aaftf filter URL issue
Opened this issue · 2 comments
Hello! I tried to run the script for aaftf filter but terminal gave me always the same error:
Running AAFTF v0.5.0
error with url https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/819/615/GCF_000819615.1_ViralProj14015/GCF_000819615.1_ViralProj14015_genomic.fna.gz aaftf-filter_85caa12f/GCF_000819615.1_ViralProj14015_genomic.fna.gz
Traceback (most recent call last):
File "/mnt/home/dematth2/anaconda3/envs/aaftf/bin/AAFTF", line 8, in
sys.exit(main())
File "/mnt/home/dematth2/anaconda3/envs/aaftf/lib/python3.7/site-packages/AAFTF/AAFTF_main.py", line 1113, in main
args.func(parser, args)
File "/mnt/home/dematth2/anaconda3/envs/aaftf/lib/python3.7/site-packages/AAFTF/AAFTF_main.py", line 53, in run_subtool
submodule.run(parser, args)
File "/mnt/home/dematth2/anaconda3/envs/aaftf/lib/python3.7/site-packages/AAFTF/filter.py", line 65, in run
earliest_file_age = os.path.getctime(acc_file)
File "/mnt/home/dematth2/anaconda3/envs/aaftf/lib/python3.7/genericpath.py", line 65, in getctime
return os.stat(filename).st_ctime
FileNotFoundError: [Errno 2] No such file or directory: 'aaftf-filter_85caa12f/GCF_000819615.1_ViralProj14015_genomic.fna.gz'
======= This is where my script ends! =========
I tried to modify the link because, if i delete the last part and i copy on my internet page i can download the Escherichia coli's sequence but never has changed on the terminal...i obtained the same error.
I tried also to modify the script first by adding the genome directory (before i downloaded it) with the options -u but it keeps insisting on the URL and then i tried to add the right URL instead, but it keeps giving an error on that initial URL.
Thank you 👍
I’ll see why the downloads may have an issue. You can also download manually.
Thank you. Is there a manual, or a more detailed documentation, for this pipeline I can use? Or maybe is it included in a publication?
Thanks again,
Martina