Blast db build fail

Microbial community profiling ShortBRED
1

Blast DB failed due to insufficient memory allocation.

example_identify/goidb.log says:

Building a new DB, current time: 03/21/2021 20:37:02
New DB name:   /home/amirza/CAZymes/example_identify/clustdb/goidb
New DB title:  example_identify/clust/clust.faa
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B

No volumes were created.

Error: mdb_env_open: Cannot allocate memory

I am creating markers using the full CAZymes database (dbCAN) using the full uniref90 db as the reference. My aim is to compare the diversity and composition of the stool CAZymes profiles between two groups of people. My command was: shortbred_identify.py --goi dbCAN_seq/CAZyme_seq_list/GCF.deduplicated.fasta -ref uniref90.fasta --markers CAZymes_uniref90.faa --tmp example_identify --usearch /home/amirza/CAZymes

I ran the job with 16 cores with 4GM memory (RAM) allocation per core. What command should I use to rerun the code with restarting from the beginning and should I allocate more memory to prevent the memory problem? My blastp version is 2.10.1+

3

I resolved the error with export BLASTDB_LMDB_MAP_SIZE=100000000. I think BLAST wanted to allocate a too much virtual memory and my machine didnt like that. Now I understand the wisdom behind why you have been delaying your response, you wanted me to take the time to resolve the issue myself :grin: