Yesterday I started running a job with a script for blast. An output file was created. now, almost 24 hours later, the file is still empty, no other files were created, and the job keeps running. I think it won't stop unless I'll stop it. I was told that it might be due to a contig that's too long.
Maybe it's important to note that initially I couldn't keep the job running, since it kept failing due to memory limit exceeding. To overcome this I set a higher limit of 100gb. That's the highest I ever had to set.
#!/bin/bash #PBS -q ... #PBS -N ... #PBS -e ... #PBS -o ... #PBS -l nodes=1:ppn=20,mem=100gb module load blast/blast-2.10.0 cd /some/path/ blastx -query A1/scaffold.fa \ -db /root/BLAST/Proteins2/nr \ -max_hsps 1 -max_target_seqs 1 -num_threads 20 \ -out just_trying.txt \ -outfmt "6 std staxids qseqid sseqid staxids sscinames scomnames stitle"
Does anyone have an idea what to do?