GISAID-download使用

于 2024-08-05 19:43:13 发布
阅读量138 收藏
点赞数
分类专栏： 生物信息 文章标签： Ubuntu GISAID
版权声明：本文为博主原创文章，遵循 CC 4.0 BY-SA 版权协议，转载请附上原文出处链接和本声明。
本文链接：https://blog.csdn.net/yin1331102028yin/article/details/140932598
版权
  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
 2023.08.07.552204v1.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   HJCB20210100000_11480634.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
病树前头
关注
  • 0
    点赞
  • 踩
  • 0
    收藏
    觉得还不错? 一键收藏
  • 0
    评论
专栏目录
Mercedes-Benz-Download-Manager
01-04
Benz地图包下载。奔驰官方下载器，地图包下载，奔驰地图
force-download:强制下载PHP文件
05-13
将artdarek / force-download添加到您的composer.json文件： "require": { "artdarek/force-download": "dev-master" } 使用安装此软件包。 $ composer update 用法 创建名为ie的文件。 “ download.php”。 ...
shimo-cloud-files-download-v0.0.7.exe
05-21
加速站：https://nfazq6ef.fast-github.ml/ 源地址：...昨晚上折腾了好长时间都没下载成，现在终于弄好了以便大家使用，放CSDN上。 用于石墨文档、腾讯文档批量导出
Thunder-Download-Extension-for-Chrome_v3.1等.zip
01-21
【Thunder-Download-Extension-for-Chrome_v3.1等.zip】这个压缩包文件包含的是针对谷歌浏览器（Chrome）的迅雷下载扩展程序的版本v3.1。迅雷下载工具是一款在中国广泛使用的下载管理器，它以其高速下载能力和对各种...
electronic-download-manager：无需用户交互即可从Electron的BrowserWindows管理下载项，从而允许单文件下载和批量下载
02-04
电子下载管理器无需用户交互即可从的...安装$ npm install electron-download-manager用法注册所有窗口注册侦听器（它将捕获所有DownloadItems） const electron = require ( "electron" ) ;const { app , B
基于Matlab的模糊PID控制系统设计及仿真.pdf
08-05
基于Matlab的模糊PID控制系统设计及仿真
黑马头条，黑马头条，黑马头条
08-05
黑马头条，黑马头条，黑马头条
基于ppo算法的计算卸载策略研究python
08-05
ppo算法 基于ppo算法的计算卸载策略研究 适用人群：学习不同技术领域的小白或进阶学习者；可作为毕设项目、课程设计、大作业、工程实训或初期项目立项。
SQLTools插件下载与使用说明
08-05
1
超声波测试方案+气体+液体
08-05
超声波流量计应用的集成式超声波感应解决方案 (USS) 子系统
计算机网络开发 -Socket编程介绍.pdf
08-05
计算机网络开发 -Socket编程介绍
2023-04-06-项目笔记 - 第二百一十六阶段 - 4.4.2.214全局变量的作用域-214 -2024.08.05
08-05
2023-04-06-项目笔记-第二百一十六阶段-课前小分享_小分享1.坚持提交gitee 小分享2.作业中提交代码 小分享3.写代码注意代码风格 4.3.1变量的使用 4.4变量的作用域与生命周期 4.4.1局部变量的作用域 4.4.2全局变量的作用域 4.4.2.1全局变量的作用域_1 4.4.2.214局变量的作用域_214- 2024-08-05
CRCTool modbus通讯工具
最新发布
08-05
CRCTool modbus通讯工具
爬取豆瓣电影源代码数据-项目实战7-爬取源代码数据-ipynb格式-Python语法-用Jupyter notebook打开
08-05
爬取豆瓣电影TOP250源代码数据-项目实战7-爬取源代码数据-ipynb格式-Python语法-用Jupyter notebook打开 用来练习如何爬取源代码数据，可用Pycharm，也可用 Jupyter notebook进行编写代码，相关代码已给出，拿到豆瓣电影TOP250页面的源代码之后，从而得到可供下一步分析的数据。 整个流程清晰，每个步骤均用Make down编辑器进行编辑文字，相关部分会加以图片讲解，并给出了相关代码 最后祝您变得更强
2024电赛 不要让M0G3507成为阻碍.zip
08-05
