I'm trying to run blastn using an own fasta file, but each time I try, I get an empty output file with the response 'Killed' on the terminal, and no other information. Here's the command I'm giving:
blastn -query sus_DEseqs.txt -subject mastertranscriptome.fasta -outfmt 6 -out sus_v_master.csv
I've also tried adding
-task blastn to this command, but it produces the same output. The reference fasta file is about 2.1 Gb. Running
makeblastdb produced the db files too. Also, it's not like blastn crashes immediately. It runs for roughly 30 minutes before outputting the empty file and the 'Killed' message.
My guesses on the issue at hand are:
- improperly formatted fasta file (but this seems unlikely because this file doesn't give me issues with other tools)
- we had memory issues on the HPC recently, so maybe carried over from that? Although if I run
htop, I see it using 50-95% CPU and memory. It's a lot, but at least it's working.
Any ideas what's wrong/how I can fix it? Thanks!