File doesn't exist

Question

[hebatullah.esmail]

I'm creating a blast-database of Virulent factors. 1- I downloaded the virulent factors sequences
2- I transferred the sequence file from my desktop to the terminal (Putty) through winSCP (drag and drop). I'm not sure that this is the right way. 3- Then I started creating the blast database using the following command line

   makeblastdb -in VFDB_setA_pro.fas -title   VFDB -parse_seqids -out VFs -dbtype prot

Then I get the following errors BLAST options error: File VFDB_setA_pro.fas does not exist

I need help please.

Thanks!

[GenoMax]

I suggest that you familiarize yourself with some basics of UNIX. This would be the best few hours you will spend. Even though the tutorial uses mac os as an example do everything in it in Putty after you log into your server.

Problem here is you are trying to run this command from a directory which may not contain the file in question. This should be an easy fix, once you understand directory structure/navigation in unix.

To answer your question you need to do this (provide a value for path_to from your server or change to the directory where that file is present.)

makeblastdb -in /path_to/VFDB_setA_pro.fas -title   VFDB -parse_seqids -out VFs -dbtype prot

Answer 1

[Ram]

Drag-drop is not the problem here. When you SCP a file, you're copying it from a source (in your case, your computer - this is where you used drag-drop) to a destination (the remote computer). You've got to figure out where WinSCP transferred that file to. It should have a log file/logging console where it logged the transfer. That should tell you the destination.

If not, drag drop the file again and see where it goes. Ideally, you should be using scp <sourcefile> <remote_username>@<remote_host>:<remote_location> to copy the file to a remote location and swap the parameters to copy the file from a remote location.