blastn 2.11.0 in Docker hangs phoning home

[zwets]

My apologies if this is not the correct place to report this, but I would expect the issue to show up in this project too.

I am running blastn in a docker container, copying it in from the binary tarball from https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+.

Since upgrading to 2.11.0, blastn calls take excessively long to finish, or do not complete at all.

Setting BLAST_USAGE_REPORT=false resolves the issue. This raises the strong suspicion that the new usage reporting feature is the culprit.

The issue can be reproduced by creating a docker image with a simple Dockerfile:

FROM ubuntu  # or your preferred starting image
COPY blastn /usr/local/bin
USER nobody:nogroup

After building the container with docker build -t test-bug ".", observe the difference between:

docker run -ti --rm --read-only -e BLAST_USAGE_REPORT=false test-bug blastn -help

and

docker run -ti --rm --read-only test-bug blastn -help

The hiccup is sub-second but already noticeable. Start a longer running local blastn call, and runtimes of normally e.g. 15s go up to many minutes, while top shows the processes as mostly sleeping.

Update for the record: the excessively long run times were not for single runs of blastn. They happened in our pipeline where we do a few dozen calls in series. These should take ~20s altogether, but their added up "hang time" made the job timeout after 20mn.