk= If-Modified-Since: Fri, 28 Oct 2022 15:33:23 GMT If-None-Match: W/"93476d5e7aa8d3f8bc0c04afafc94d26"

<<HTTPS 304 Not Modified < Age: 950599 < Cache-Control: public, max-age=30 < CF-Cache-Status: HIT < CF-RAY: 773d7182c8322249-ORD < Date: Sat, 03 Dec 2022 15:47:53 GMT < ETag: "93476d5e7aa8d3f8bc0c04afafc94d26" < Expires: Sat, 03 Dec 2022 15:48:23 GMT < Last-Modified: Fri, 28 Oct 2022 15:33:23 GMT < Server: cloudflare < Vary: Accept-Encoding < x-amz-id-2: D6P8KXSXC8gI7KOzlv0g5TO90T3ZSLUoRW6bdyxr5QPE9G0npKKYCVCJxA2sG2SUDPMQvTjcbxg= < x-amz-request-id: PRT6QH04241S05D7 < x-amz-version-id: gruUyeXEAuhL5g34laDjUOasClLQRFQz < Connection: keep-alive < Elapsed: 00:00.039491

DEBUG conda.core.subdir_data:_load(293): 304 NOT MODIFIED for 'https://repo.anaconda.com/pkgs/r/noarch/repodata.json'. Updating mtime and loading from disk DEBUG conda.core.subdir_data:_read_pickled(357): found pickle file /home/bguthrie/anaconda3/pkgs/cache/4ea078d6.q DEBUG conda.resolve:init(111): restricting to unmanageable packages: linux DEBUG conda.resolve:init(111): restricting to unmanageable packages: glibc DEBUG conda.resolve:init(111): restricting to unmanageable packages: unix DEBUG conda.resolve:init(111): restricting to unmanageable packages: archspec done Solving environment: ...working... DEBUG conda.resolve:get_reduced_index(575): Retrieving packages for:

<<HTTPS 304 Not Modified < Age: 3291 < Cache-Control: public, max-age=1200 < CF-Cache-Status: HIT < CF-Ray: 773da3b8cd051407-ORD < Date: Sat, 03 Dec 2022 16:22:10 GMT < ETag: "6bbde2b0f2e0ff0e4d3b5cebe8af5c48" < Expires: Sat, 03 Dec 2022 16:42:10 GMT < Last-Modified: Sat, 03 Dec 2022 15:26:48 GMT < Server: cloudflare < Set-Cookie: __cf_bm=g0nzfVAmX_CIryG6v6x5qQvY7dTWdziGgWWDvTUN7e0-1670084530-0-AdlvC5QT+VA94heinxWxv0FDVgsDdgtkBIKFAj1NK91/7yqa4BypnutiariAzeIJFLL5/jSyEYVYYr+ZtOQJ6kNTLBTjBIAFfDZGwhb/zSjF; path=/; expires=Sat, 03-Dec-22 16:52:10 GMT; domain=.anaconda.org; HttpOnly; Secure; SameSite=None < Vary: Accept-Encoding < x-amz-id-2: Oc+VSDhXGU/AEih8sCTb4BlxRuOcURsQN7/N6irU7Kb657wV7qvOp9f0opFjOORLFo/MA+Z1eS0= < x-amz-request-id: 6EGKB91DTGD4Y6A4 < x-amz-version-id: null < Connection: keep-alive < Elapsed: 00:00.980958

DEBUG conda.core.subdir_data:_load(293): 304 NOT MODIFIED for 'https://conda.anaconda.org/conda-forge/linux-64/repodata.json'. Updating mtime and loading from disk DEBUG conda.core.subdir_data:_read_pickled(357): found pickle file /home/bguthrie/anaconda3/pkgs/cache/497deca9.q DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://conda.anaconda.org/conda-forge/noarch/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/09cdf8bf.json DEBUG urllib3.connectionpool:_make_request(393): https://conda.anaconda.org:443 "GET /conda-forge/noarch/repodata.json HTTP/1.1" 200 None DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /conda-forge/noarch/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive Cookie: __cf_bm=g0nzfVAmX_CIryG6v6x5qQvY7dTWdziGgWWDvTUN7e0-1670084530-0-AdlvC5QT+VA94heinxWxv0FDVgsDdgtkBIKFAj1NK91/7yqa4BypnutiariAzeIJFLL5/jSyEYVYYr+ZtOQJ6kNTLBTjBIAFfDZGwhb/zSjF If-Modified-Since: Sat, 03 Dec 2022 15:07:04 GMT If-None-Match: W/"cc18cc539823ecf8d02e285cc83cffbf"