对于计算机专业的学生而言，参加各类比赛能够带来多方面的益处，具体包括但不限于以下几点： 技能提升： 参与比赛促使学生深入学习和掌握计算机领域的专业知识与技能，如编程语言、算法设计、软件工程、网络安全等。 比赛通常涉及实际问题的解决，有助于将理论知识应用于实践中，增强问题解决能力。 实践经验： 大多数比赛都要求参赛者设计并实现解决方案，这提供了宝贵的动手操作机会，有助于积累项目经验。 实践经验对于计算机专业的学生尤为重要，因为雇主往往更青睐有实际项目背景的候选人。 团队合作： 许多比赛鼓励团队协作，这有助于培养学生的团队精神、沟通技巧和领导能力。 团队合作还能促进学生之间的知识共享和思维碰撞，有助于形成更全面的解决方案。 职业发展： 获奖经历可以显著增强简历的吸引力，为求职或继续深造提供有力支持。 某些比赛可能直接与企业合作，提供实习、工作机会或奖学金，为学生的职业生涯打开更多门路。 网络拓展： 比赛是结识同行业人才的好机会，可以帮助学生建立行业联系，这对于未来的职业发展非常重要。 奖金与荣誉： 许多比赛提供奖金或奖品，这不仅能给予学生经济上的奖励，还能增强其成就感和自信心。 荣誉证书或奖状可以证明学生的成就，对个人品牌建设有积极作用。 创新与研究： 参加比赛可以激发学生的创新思维，推动科研项目的开展，有时甚至能促成学术论文的发表。 个人成长： 在准备和参加比赛的过程中，学生将面临压力与挑战，这有助于培养良好的心理素质和抗压能力。 自我挑战和克服困难的经历对个人成长有着深远的影响。 综上所述，参加计算机领域的比赛对于学生来说是一个全面发展的平台，不仅可以提升专业技能，还能增强团队协作、沟通、解决问题的能力，并为未来的职业生涯奠定坚实的基础。
Huawei网络设备安全加固规范.doc
08-05
Huawei网络设备安全加固规范.doc
在 IntelliJ IDEA 中集成 Maven 环境，可以按照以下步骤进行操作： 安装 Maven
08-05
文章目录 配置Maven环境 方法一（当前工程） 方法二（全局） IDEA创建Maven项目 写入代码 Maven坐标 导入Maven项目： 在这里插入图片描述在 IntelliJ IDEA 中集成 Maven 环境，可以按照以下步骤进行操作： 安装 Maven：首先，确保你已经在本地计算机上安装了 Maven。你可以从 Maven 官方网站（https://maven.apache.org）下载最新版本的 Maven，并按照官方文档进行安装。 配置 Maven 路径：在 IntelliJ IDEA 中打开设置（Settings）窗口，选择 “Build, Execution, Deployment” -> “Build Tools” -> “Maven”。在这里，你可以设置 Maven 的安装路径。点击 “Apply” 或 “OK” 按钮保存设置。 创建 Maven 项目：在 IntelliJ IDEA 主界面，选择 “File” -> “New” -> “Project”，然后在弹出的对话框中选择 “Maven” 选项，并点击 “Next”。在下一步中，可以选择基于 Ma
基于java开发的紧急救援基站定位搜索系统
08-05
基于java开发的紧急救援基站定位搜索系统 数据库采用mysql5.5 jdk1.8 maven3.6.1
销售员各月销售提成计算.xlsx.xlsx
08-05
销售管理表，财务报表，占比分析，消费能力分析，日程安排，提成表，考核表 适用人群：学习不同技术领域的小白或进阶学习者；可作为毕设项目、课程设计、大作业、工程实训或初期项目立项。
js-file-download使用方法
05-30
js-file-download 是一个 JavaScript 库，用于从 Web 应用程序中下载文件。它允许您使用 JavaScript 在客户端创建和下载文件。 要使用 js-file-download，您需要遵循以下步骤： 1. 下载 js-file-download 库，包括 js-file-download.js 和 FileSaver.js。 2. 在您的 HTML 文件中，将 js-file-download.js 和 FileSaver.js 文件链接到您的页面。 ```html <script src="js/FileSaver.js"></script> <script src="js/js-file-download.js"></script> ``` 3. 在您的 JavaScript 代码中，使用以下语法来下载文件： ```javascript fileDownload(data, filename, mimeType); ``` 其中： - data：要下载的文件内容，可以是字符串、Blob 或 ArrayBuffer。 - filename：要保存的文件名，包括扩展名。 - mimeType：文件的 MIME 类型，例如 "text/plain" 或 "application/pdf"。 例如，要下载一个名为 "example.txt" 的文本文件，您可以使用以下代码： ```javascript var fileContent = "This is an example file."; fileDownload(fileContent, "example.txt", "text/plain"); ``` 这将提示用户下载一个名为 "example.txt" 的文本文件，其中包含 "This is an example file." 的内容。 希望这可以帮助您使用 js-file-download 库下载文件。
评论
添加红包

请填写红包祝福语或标题

个

红包个数最小为10个

元

红包金额最低5元

当前余额3.43元 前往充值 >
需支付：10.00元
成就一亿技术人!
领取后你会自动成为博主和红包主的粉丝 规则
hope_wisdom
发出的红包
实付元
使用余额支付
点击重新获取
扫码支付
钱包余额 0

抵扣说明：

1.余额是钱包充值的虚拟货币，按照1:1的比例进行支付金额的抵扣。
2.余额无法直接购买下载，可以购买VIP、付费专栏及课程。

余额充值