Blast#
Introduction#
BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
Databases#
Local copies of blast databases can be found in the directory /cluster/tufts/biocontainers/datasets/blast/latest/.
In blast modulefiles, we defined the environment variable BLASTDB as /cluster/tufts/biocontainers/datasets/blast/latest, so that you can use the blast databases such as nr and nt without specifying the full path.
Versions#
2.15.0
2.16.0
Commands#
amino-acid-composition
between-two-genes
blastdb_aliastool
blastdbcheck
blastdbcmd
blast_formatter
blastn
blastp
blastx
cleanup-blastdb-volumes.py
deltablast
dustmasker
eaddress
eblast
get_species_taxids.sh
legacy_blast.pl
makeblastdb
makembindex
makeprofiledb
psiblast
rpsblast
rpstblastn
run-ncbi-converter
segmasker
tblastn
tblastx
update_blastdb.pl
windowmasker
Memory requirements for blast#
Ensure that you allocate sufficient memory for the BLAST database being used. Insufficient memory will force the database to be repeatedly read from disk, leading to intensive I/O operations that significantly slow down your job. This can also cause severe strain on the filesystem, especially when running multiple jobs concurrently. Such issues may disrupt other users and prompt intervention from the Research Technology (RT) staff.
Calculate the memory required by totalling the size of the .nsq (for nucleotide databases) or .psq (for protein databases) files. e.g.:
$ du -sh --total /fdb/blastdb/nt*.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.000.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.001.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.002.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.003.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.004.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.005.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.006.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.007.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.008.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.009.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.010.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.011.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.012.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.013.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.014.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.015.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.016.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.017.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.018.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.019.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.020.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.021.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.022.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.023.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.024.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.025.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.026.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.027.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.028.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.029.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.030.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.031.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.032.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.033.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.034.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.035.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.036.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.037.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.038.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.039.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.040.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.041.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.042.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.043.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.044.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.045.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.046.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.047.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.048.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.049.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.050.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.051.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.052.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.053.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.054.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.055.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.056.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.057.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.058.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.059.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.060.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.061.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.062.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.063.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.064.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.065.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.066.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.067.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.068.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.069.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.070.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.071.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.072.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.073.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.074.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.075.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.076.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.077.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.078.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.079.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.080.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.081.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.082.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.083.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.084.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.085.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.086.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.087.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.088.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.089.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.090.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.091.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.092.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.093.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.094.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.095.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.096.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.097.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.098.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.099.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.100.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.101.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.102.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.103.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.104.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.105.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.106.