Last night I set a blast running through the command line and when after half an hour it seemed to be running fine I went home. I have just come in to check on it and it is displaying the warning message:
Warning: (307.8) [HTTP; http://www.ncbi.nlm.nih.gov/Service/dispd.cgi?service=blast4&address=(sever_address)&platform=x86_64-unknown-linux-gnu] Cannot read header (Timeout)
(I removed the sever address but it was correct).
The command appears to still be running and the output file has stuff in it (the sort of outputs I was expecting). Has anyone any idea what is causing this and if I should be worried about it?
The command I used was:
blastp -query proteins_fasta.fa -out protiens_blasted -db refseq_protein -outfmt 5 -remote