<<HTTPS 200 OK < Age: 1555 < Cache-Control: public, max-age=1200 < CF-Cache-Status: HIT < CF-Ray: 773da4159f0d1407-ORD < Content-Encoding: gzip < Content-Type: application/json < Date: Sat, 03 Dec 2022 16:22:24 GMT < ETag: W/"e77bd819d372dee4cb2998a4da0f69f5" < Expires: Sat, 03 Dec 2022 16:42:24 GMT < Last-Modified: Sat, 03 Dec 2022 15:55:52 GMT < Server: cloudflare < Transfer-Encoding: chunked < Vary: Accept-Encoding < x-amz-id-2: AB2GbEKWXAiWMNZQeNLNM62kZMTscpB3SsZPf2w/S8iYiqiYxH22H9cUFHSt7ENb/PEHsm4Koeg= < x-amz-request-id: 3T3WCRACYSGZVPHE < x-amz-version-id: null < Connection: keep-alive < Elapsed: 00:00.077087

{ "info": { "subdir": "noarch" }, "packages": { "_current_repodata_hack_gcc_linux_64_75-0.0.1-0.tar.bz2": { "build": "0", "build_number": 0, "depends": [ "gcc_linux-64 7.5.*" ], "license": "LicenseRef-OTH

DEBUG conda.core.subdir_data:_pickle_me(317): Saving pickled state for https://conda.anaconda.org/conda-forge/noarch/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/09cdf8bf.q DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://conda.anaconda.org/bioconda/linux-64/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/ffeee55f.json DEBUG urllib3.connectionpool:_make_request(393): https://conda.anaconda.org:443 "GET /bioconda/linux-64/repodata.json HTTP/1.1" 304 0 DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /bioconda/linux-64/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive Cookie: __cf_bm=g0nzfVAmX_CIryG6v6x5qQvY7dTWdziGgWWDvTUN7e0-1670084530-0-AdlvC5QT+VA94heinxWxv0FDVgsDdgtkBIKFAj1NK91/7yqa4BypnutiariAzeIJFLL5/jSyEYVYYr+ZtOQJ6kNTLBTjBIAFfDZGwhb/zSjF If-Modified-Since: Sat, 03 Dec 2022 01:27:36 GMT If-None-Match: W/"b57a947f36d9cb49386297a34639c13e-4"

<<HTTPS 304 Not Modified < Age: 52764 < Cache-Control: public, max-age=1200 < CF-Cache-Status: HIT < CF-Ray: 773da4b57bae1407-ORD < Date: Sat, 03 Dec 2022 16:22:50 GMT < ETag: "b57a947f36d9cb49386297a34639c13e-4" < Expires: Sat, 03 Dec 2022 16:42:50 GMT < Last-Modified: Sat, 03 Dec 2022 01:27:36 GMT < Server: cloudflare < Vary: Accept-Encoding < x-amz-id-2: vFklTtppYM50YxXyaPO5VqbVCr67t9z9r7K+EkB3NjpNh3+QxLo4nED4TtXtgPnaXL7l70iL/Ms= < x-amz-request-id: AJP664Z7X81S688E < x-amz-version-id: null < Connection: keep-alive < Elapsed: 00:00.090997

DEBUG conda.core.subdir_data:_load(293): 304 NOT MODIFIED for 'https://conda.anaconda.org/bioconda/linux-64/repodata.json'. Updating mtime and loading from disk DEBUG conda.core.subdir_data:_read_pickled(357): found pickle file /home/bguthrie/anaconda3/pkgs/cache/ffeee55f.q DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://conda.anaconda.org/bioconda/noarch/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/2a957770.json DEBUG urllib3.connectionpool:_make_request(393): https://conda.anaconda.org:443 "GET /bioconda/noarch/repodata.json HTTP/1.1" 304 0 DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /bioconda/noarch/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive Cookie: __cf_bm=g0nzfVAmX_CIryG6v6x5qQvY7dTWdziGgWWDvTUN7e0-1670084530-0-AdlvC5QT+VA94heinxWxv0FDVgsDdgtkBIKFAj1NK91/7yqa4BypnutiariAzeIJFLL5/jSyEYVYYr+ZtOQJ6kNTLBTjBIAFfDZGwhb/zSjF If-Modified-Since: Sat, 03 Dec 2022 14:28:34 GMT If-None-Match: W/"c4aa049a94fef698f7fe61950c684bcb-4"

