GISAID-download使用

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1. gisaid-download这个也折腾了大半天而且还没有解决，有一些原始参数我用不到，脚本硬要我提供，提供一个假的呢，它一直提示不对：

(base) xxx@xxx-ThinkCentre-E97:~$ pip install gisaid-download Collecting gisaid-download Downloading gisaid_download-0.3.0-py3-none-any.whl (17 kB) Collecting hpc-interact>=0.1.0 (from gisaid-download) Downloading hpc_interact-0.1.1-py3-none-any.whl (8.8 kB) Collecting pypdf>=3.1.0 (from gisaid-download) Downloading pypdf-4.3.1-py3-none-any.whl (295 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 295.8/295.8 kB 1.2 MB/s eta 0:00:00 Requirement already satisfied: typing_extensions>=4.0 in ./anaconda3/lib/python3.9/site-packages (from pypdf>=3.1.0->gisaid-download) (4.3.0) Installing collected packages: pypdf, hpc-interact, gisaid-download Successfully installed gisaid-download-0.3.0 hpc-interact-0.1.1 pypdf-4.3.1 [notice] A new release of pip is available: 22.0.3 -> 24.1.2 [notice] To update, run: pip install --upgrade pip (base) xxx@xxx-ThinkCentre-E97:~$ pip install --upgrade pip Requirement already satisfied: pip in ./anaconda3/lib/python3.9/site-packages (22.0.3) Collecting pip Downloading pip-24.2-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 1.2 MB/s eta 0:00:00 Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 22.0.3 Uninstalling pip-22.0.3: Successfully uninstalled pip-22.0.3 Successfully installed pip-22.1.2 (base) xxx@xxx-ThinkCentre-E97:~$ ls 13D_02M_2024Y_14h_09m_07s.tar.gz add_fasta clustalw GISAID_EpiFluDB_DAA.pdf Hmm3 OSCAR_RFV pydata-book sensors Vim-0.png 2023.08.07.v1.full.pdf AI clustalx group_1.tar.gz influenza Pictures Pytorch.ipynb snap Vscode 3RRR_4JHW.pse anaconda3 cmake 'HA_1 (copy).pse' jalview 'Prefusion (copy).xlsx' QUILT 'Sunlogin Files' xingzh 6ZV9.pse bin Desktop HA_1.pse Ligplot Prefusion.xlsx RecordPlayer-linux64 temp xpProteinDesign 9375_antibody_design_using_a_score_.pdf BPE.ipynb Documents 'HA (copy).pse' Literatures Protein_design RMSD Templates 证件照片 9454_carbonnovo_joint_design_of_pro.pdf CDHIT Downloads HA.pse NOTE Public RSV Understand ABACUS2 clash EasyConnect HJCB_.pdf obsutil pycharm s42003-023-05332-w.pdf Videos (base) xxx@xxx-ThinkCentre-E97:~$ vi gisaid_config.ini (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download --example -o gisaid/ Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 181, in getVariables return args.date,args.location,args.downloads,filetype_choices,meta_files,args.get_epi_set,args.epicov_dir,ssh_vars,args.wait,args.skip_local_update,followup_command,args.cluster_interact,custom_filters,example,args.outdir UnboundLocalError: local variable 'meta_files' referenced before assignment (base) xxx@xxx-ThinkCentre-E97:~$ vi /home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download --example -o gisaid/directory Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 181, in getVariables return args.date,args.location,args.downloads,filetype_choices,meta_files,args.get_epi_set,args.epicov_dir,ssh_vars,args.wait,args.skip_local_update,followup_command,args.cluster_interact,custom_filters,example,args.outdir UnboundLocalError: local variable 'meta_files' referenced before assignment (base) xxx@xxx-ThinkCentre-E97:~$ vi .gisaid_config (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config --example -o gisaid usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] gisaid_download_basic.py: error: unrecognized arguments: -c /home/xxx/.gisaid_config (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download --example -c ~/.gisaid_config -o gisaid usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] gisaid_download_basic.py: error: unrecognized arguments: -c /home/xxx/.gisaid_config (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid --start-date 1999-01-01 --end-state 2010-01-01 usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: unrecognized arguments: --start-date --end-state 2010-01-01 (base) xxx@xxx-ThinkCentre-E97:~$ sample-date='1999-01-01' sample-date=1999-01-01: command not found (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid 1999-01-01 2009-01-01 usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: unrecognized arguments: 2009-01-01 (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid 1999-01-01 Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 155, in getVariables followup_command = config["Misc"].get("followup_command") File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 963, in __getitem__ raise KeyError(key) KeyError: 'Misc' (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta 1999-01-01 usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta [1999-01-01] usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta { 