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.107.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.108.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.109.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.110.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.111.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.112.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.113.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.114.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.115.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.116.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.117.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.118.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.119.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.120.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.121.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.122.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.123.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.124.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.125.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.126.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.127.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.128.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.129.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.130.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.131.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.132.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.133.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.134.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.135.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.136.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.137.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.138.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.139.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.140.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.141.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.142.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.143.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.144.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.145.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.146.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.147.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.148.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.149.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.150.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.151.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.152.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.153.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.154.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.155.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.156.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.157.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.158.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.159.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.160.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.161.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.162.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.163.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.164.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.165.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.166.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.167.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.168.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.169.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.170.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.171.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.172.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.173.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.174.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.175.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.176.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.177.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.178.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.179.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.180.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.181.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.182.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.183.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.184.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.185.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.186.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.187.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.188.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.189.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.190.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.191.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.192.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.193.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.194.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.195.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.196.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.197.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.198.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.199.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.200.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.201.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.202.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.203.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.204.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.205.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.206.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.207.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.208.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.209.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.210.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.211.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.212.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.213.nsq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nt.214.nsq
760M /cluster/tufts/biocontainers/datasets/blast/latest/nt.215.nsq
601G total
$ du -sh --total /cluster/tufts/biocontainers/datasets/blast/latest/nr*.psq
3.4G /cluster/tufts/biocontainers/datasets/blast/latest/nr.000.psq
3.5G /cluster/tufts/biocontainers/datasets/blast/latest/nr.001.psq
3.2G /cluster/tufts/biocontainers/datasets/blast/latest/nr.002.psq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.003.psq
3.2G /cluster/tufts/biocontainers/datasets/blast/latest/nr.004.psq
3.1G /cluster/tufts/biocontainers/datasets/blast/latest/nr.005.psq
3.0G /cluster/tufts/biocontainers/datasets/blast/latest/nr.006.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.007.psq
47M /cluster/tufts/biocontainers/datasets/blast/latest/nr.008.psq
3.2G /cluster/tufts/biocontainers/datasets/blast/latest/nr.009.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.010.psq
649M /cluster/tufts/biocontainers/datasets/blast/latest/nr.011.psq
3.2G /cluster/tufts/biocontainers/datasets/blast/latest/nr.012.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.013.psq
556M /cluster/tufts/biocontainers/datasets/blast/latest/nr.014.psq
3.3G /cluster/tufts/biocontainers/datasets/blast/latest/nr.015.psq
3.4G /cluster/tufts/biocontainers/datasets/blast/latest/nr.016.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.017.psq
756M /cluster/tufts/biocontainers/datasets/blast/latest/nr.018.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.019.psq
126M /cluster/tufts/biocontainers/datasets/blast/latest/nr.020.psq
3.6G /cluster/tufts/biocontainers/datasets/blast/latest/nr.021.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.022.psq
517M /cluster/tufts/biocontainers/datasets/blast/latest/nr.023.psq
3.1G /cluster/tufts/biocontainers/datasets/blast/latest/nr.024.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.025.psq
320M /cluster/tufts/biocontainers/datasets/blast/latest/nr.026.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.027.psq
970M /cluster/tufts/biocontainers/datasets/blast/latest/nr.028.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.029.psq
563M /cluster/tufts/biocontainers/datasets/blast/latest/nr.030.psq
2.6G /cluster/tufts/biocontainers/datasets/blast/latest/nr.031.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.032.psq
308M /cluster/tufts/biocontainers/datasets/blast/latest/nr.033.psq
3.6G /cluster/tufts/biocontainers/datasets/blast/latest/nr.034.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.035.psq
484M /cluster/tufts/biocontainers/datasets/blast/latest/nr.036.psq
3.5G /cluster/tufts/biocontainers/datasets/blast/latest/nr.037.psq
3.0G /cluster/tufts/biocontainers/datasets/blast/latest/nr.038.psq
3.0G /cluster/tufts/biocontainers/datasets/blast/latest/nr.039.psq
3.0G /cluster/tufts/biocontainers/datasets/blast/latest/nr.040.psq
3.3G /cluster/tufts/biocontainers/datasets/blast/latest/nr.041.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.042.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.043.psq
103M /cluster/tufts/biocontainers/datasets/blast/latest/nr.044.psq
2.7G /cluster/tufts/biocontainers/datasets/blast/latest/nr.045.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.046.psq
120M /cluster/tufts/biocontainers/datasets/blast/latest/nr.047.psq
3.7G /cluster/tufts/biocontainers/datasets/blast/latest/nr.048.psq
2.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.049.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.050.psq
62M /cluster/tufts/biocontainers/datasets/blast/latest/nr.051.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.052.psq
113M /cluster/tufts/biocontainers/datasets/blast/latest/nr.053.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.054.psq
212M /cluster/tufts/biocontainers/datasets/blast/latest/nr.055.psq
2.7G /cluster/tufts/biocontainers/datasets/blast/latest/nr.056.psq
3.4G /cluster/tufts/biocontainers/datasets/blast/latest/nr.057.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.058.psq
384M /cluster/tufts/biocontainers/datasets/blast/latest/nr.059.psq
3.7G /cluster/tufts/biocontainers/datasets/blast/latest/nr.060.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.061.psq
96M /cluster/tufts/biocontainers/datasets/blast/latest/nr.062.psq
3.7G /cluster/tufts/biocontainers/datasets/blast/latest/nr.063.psq
3.5G /cluster/tufts/biocontainers/datasets/blast/latest/nr.064.psq
3.6G /cluster/tufts/biocontainers/datasets/blast/latest/nr.065.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.066.psq
140M /cluster/tufts/biocontainers/datasets/blast/latest/nr.067.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.068.psq
140M /cluster/tufts/biocontainers/datasets/blast/latest/nr.069.psq
3.7G /cluster/tufts/biocontainers/datasets/blast/latest/nr.070.psq
3.1G /cluster/tufts/biocontainers/datasets/blast/latest/nr.071.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.072.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.073.psq
51M /cluster/tufts/biocontainers/datasets/blast/latest/nr.074.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.075.psq
740M /cluster/tufts/biocontainers/datasets/blast/latest/nr.076.psq
3.3G /cluster/tufts/biocontainers/datasets/blast/latest/nr.077.psq
3.2G /cluster/tufts/biocontainers/datasets/blast/latest/nr.078.psq
3.4G /cluster/tufts/biocontainers/datasets/blast/latest/nr.079.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.080.psq
385M /cluster/tufts/biocontainers/datasets/blast/latest/nr.081.psq
3.7G /cluster/tufts/biocontainers/datasets/blast/latest/nr.082.psq
3.4G /cluster/tufts/biocontainers/datasets/blast/latest/nr.083.psq
3.1G /cluster/tufts/biocontainers/datasets/blast/latest/nr.084.psq
3.3G /cluster/tufts/biocontainers/datasets/blast/latest/nr.085.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.086.psq
269M /cluster/tufts/biocontainers/datasets/blast/latest/nr.087.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.088.psq
13M /cluster/tufts/biocontainers/datasets/blast/latest/nr.089.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.090.psq
106M /cluster/tufts/biocontainers/datasets/blast/latest/nr.091.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.092.psq
390M /cluster/tufts/biocontainers/datasets/blast/latest/nr.093.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.094.psq
513M /cluster/tufts/biocontainers/datasets/blast/latest/nr.095.psq
2.9G /cluster/tufts/biocontainers/datasets/blast/latest/nr.096.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.097.psq
895M /cluster/tufts/biocontainers/datasets/blast/latest/nr.098.psq
3.2G /cluster/tufts/biocontainers/datasets/blast/latest/nr.099.psq
3.3G /cluster/tufts/biocontainers/datasets/blast/latest/nr.100.psq
3.3G /cluster/tufts/biocontainers/datasets/blast/latest/nr.101.psq
2.5G /cluster/tufts/biocontainers/datasets/blast/latest/nr.102.psq
2.9G /cluster/tufts/biocontainers/datasets/blast/latest/nr.103.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.104.psq
136M /cluster/tufts/biocontainers/datasets/blast/latest/nr.105.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.106.psq
3.2G /cluster/tufts/biocontainers/datasets/blast/latest/nr.107.psq
3.5G /cluster/tufts/biocontainers/datasets/blast/latest/nr.108.psq
3.5G /cluster/tufts/biocontainers/datasets/blast/latest/nr.109.psq
3.6G /cluster/tufts/biocontainers/datasets/blast/latest/nr.110.psq
3.1G /cluster/tufts/biocontainers/datasets/blast/latest/nr.111.psq
3.7G /cluster/tufts/biocontainers/datasets/blast/latest/nr.112.psq
3.1G /cluster/tufts/biocontainers/datasets/blast/latest/nr.113.psq
3.8G /cluster/tufts/biocontainers/datasets/blast/latest/nr.114.psq
702M /cluster/tufts/biocontainers/datasets/blast/latest/nr.115.psq
1.3G /cluster/tufts/biocontainers/datasets/blast/latest/nr.116.psq
302G total
As you can see, if you want to run blastn with the nt database, you need to allocate at least 601GB of memory, or better yet, 610GB for safety.
If you want to run blastp with the nr database, you need to allocate at least 302GB of memory, or better yet, 310GB for safety.
Example job#
If you want to run a blast job with the nr or nr database, it is recommended to use the largemem partition.
Adjust slurm options based on job requirements (slurm cheat sheet):
#!/bin/bash
#SBATCH -p largemem # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00 # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1 # Number of nodes
#SBATCH -n 1 # Number of tasks per node
#SBATCH -c 24 # Number of CPU cores per task
#SBATCH --mem=400G # Memory required per node
#SBATCH --job-name=blast # Job name
#SBATCH --mail-type=FAIL,BEGIN,END # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu # Email address for notifications
#SBATCH --error=%x-%J-%u.err # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out # Standard output file: <job_name>-<job_id>-<username>.out
module purge ### Optional, but highly recommended.
module load blast/XXXX ### Latest version is recommended.
blastp -query query.fasta -db nr -out blastp_results.txt -evalue 1e-5 -outfmt 6 -num_threads 24