BLAST 2.11.0:

Question

[slin023]

Hi, I am currently running BLAST 2.11.0 thru conda at HPC. I just downloaded pre-complied database from NCBI a month ago (using

wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.??.tar.gz" -P nt/ && \ for file in nt/*.tar.gz; \ do tar xf $file -C nt && rm $file; \ done )

and run it locally. However, I keep receiving these error messages:

/tmp/slurmd/job5370717/slurm_script: line 21: 39561 Segmentation fault      blastn -db /scratch/mdegenna/slin023/nucleotide/nt -query /scratch/mdegenna/slin023/smallGenomecontig/half_genome.fa -outfmt "6 qseqid staxids bitscore std" -max_target_seqs 10 -max_hsps 1 -evalue 1e-25 -num_threads 40 -out /scratch/mdegenna/slin023/BTK_TUTORIAL/FILES/ASSEMBLY_NAME5.ncbi.blastn.out

Which might indicate core dump, so I switched to a different partition with higher mem. still the same messages. Here is my script:

any suggestions will be very helpful! thank you for your time!

[GenoMax]

Can you make sure your index files are intact and present?

$ blastdbcmd -db yourDb -info

You should see something like the following. There should be 51 files in total. Example below is truncated to save space.

$ blastdbcmd -db nt -info
Database: Nucleotide collection (nt)
        77,026,053 sequences; 608,810,694,332 total bases

Date: Dec 12, 2021  5:39 AM     Longest sequence: 99,791,824 bases

BLASTDB Version: 5

Volumes:
        /nas/longleaf/data/blast/nt.00
        /nas/longleaf/data/blast/nt.01
        /nas/longleaf/data/blast/nt.02
        /nas/longleaf/data/blast/nt.03

[slin023]

Hi, I have tried. All 51 files are in there.

[GenoMax]

Then next thing is to try and assign more RAM for your process. So add the following in your script and see what happens.

#SBATCH mem=30g

This will assign 30G of RAM to this job. You may need to adjust this up if you still get a seg fault.

[slin023]

Hi, I keep adjusting, switching to highest memory partition, then to 1500G, tried 500G, none of them worked.

#SBATCH --partition IB_40C_1.5T
#SBATCH --mem=1500G
#SBATCH -n 40
#SBATCH -N 1

[GenoMax]

Are you able to start a small test job? Use a single sequence and see what happens. Perhaps there is a problem with your blast+ install.

[slin023]

I tested out all possible problems, I found out it was the V5 database corrupted, so I used update_blastdb.pl command to fix it, then issue resolved. thank you!