DRAM 1.5.0 installation issues #330
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I ran to same issue. Apparently, DRAM-setup.py lines 123-127 were broken (release v1.5.0): this typo is fixed now with 9ff00c9, if you install from master. Thanks DRAM developers! |
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@tpall Did you have the same issue with the json.decoder bit too? |
No, after installing development version from Github, DRAM-setup.py script runs alright. I modified the last line of the environment.yaml file to install from Github. |
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I ran into this same issue. But when I tired manually editing the last line of the environment.yaml file, and re-installing with conda, I ended up with the following error message: >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
environment variables: populated config files : /datastore/tools/miniforge/.condarc An unexpected error has occurred. Conda has prepared the above report. If submitted, this report will be used by core maintainers to improve No report sent. To permanently opt-out, use |
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I ended up using the edit provided by @tpall in the environment.yaml, but I could not verify manually in the DRAM-setup.py whether the change took effect. Following the error above for conda, I tried re-creating the environment using mamba and it seems to have fixed the issue and I am setting up the databases from scratch just to make sure the entire setupworkflow is still proceeding. |
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Thank you for choosing to use DRAM. Unfortunately, at this time, we do not have the capacity to provide support for DRAM. We appreciate your understanding and encourage you to stay tuned for the release of DRAM2, expected in 2025. Best regards, DRAM dev team |
Hi, I've recently installed DRAM 1.5.0. using
wget https://raw.githubusercontent.com/WrightonLabCSU/DRAM/master/environment.yamlconda env create -f environment.yaml -n DRAMWhen I started
DRAM-setup.py prepare_databases --output_dir DRAM_data --uniref_loc uniref90.fasta.gzI had this error:
File "/home/karenhn/.conda/envs/DRAM/bin/DRAM-setup.py", line 124 set_db_locs_parser.add_argument('--camper_tar_gz_loc', default=None, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ SyntaxError: invalid syntax. Perhaps you forgot a comma?I found in the script for DRAM-setup.py there's two lines which have been transposed [there are two help=mmseqs2... lines following each other, and one should be after the --viral_loc line]. Once I fixed that, I ran the script again but got a different error:
Traceback (most recent call last): File "/home/karenhn/.conda/envs/DRAM/bin/DRAM-setup.py", line 187, in <module> args.func(**args_dict) File "/home/karenhn/.conda/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 5 31, in prepare_databases db_handler = DatabaseHandler(logger=LOGGER) File "/home/karenhn/.conda/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_handler.py", line 77, in __init__ self.load_config(config_loc) File "/home/karenhn/.conda/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_handler.py", line 82, in load_config conf = json.loads(open(config_file).read()) File "/home/karenhn/.conda/envs/DRAM/lib/python3.10/json/__init__.py", line 346, in loads return _default_decoder.decode(s) File "/home/karenhn/.conda/envs/DRAM/lib/python3.10/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/home/karenhn/.conda/envs/DRAM/lib/python3.10/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)I have no idea what this means! The database_files and the database_processing.log are empty, and I tried
DRAM-setup.py export_config --output_file fix_me.txtbut that file is empty too.Am I missing something obvious? Any help would be appreciated.
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