<<HTTPS 304 Not Modified < Age: 2104 < Cache-Control: public, max-age=1200 < CF-Cache-Status: HIT < CF-Ray: 773da4c6ded41407-ORD < Date: Sat, 03 Dec 2022 16:22:53 GMT < ETag: "c4aa049a94fef698f7fe61950c684bcb-4" < Expires: Sat, 03 Dec 2022 16:42:53 GMT < Last-Modified: Sat, 03 Dec 2022 14:28:34 GMT < Server: cloudflare < Vary: Accept-Encoding < x-amz-id-2: oV4U2kepMhmsFZdV3BjEFpVrZqYVjhZ5MZEyg0AM/MpmjwlcKFhfExUzp5L8NNwx81/XwPljOI4= < x-amz-request-id: Y6R8DMMQMX6J836B < x-amz-version-id: null < Connection: keep-alive < Elapsed: 00:00.055352

DEBUG conda.core.subdir_data:_load(293): 304 NOT MODIFIED for 'https://conda.anaconda.org/bioconda/noarch/repodata.json'. Updating mtime and loading from disk DEBUG conda.core.subdir_data:_read_pickled(357): found pickle file /home/bguthrie/anaconda3/pkgs/cache/2a957770.q DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://repo.anaconda.com/pkgs/main/linux-64/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/47929eba.json DEBUG urllib3.connectionpool:_new_conn(813): Starting new HTTPS connection (1): repo.anaconda.com:443 DEBUG urllib3.connectionpool:_make_request(393): https://repo.anaconda.com:443 "GET /pkgs/main/linux-64/repodata.json HTTP/1.1" 304 0 DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /pkgs/main/linux-64/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive If-Modified-Since: Sat, 03 Dec 2022 00:13:30 GMT If-None-Match: W/"2c24fef494030b498e59f430dc68dbfa"

<<HTTPS 304 Not Modified < Age: 58106 < Cache-Control: public, max-age=30 < CF-Cache-Status: HIT < CF-RAY: 773da4ce0a27e24b-ORD < Date: Sat, 03 Dec 2022 16:22:54 GMT < ETag: "2c24fef494030b498e59f430dc68dbfa" < Expires: Sat, 03 Dec 2022 16:23:24 GMT < Last-Modified: Sat, 03 Dec 2022 00:13:30 GMT < Server: cloudflare < Set-Cookie: __cf_bm=jYNCY4TvvH2MNoliEK20QcWBR7yA9Eau5p7ZuMwYC5Y-1670084574-0-AYRkO+aZ4AwT2h9cUcXRNXIzMMrg2lpgq+44kSakICHCTvCqr1bn+AI9uVuO3zMbWf+fVxaX4Twzg6mWC0Rzt6g=; path=/; expires=Sat, 03-Dec-22 16:52:54 GMT; domain=.anaconda.com; HttpOnly; Secure; SameSite=None < Vary: Accept-Encoding < x-amz-id-2: sKgWVxpb3hoRBjZy3oJluOD+NKmxzjms68R4IRioEQ9i0jY4B9oD1FiI4/paQHXzovUYR0acio0= < x-amz-request-id: 8D9WAF9BA3PP7DBW < x-amz-version-id: WgCH7Zg_Dv3mM9AYLjSEQMXvjvioTNAL < Connection: keep-alive < Elapsed: 00:00.334020

DEBUG conda.core.subdir_data:_load(293): 304 NOT MODIFIED for 'https://repo.anaconda.com/pkgs/main/linux-64/repodata.json'. Updating mtime and loading from disk DEBUG conda.core.subdir_data:_read_pickled(357): found pickle file /home/bguthrie/anaconda3/pkgs/cache/47929eba.q DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://repo.anaconda.com/pkgs/main/noarch/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/3e39a7aa.json DEBUG urllib3.connectionpool:_make_request(393): https://repo.anaconda.com:443 "GET /pkgs/main/noarch/repodata.json HTTP/1.1" 304 0 DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /pkgs/main/noarch/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive Cookie: __cf_bm=jYNCY4TvvH2MNoliEK20QcWBR7yA9Eau5p7ZuMwYC5Y-1670084574-0-AYRkO+aZ4AwT2h9cUcXRNXIzMMrg2lpgq+44kSakICHCTvCqr1bn+AI9uVuO3zMbWf+fVxaX4Twzg6mWC0Rzt6g= If-Modified-Since: Tue, 29 Nov 2022 16:03:07 GMT If-None-Match: W/"6e04ba60f4112b8b66a702155b149789"