   1999-01-01} usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -h usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] Download EpiCoV sequences from GISAID. WARNING: By using this software you agree GISAID's Terms of Use and reaffirm your understanding of these terms. positional arguments: date: [YYYY-MM-DD] download sequences up to this date optional arguments: -h, --help show this help message and exit -V, --version show program's version number and exit --example writes out an example 'gisaid_config.ini' to `outdir` -o OUTDIR, --outdir OUTDIR outdir for example config file (default: current working directory) -f [FILETYPES ...], --filetypes [FILETYPES ...] space delimited list of files to download - options: ['fasta','meta','date_loc','patient','seq_tech','ackno','all','none'] -l [ ...], --location [ ...] space delimited list of state(s) for which data is desired (standard abbreviations allowed) -e, --episet request EPI_SET for selection after any downloads -d [DOWNLOADS], --downloads [DOWNLOADS] path to where you recieve downloads from your web browser -w EPICOV_DIR, --epicov_dir EPICOV_DIR local directory containing all related downloads - will be created if absent -b CLUSTER_EPICOV_DIR, --cluster_epicov_dir CLUSTER_EPICOV_DIR local directory containing all related downloads - will be created if absent -c CONFIG_FILE, --config_file CONFIG_FILE path to config (default: ./gisaid_config.ini) -q, --quick don't wait for user to hit enter between each step -s, --skip_local_update don't update local list of downloaded accessions (if unset, files will be retrieved from the cluster before the EpiCoV download steps) -n, --no_cluster don't interact trasfer any files to/from the cluster (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta date:1999-01-01 usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta date:[1999-01-01] usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta -date 2010-01-01 Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 155, in getVariables followup_command = config["Misc"].get("followup_command") File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 963, in __getitem__ raise KeyError(key) KeyError: 'Misc' (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta 2010-01-01 usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta date: [2010-01-01} usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta date: [2010-01-01] usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta [2010-01-01] usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta date:2010-01-01 usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta date: 2010-01-01 usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta 2010-01-01 usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download -c ~/.gisaid_config -o gisaid -f fasta date:2010-01-01 usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: the following arguments are required: date: [YYYY-MM-DD] (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download 2010-01-01 -c ~/.gisaid_config -o gisaid -f fasta Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 155, in getVariables followup_command = config["Misc"].get("followup_command") File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 963, in __getitem__ raise KeyError(key) KeyError: 'Misc' (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download date 2010-01-01 -c ~/.gisaid_config -o gisaid -f fasta usage: gisaid_download_basic.py [-h] [-V] [--example] [-o OUTDIR] [-f [FILETYPES ...]] [-l [...]] [-e] [-d [DOWNLOADS]] [-w EPICOV_DIR] [-b CLUSTER_EPICOV_DIR] [-c CONFIG_FILE] [-q] [-s] [-n] date: [YYYY-MM-DD] gisaid_download_basic.py: error: unrecognized arguments: 2010-01-01 (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download date:2010-01-01 -c ~/.gisaid_config -o gisaid -f fasta WARNING: `date` (date:2010-01-01) not in expected format 'YYYY-MM-DD' Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 155, in getVariables followup_command = config["Misc"].get("followup_command") File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 963, in __getitem__ raise KeyError(key) KeyError: 'Misc' (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download 2010-01-01 -c ~/.gisaid_config -o gisaid -f fasta Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 155, in getVariables followup_command = config["Misc"].get("followup_command") File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 963, in __getitem__ raise KeyError(key) KeyError: 'Misc' (base) xxx@xxx-ThinkCentre-E97:~$ vi ~/.gisaid.config (base) xxx@xxx-ThinkCentre-E97:~$ vi ~/.gisaid_config (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download 2010-01-01 -c ~/.gisaid_config -o gisaid -f fasta Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 156, in getVariables ssh_vars = get_elements(config,"SSH",("site","group","login_config","save_credentials")) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 89, in get_elements value = config[section][element] File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 963, in __getitem__ raise KeyError(key) KeyError: 'SSH' (base) xxx@xxx-ThinkCentre-E97:~$ mv .gisaid_config gisaid_config.ini (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download 2010-01-01 -c gisaid_config.ini -o gisaid -f fasta Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 156, in getVariables ssh_vars = get_elements(config,"SSH",("site","group","login_config","save_credentials")) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 89, in get_elements value = config[section][element] File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 963, in __getitem__ raise KeyError(key) KeyError: 'SSH' (base) xxx@xxx-ThinkCentre-E97:~$ vi gisaid_config.ini (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download 2010-01-01 -c gisaid_config.ini -o gisaid -f fasta Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 158, in getVariables path_vars = get_elements(config,"Paths",path_var_list) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 89, in get_elements value = config[section][element] File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 963, in __getitem__ raise KeyError(key) KeyError: 