atice
commented
1 year ago Hi!
It looks like you are providing config.py with metadata.tsv instead of the input_metadata.tsv. Check the documentation again for more information. Let us know if this solves the issue.
Alex
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From: Carlos Fernandez-Lozano @.> Sent: Friday, June 9, 2023 3:22:50 AM To: TheBrownLab/PhyloFisher @.> Cc: Subscribed @.***> Subject: [TheBrownLab/PhyloFisher] Non-reproducible baseline example (Issue #82)
Hi!
I tried to reproduce the baseline example using the docker image 1.2.8--pyhdfd78af_0 (and others) available at https://bioconda.github.io/recipes/phylofisher/README.htmlhttps://secure-web.cisco.com/1lPtm9pb6t_U-NvudOhRs553vV1S_cNciQScyjA9n5M1MdMEX5EYN97Yh0NNk4Wd0UlpuJpHhHCwuh_Cb9nvVonwI2oGr_cZahrU7ityjXYD3T4h7USIbiv4MGXsVkjSZwMPX6wUeEj-bOypiU_nTCLe-sYBOXkcVh69IW36e9aGgbIU7pVj3HytYipQqjZRsn7-6qfJCk_x9xqyyexhu_Z991qUUrSPA21E36ylIkFhms0dWJrjXbtK2gwUgeFyk9_2euqUe5CDu4jUyfo-TC-6yN-a6oXnc9upeF0Q_WkW-fheUp4LSPlVldlGWqf-s/https%3A%2F%2Fbioconda.github.io%2Frecipes%2Fphylofisher%2FREADME.html but:
- explore_database.py was able to parse the metadata file
- config.py raise an illegal character error
`docker run -it --rm quay.io/biocontainers/phylofisher:1.2.8--pyhdfd78af_0 /bin/sh sh-5.0# wget https://ndownloader.figshare.com/files/29093409https://secure-web.cisco.com/1XrzlyzmYEYRqysT0kiIsDb9jztQCNyCKedWKWSUIlHj87EIXHJCPkssR8_nE_VYLcQTikrjiUuVDCPvnmZgSy3IsauzeW2lIXxyzgNB7Nou4GJC_cHAoDZ7NTNWpE5W8G0PbyRJ-LpAWurJdjlgzyvQNoZws6W9F9IcYead7pBErhR2E5KAJgNfJeF_S79mzhOAf8HutcHAPJkA1EnY02-XK4cEhkMavAjz0xnhLcUu400fG6_TFAJloXA-RLcYIb-nl-XO9KuJvJ2NQ4mbpLZP0XGgiI6Tfu17e9_wb_3BIYuD0UxRtsOEErnPdkRVb/https%3A%2F%2Fndownloader.figshare.com%2Ffiles%2F29093409 Saving to: ‘29093409’
29093409 100%[============================================================================>] 2.15G 10.2MB/s in 3m 18s
2023-06-09 08:14:31 (11.1 MB/s) - ‘29093409’ saved [2305051083/2305051083]
sh-5.0# tar -xzf 29093409 sh-5.0# cd PhyloFisherDatabase_v1.0/ sh-5.0# explore_database.py -d database/ -t Higher Taxonomy Organisms Alveida 1 Alveolata 27 Amoebozoa 42 Ancyromonadida 4 CRuMs 4 Chloroplastida 17 Cryptista 9 Discoba 19 Glaucophyta 4 Haptista 14 Hemimastigophora 2 Malawimonadida 3 Metamonada 10 Obazoa 49 Picozoa 1 Rhizaria 18 Rhodelphidia 2 Rhodophyta 15 Stramenopiles 60 Telonemia 3 sh-5.0# config.py -d database/ -i database/metadata.tsv ERROR: illegal character in Higher Taxonomy`
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Hi!
I tried to reproduce the baseline example using the docker image 1.2.8--pyhdfd78af_0 (and others) available at https://bioconda.github.io/recipes/phylofisher/README.html but:
`docker run -it --rm quay.io/biocontainers/phylofisher:1.2.8--pyhdfd78af_0 /bin/sh sh-5.0# wget https://ndownloader.figshare.com/files/29093409 Saving to: ‘29093409’
29093409 100%[============================================================================>] 2.15G 10.2MB/s in 3m 18s
2023-06-09 08:14:31 (11.1 MB/s) - ‘29093409’ saved [2305051083/2305051083]
sh-5.0# tar -xzf 29093409 sh-5.0# cd PhyloFisherDatabase_v1.0/ sh-5.0# explore_database.py -d database/ -t Higher Taxonomy Organisms Alveida 1 Alveolata 27 Amoebozoa 42 Ancyromonadida 4 CRuMs 4 Chloroplastida 17 Cryptista 9 Discoba 19 Glaucophyta 4 Haptista 14 Hemimastigophora 2 Malawimonadida 3 Metamonada 10 Obazoa 49 Picozoa 1 Rhizaria 18 Rhodelphidia 2 Rhodophyta 15 Stramenopiles 60 Telonemia 3 sh-5.0# config.py -d database/ -i database/metadata.tsv ERROR: illegal character in Higher Taxonomy`