A Rare Error Reporting while using local BLAST Software

Preface
The NCBI provide the command-line tools to run BLAST locally instead of using the online version. With the local BLAST software, any sequence alignment can be run easily and fleetly. Currently, there are hundreds of courses or tutorials about how to correctly use the local BLAST software. However, I recently encountered a error when using this software and there is no online solution to fix the error. Fortunately, I finally figure out the best solution by myself. Thus, I will record the incident as a supplementary tutorial of BLAST software.

An error occurred after updating the database

    BLAST databases are updated daily and need be downloaded via FTP. Database sets may be retrieved automatically with update_blastdb.pl, which is part of the BLAST+ suite. As a consumer, it is worthwhile to update the database regularly. The recent update from NCBI was in 17th January, 2022.Considering my latest local database was downloaded half a year ago. Therefore, I updated the database by using the update_blastdb.pl several days ago.
    With the new version of the database, the first thing is to confirm whether the database would be read and analyzed by the BLAST software. However, a error occurred when I used the blastn software to search a sets of nucleotide sequences. The command I input was highlighted as follows:

blastn -query myseqs.fa -db /path/to/my/nt/db -num_threads 15 -outfmt 8 -out searched.m8

    I never meet this error before, it looks like something wrong with the database. Maybe the uncompleted nt files were downloaded. I immediately run the md5 related command to check the file integrity.

md5sum -c *gz

    Not as expected, all nt subfiles were complete.

Debug

    I noted that the error occurred about 5 minutes after ran the command. Since the each nt subfile was read individuallyi by the blastn script, may be some of the subdatabase were not read correctly by blastn. Thus, I used the command to check which file was reading error.

for my i in `seq 1 53`; do echo ${i}; blastn -query myseqs.fa -db /path/to/my/nt/db/nt.${i} -num_threads 15 -outfmt 8 -out search.subdb${i}.m8

    As predicted, some files were successfully read by blastn, but others failed. All the files which were failed to be read were compared to the previous version before update. I finally found the difference. The best and simplest way to fix the bug is to update the version of the BLASTN software.

    The version 2.12 of BLAST was downloaded by the ftp. I again run the previous command, the sequence alignment were successfully performed without any warning or error.

Epilogue
The Local BLAST provides the great convenience for users to align a large number of sequences without the network. But it also limits the real-time update of the local database. Therefore, it is necessary to periodically download the new database to expand the sequences information. To avoid the errors in this push, It is better to update the version of the BLAST software when update the database.