Question: Blast job never stops
0
langziv • 0 wrote:
Hi.
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.
The script:
#!/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?
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modified 9 weeks ago
by
Mensur Dlakic • 8.4k
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written
9 weeks ago by
langziv • 0
not directly related to your issue but a few points to be aware of:
be caution (or at least know very well what it implies) with using parameters as
-max_hsps 1and/or-max_target_seqs 1, they can cause 'unexpected' results (google for it for details)Also: using up to 20 threads will likely not give much speed increase, blast is only for a small part parallelised and with 20 you for sure are on the plateau of speed increase (it has been said that anything above 4-5 threads is likely not adding much)
Give us more info or flip a coin.
I added the job's script.
Log onto the cluster node your job has been allocated and check what's happening there (e.g. with top).