kubu4
commented
3 years ago Just documenting discussion from class today.
A couple of things. One problem was that the download directory specified in your curl command didn't exist. This was a common problem that other encountered. Making the desired directory structure before downloading files is helpful to avoid this. Also, using tab completion when typing the destination location can be a useful "check" to see if the specified location exists before you start downloading.
Another problem was the curl command for the FASTA file. For some reason, the curl command also needed an additional argument (-k) to deal with a weird server certificate issue. Totally non-intuitive, but the error message suggested this as a possible fix and it worked!
I was unable to work with blast, the .fa file from washington.edu and the Swiss-Prot sequences. I am not sure why these issues are occuring. I am trying to replicate the code shown in the tutorial and in the jupyter notebooks from other students, but I keep running into errors.