'Paths' (base) xxx@xxx-ThinkCentre-E97:~$ vi gisaid_config.ini (base) xxx@xxx-ThinkCentre-E97:~$ vi gisaid_config.ini (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download 2010-01-01 -c gisaid_config.ini -o gisaid -f fasta Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 152, in getVariables config.read(args.config_file) File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 697, in read self._read(fp, filename) File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 1070, in _read raise DuplicateSectionError(sectname, fpname, configparser.DuplicateSectionError: While reading from PosixPath('gisaid_config.ini') [line 26]: section 'Misc' already exists (base) xxx@xxx-ThinkCentre-E97:~$ vi gisaid_config.ini (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download 2010-01-01 -c gisaid_config.ini -o gisaid -f fasta Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 169, in getVariables raise AttributeError(f"Attribute `{var}` must be provided in config or arguments.") AttributeError: Attribute `epicov_dir` must be provided in config or arguments. (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download 2010-01-01 -c gisaid_config.ini -o gisaid -f fasta Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 169, in getVariables raise AttributeError(f"Attribute `{var}` must be provided in config or arguments.") AttributeError: Attribute `epicov_dir` must be provided in config or arguments. (base) xxx@xxx-ThinkCentre-E97:~$ vi gisaid_config.ini (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download 2010-01-01 -c gisaid_config.ini -o gisaid -f fasta Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 169, in getVariables raise AttributeError(f"Attribute `{var}` must be provided in config or arguments.") AttributeError: Attribute `cluster_epicov_dir` must be provided in config or arguments. (base) xxx@xxx-ThinkCentre-E97:~$ vi gisaid_config.ini (base) xxx@xxx-ThinkCentre-E97:~$ mv gisaid_config.ini gisaid_config_backup.ini (base) xxx@xxx-ThinkCentre-E97:~$ vi gisaid_config.ini (base) xxx@xxx-ThinkCentre-E97:~$ vi gisaid_config_backup.ini (base) xxx@xxx-ThinkCentre-E97:~$ vi gisaid_config.ini (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config.ini -o gisaid -f fasta Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 155, in getVariables followup_command = config["Misc"].get("followup_command") File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 963, in __getitem__ raise KeyError(key) KeyError: 'Misc' (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download --example -o gisaid/example Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 181, in getVariables return args.date,args.location,args.downloads,filetype_choices,meta_files,args.get_epi_set,args.epicov_dir,ssh_vars,args.wait,args.skip_local_update,followup_command,args.cluster_interact,custom_filters,example,args.outdir UnboundLocalError: local variable 'meta_files' referenced before assignment (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download --example -o gisaid/ Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 181, in getVariables return args.date,args.location,args.downloads,filetype_choices,meta_files,args.get_epi_set,args.epicov_dir,ssh_vars,args.wait,args.skip_local_update,followup_command,args.cluster_interact,custom_filters,example,args.outdir UnboundLocalError: local variable 'meta_files' referenced before assignment (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download --example -o gisaid Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 181, in getVariables return args.date,args.location,args.downloads,filetype_choices,meta_files,args.get_epi_set,args.epicov_dir,ssh_vars,args.wait,args.skip_local_update,followup_command,args.cluster_interact,custom_filters,example,args.outdir UnboundLocalError: local variable 'meta_files' referenced before assignment (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2000-01-01' Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 155, in getVariables followup_command = config["Misc"].get("followup_command") File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 963, in __getitem__ raise KeyError(key) KeyError: 'Misc' (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2000-01-01' -n Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 155, in getVariables followup_command = config["Misc"].get("followup_command") File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 963, in __getitem__ raise KeyError(key) KeyError: 'Misc' (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config.ini -o gisaid -f fasta -n Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 155, in getVariables followup_command = config["Misc"].get("followup_command") File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 963, in __getitem__ raise KeyError(key) KeyError: 'Misc' (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config_baacup.ini -o gisaid -f fasta -n Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 150, in getVariables if not args.config_file.exists(): raise FileNotFoundError(args.config_file) FileNotFoundError: gisaid_config_baacup.ini (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config_backup.ini -o gisaid -f fasta -n Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 169, in getVariables raise AttributeError(f"Attribute `{var}` must be provided in config or arguments.") AttributeError: Attribute `cluster_epicov_dir` must be provided in config