metabinkit_blastgendb not creating db

[envmetagen]

metabinkit_blastgendb not creating db

[nunofonseca]

Hi,
Yes, it is a BLAST error:
https://www.ncbi.nlm.nih.gov/books/NBK279684/
"If makeblastdb cannot access enough virtual memory, it will produce a message containing the string “mdb_env_open”. Virtual memory is just that (virtual) and doesn’t depend on the hardware in your system. In general, we recommend that BLAST users simply set the virtual memory to unlimited. The other alternative is to use an environment variable (BLASTDB_LMDB_MAP_SIZE) to set the required virtual memory lower, but this runs the risk of LMDB not being able to complete indexing the database."
Before generatating the BLAST database you can increase the VM limit by running
export BLASTDB_LMDB_MAP_SIZE=1000000

[bastianegeter]

unfortunately this did not solve it for me. Maybe something to do with my virtualbox virtual machine.

[nunofonseca]

Yes, it looks like an issue related to the virtual environment. Try to increase the VM resources or run makeblastdb in a docker image. Will close this issue since it is not a metabinkit issue per se but a Blast/VM one. If necessary we can discuss this on Slack.

[bastianegeter]

well, it appears this happens only when I try to write the database to the host machine shared folder. runs fine when I write to virtual machine hard disk!