<<HTTPS 304 Not Modified < Age: 346747 < Cache-Control: public, max-age=30 < CF-Cache-Status: HIT < CF-RAY: 773da4dc5bf6e24b-ORD < Date: Sat, 03 Dec 2022 16:22:56 GMT < ETag: "6e04ba60f4112b8b66a702155b149789" < Expires: Sat, 03 Dec 2022 16:23:26 GMT < Last-Modified: Tue, 29 Nov 2022 16:03:07 GMT < Server: cloudflare < Vary: Accept-Encoding < x-amz-id-2: XOcwXl6k5xoUe4CZu165pl5DxNRL491AX2Bo9oR0kKVB7C17o3jsWbDG9NiZYZJdTx5oBpaxcqA= < x-amz-request-id: GVVB079XW40XCD4Q < x-amz-version-id: Q4_RUh4DCA9G9p4t7FVjTf1kw3tFux.. < Connection: keep-alive < Elapsed: 00:00.046687

DEBUG conda.core.subdir_data:_load(293): 304 NOT MODIFIED for 'https://repo.anaconda.com/pkgs/main/noarch/repodata.json'. Updating mtime and loading from disk DEBUG conda.core.subdir_data:_read_pickled(357): found pickle file /home/bguthrie/anaconda3/pkgs/cache/3e39a7aa.q DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://repo.anaconda.com/pkgs/r/linux-64/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/2ce54b42.json DEBUG urllib3.connectionpool:_make_request(393): https://repo.anaconda.com:443 "GET /pkgs/r/linux-64/repodata.json HTTP/1.1" 304 0 DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /pkgs/r/linux-64/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive Cookie: __cf_bm=jYNCY4TvvH2MNoliEK20QcWBR7yA9Eau5p7ZuMwYC5Y-1670084574-0-AYRkO+aZ4AwT2h9cUcXRNXIzMMrg2lpgq+44kSakICHCTvCqr1bn+AI9uVuO3zMbWf+fVxaX4Twzg6mWC0Rzt6g= If-Modified-Since: Fri, 19 Aug 2022 21:27:15 GMT If-None-Match: W/"ba836b3510aff2e8ebc178babf77105f"

<<HTTPS 304 Not Modified < Age: 1622600 < Cache-Control: public, max-age=30 < CF-Cache-Status: HIT < CF-RAY: 773da4dd3d0ee24b-ORD < Date: Sat, 03 Dec 2022 16:22:56 GMT < ETag: "ba836b3510aff2e8ebc178babf77105f" < Expires: Sat, 03 Dec 2022 16:23:26 GMT < Last-Modified: Fri, 19 Aug 2022 21:27:15 GMT < Server: cloudflare < Vary: Accept-Encoding < x-amz-id-2: +KtR967NdF71FB9AeJ15EmUnCJSQ/ypK0MtA+cM6p0KNQaosQZxnohZigZUBc/iaELvajSMzLjA= < x-amz-request-id: 6K7C4Y1JX9F42R4R < x-amz-version-id: opgyjS.I6OVxKa0A2_7J5ZzdMWds2WBO < Connection: keep-alive < Elapsed: 00:00.044204

DEBUG conda.core.subdir_data:_load(293): 304 NOT MODIFIED for 'https://repo.anaconda.com/pkgs/r/linux-64/repodata.json'. Updating mtime and loading from disk DEBUG conda.core.subdir_data:_read_pickled(357): found pickle file /home/bguthrie/anaconda3/pkgs/cache/2ce54b42.q DEBUG conda.core.subdir_data:_load(274): Local cache timed out for https://repo.anaconda.com/pkgs/r/noarch/repodata.json at /home/bguthrie/anaconda3/pkgs/cache/4ea078d6.json DEBUG urllib3.connectionpool:_make_request(393): https://repo.anaconda.com:443 "GET /pkgs/r/noarch/repodata.json HTTP/1.1" 304 0 DEBUG conda.core.subdir_data:fetch_repodata_remote_request(530):

GET /pkgs/r/noarch/repodata.json HTTPS User-Agent: conda/22.9.0 requests/2.22.0 CPython/3.7.4 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.5 glibc/2.31 Accept: application/json Accept-Encoding: gzip, deflate, compress, identity Connection: keep-alive Cookie: __cf_bm=jYNCY4TvvH2MNoliEK20QcWBR7yA9Eau5p7ZuMwYC5Y-1670084574-0-AYRkO+aZ4AwT2h9cUcXRNXIzMMrg2lpgq+44kSakICHCTvCqr1bn+AI9uVuO3zMbWf+fVxaX4Twzg6mWC0Rzt6g= If-Modified-Since: Fri, 28 Oct 2022 15:33:23 GMT If-None-Match: W/"93476d5e7aa8d3f8bc0c04afafc94d26"

<<HTTPS 304 Not Modified < Age: 694155 < Cache-Control: public, max-age=30 < CF-Cache-Status: HIT < CF-RAY: 773da4deaee5e24b-ORD < Date: Sat, 03 Dec 2022 16:22:57 GMT < ETag: "93476d5e7aa8d3f8bc0c04afafc94d26" < Expires: Sat, 03 Dec 2022 16:23:27 GMT < Last-Modified: Fri, 28 Oct 2022 15:33:23 GMT < Server: cloudflare < Vary: Accept-Encoding < x-amz-id-2: D6P8KXSXC8gI7KOzlv0g5TO90T3ZSLUoRW6bdyxr5QPE9G0npKKYCVCJxA2sG2SUDPMQvTjcbxg= < x-amz-request-id: PRT6QH04241S05D7 < x-amz-version-id: gruUyeXEAuhL5g34laDjUOasClLQRFQz < Connection: keep-alive < Elapsed: 00:00.047203

DEBUG conda.core.subdir_data:_load(293): 304 NOT MODIFIED for 'https://repo.anaconda.com/pkgs/r/noarch/repodata.json'. Updating mtime and loading from disk DEBUG conda.core.subdir_data:_read_pickled(357): found pickle file /home/bguthrie/anaconda3/pkgs/cache/4ea078d6.q DEBUG conda.resolve:init(111): restricting to unmanageable packages: linux DEBUG conda.resolve:init(111): restricting to unmanageable packages: glibc DEBUG conda.resolve:init(111): restricting to unmanageable packages: unix DEBUG conda.resolve:init(111): restricting to unmanageable packages: archspec DEBUG conda.resolve:get_reduced_index(575): Retrieving packages for:

bdGut333eee commented 1 year ago

My wsl-2 has 5.32 gig of memory

bdGut333eee commented 1 year ago

Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: \ Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

Your python: python=3.10

If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that.

The following specifications were found to be incompatible with your system:

Your installed version is: 2.31

bdGut333eee commented 1 year ago

I decided that perhaps docker versions could be easier, the containers exit and don't start. Are there any youtubes or videos/docs that show a dicker version example?

PauAndrio commented 1 year ago

Hi @bdGut333eee I'm Pau Andrio another of the Biobb's developers.

Aside from docker specifics, you can find plenty of documentation, videos, slides and other resources on how to use Biobbs here: https://mmb.irbbarcelona.org/biobb/about/training

On other matters, the detail that caught my attention about your log files is your Python version (3.10). Bioconda does not provide support for Python 3.10: "Bioconda only supports python 2.7, 3.6, 3.7, 3.8 and 3.9.". On the other side, Anaconda default installation is 3.9 by default. Anaconda distributions Which led me to think that Python 3.10 was used deliberately, for some reason. Unfortunately, we can not provide support for that version yet.

To avoid future version conflicts for you and other users, We changed the environment file to also restrict the higher version of python. Commit URL

Please let us know how it works for you.

Pau

bdGut333eee commented 1 year ago

Hi PauAndrio, I tried the python version in the environment. It still failed. But it seems the python I have here is okay : bguthrie@DESKTOP-SURMM5L:~/biobb_wf_pmx_tutorial/conda_env$ python3 --version Python 3.8.10.

How could this be finding the wrong python version? Thanks for your help

PauAndrio commented 1 year ago

Hi @bdGut333eee,

I'm confused right now. Please could you, attach (please, do not copy it) here the log of creating the environment using the last conda_env/environment.yml file.

Regards, Pau

github-actions[bot] commented 1 year ago

This issue is stale because it has been open for 30 days with no activity. If there is no more activity in the following 14 days it will be automatically closed.

github-actions[bot] commented 1 year ago

This issue was closed because it has been inactive for 14 days since being marked as stale.