or arguments. (base) xxx@xxx-ThinkCentre-E97:~$ mv gisaid_config_backup.ini gisaid_config.ini (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config.ini -o gisaid -f fasta -n Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 169, in getVariables raise AttributeError(f"Attribute `{var}` must be provided in config or arguments.") AttributeError: Attribute `cluster_epicov_dir` must be provided in config or arguments. (base) xxx@xxx-ThinkCentre-E97:~$ vi gisaid_config.ini (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config.ini -o gisaid -f fasta -n Please enter the path to your downloads file now or quit and add it with parameter '-d' >quit site not found in config Please enter your site >>^CTraceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 177, in getVariables ssh_vars = checkSSH(ssh_vars) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 106, in checkSSH new_value = input(f"Please enter your {x}\n>>") KeyboardInterrupt (base) xxx@xxx-ThinkCentre-E97:~$ vi gisaid_config.ini (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config.ini -f fasta -d /home/xxx/gisaid site not found in config Please enter your site >>~/.gisaid_config.ini Requested config not found (/home/xxx/.pooPatrol/hpc_config.txt). Gathering credentials... Collecting your cluster login information to speed up future interactions: Username: > xxx The username you entered is: xxxx Is this correct? (Y/n) > y Password: > Enter a group name (or octal - must be octal for sftp) for permissions-setting or skip by hitting enter: > Command preview: (0, 'send -- "lmkdir accession_info/\n"') (1, 'send -- "lcd /home/xxx/gisaid\n"') (2, 'send -- "pwd\n"') (3, 'send -- "get -a /lustre/home/xxx/HA/gisaid/accession_info/* accession_info/ \n\n"') sh: 1: expect: not found Guiding you through downloading EpiCoV data up through 2010-01-01 Go to https://www.epicov.org/epi3/frontend and log in. Press enter in terminal to continue... ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ CONTINUE FROM HERE vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv Preparing filters - ensure these are set (or use your own filters if this is a non-standard run) Click (button) "Search" Click (checkbox) "Low coverage excluded" Click (checkbox) "Collection date complete" Fill in "Collection to (2nd box)" as: 2010-01-01 Fill in "Host" as: Human Could not find a state with name . Correct the spelling and hit enter or Press enter to continue anyway or Type 'quit' or '^C' to quit. >^CTraceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 634, in main epicov_files,new_seq_files,get_epi_set = download_data(locations,date,downloads,local_accession_dir,filetype_choices,meta_files,meta_dir,wait,get_epi_set,custom_filters) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 517, in download_data location_long = getState(location) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 51, in getState new_location = input("Correct the spelling and hit enter or \nPress enter to continue anyway or \nType 'quit' or '^C' to quit.\n>") KeyboardInterrupt (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config.ini -o gisaid -f fasta -d /home/xxx/gisaid site not found in config Please enter your site >>^CTraceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 177, in getVariables ssh_vars = checkSSH(ssh_vars) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 106, in checkSSH new_value = input(f"Please enter your {x}\n>>") KeyboardInterrupt (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config.ini -o gisaid -f fasta -d /home/xxx/gisaid --quick site not found in config Please enter your site >>^CTraceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 177, in getVariables ssh_vars = checkSSH(ssh_vars) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 106, in checkSSH new_value = input(f"Please enter your {x}\n>>") KeyboardInterrupt (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config.ini -o gisaid -f fasta -d /home/xxx/gisaid -n site not found in config Please enter your site >>^CTraceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 177, in getVariables ssh_vars = checkSSH(ssh_vars) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 106, in checkSSH new_value = input(f"Please enter your {x}\n>>") KeyboardInterrupt (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config.ini --quick Please enter the path to your downloads file now or quit and add it with parameter '-d' >/home/xxx/gisaid site not found in config Please enter your site >>^CTraceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 177, in getVariables ssh_vars = checkSSH(ssh_vars) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 106, in checkSSH new_value = input(f"Please enter your {x}\n>>") KeyboardInterrupt (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' --quick Please enter the path to your downloads file now or quit and add it with parameter '-d' >/home/xxx/gisaid site not found in config Please enter your site >>^CTraceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 177, in getVariables ssh_vars = checkSSH(ssh_vars) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 106, in checkSSH new_value = input(f"Please enter your {x}\n>>") KeyboardInterrupt (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -q Please enter the path to your downloads file now or quit and add it with parameter '-d' >/home/xxx/gisaid site not found in config Please enter your site >>^CTraceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 177, in getVariables ssh_vars = checkSSH(ssh_vars) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 106, in checkSSH new_value = input(f"Please enter your {x}\n>>") KeyboardInterrupt (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -n Please enter the path to your downloads file now or quit and add it with parameter '-d' >^CTraceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 174, in getVariables if type(args.downloads) == type(None): args.downloads = findDownloadsDir(args.downloads) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 41, in findDownloadsDir return input("Please enter the path to your downloads file now or quit and add it with parameter '-d'\n>") KeyboardInterrupt (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -n -d /home/xxx/gisaid site not found in config Please enter your site >>^CTraceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 177, in getVariables ssh_vars = checkSSH(ssh_vars) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 106, in checkSSH new_value = input(f"Please enter your {x}\n>>") KeyboardInterrupt (base) xxx@xxx-ThinkCentre-E97:~$ vi gisaid_config.ini (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config.ini -d /home/xxx/gisaid -n Traceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 609, in main date,locations,downloads,filetype_choices,meta_files,get_epi_set,epicov_dir,ssh_vars,wait,skip_local_update,followup_command,cluster_interact,custom_filters,example,outdir = getVariables() File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 156, in getVariables ssh_vars = get_elements(config,"SSH",("site","group","login_config","save_credentials")) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 89, in get_elements value = config[section][element] File "/home/xxx/anaconda3/lib/python3.9/configparser.py", line 1257, in __getitem__ raise KeyError(key) KeyError: 'site' (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config.ini -d /home/xxx/gisaid -n Guiding you through downloading EpiCoV data up through 2010-01-01 Go to https://www.epicov.org/epi3/frontend and log in. Press enter in terminal to continue... ^CTraceback (most recent call last): File "/home/xxx/anaconda3/bin/gisaid_download", line 8, in <module> sys.exit(main()) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 630, in main awaitEnter(wait=wait) File "/home/xxx/anaconda3/lib/python3.9/site-packages/gisaid_download/gisaid_download.py", line 196, in awaitEnter input("\n\tPress enter in terminal to continue...\n") KeyboardInterrupt (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config.ini -d /home/xxx/gisaid -n Guiding you through downloading EpiCoV data up through 2010-01-01 Go to https://www.epicov.org/epi3/frontend and log in. Press enter in terminal to continue... ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ CONTINUE FROM HERE vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv Preparing filters - ensure these are set (or use your own filters if this is a non-standard run) Click (button) "Search" Click (A(H1N1)) "Virus name" Could not find a state with name . Correct the spelling and hit enter or Press enter to continue anyway or Type 'quit' or '^C' to quit. > Downloading (or locating) EpiCoV accessions file for Need to download data for Fill in "Location" as: Press enter in terminal to continue... ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ CONTINUE FROM HERE vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv Determining which sequences need to be downloaded for If not done already: Check the select-all checkbox next to 'Virus name' - it's not labeled Click (button) "Select" Click (button) "CSV" Waiting for new file in downloads with extension ".csv" 60.0 seconds have passed - still waiting. Previous files: 2 - Current files: 2 120.0 seconds have passed - still waiting. Previous files: 2 - Current files: 2 ^C Script stopped by KeyboardInterrupt (base) xxx@xxx-ThinkCentre-E97:~$ gisaid_download '2010-01-01' -c gisaid_config.ini -d /home/xxx/gisaid -n Guiding you through downloading EpiCoV data up through 2010-01-01 Go to https://www.epicov.org/epi3/frontend and log in. Press enter in terminal to continue... ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ CONTINUE FROM HERE vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv Preparing filters - ensure these are set (or use your own filters if this is a non-standard run) Click (button) "Search" Fill in "Virus name" as: A(H1N1) Could not find a state with name . Correct the spelling and hit enter or Press enter to continue anyway or Type 'quit' or '^C' to quit. > Downloading (or locating) EpiCoV accessions file for Need to download data for Fill in "Location" as: Press enter in terminal to continue... ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ CONTINUE FROM HERE vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv Determining which sequences need to be downloaded for If not done already: Check the select-all checkbox next to 'Virus name' - it's not labeled Click (button) "Select" Click (button) "CSV" Waiting for new file in downloads with extension ".csv" 60.0 seconds have passed - still waiting. Previous files: 2 - Current files: 2 120.0 seconds have passed - still waiting. Previous files: 2 - Current files: 2 180.0 seconds have passed - still waiting. Previous files: 2 - Current files: 2 ^C Script stopped by KeyboardInterrupt