I can’t understand why this starts to happen sometimes and I can’t figure out what I did to get it to stop…
I had added a little debug coding in there (since it started happening) and it indicated the sys() function seemed to stop working.
def assert_blast_installed_and_compatible
begin
aa = sys(‘blastdbcmd -version’, path: config[:bin])
puts ["output: version ",aa.count]
aa.each { |item| puts item }
out, = sys(‘blastdbcmd -version’, path: config[:bin])
…
ericiam@graingenes:/data/seqserv2rc8$ bundle exec bin/sequenceserver -c /data/seqserv2rc8/gg-sequenceserver/sequenceserver.conf
[2022-02-01 07:00:15] INFO Reading configuration file: /data/seqserv2rc8/gg-sequenceserver/sequenceserver.conf.
output: version
2
<---- nothing from sys()
Something went wonky
Looks like you have encountered a bug in SequenceServer. Please could you
report this incident to our Google Group -
https://groups.google.com/forum/?fromgroups#!forum/sequenceserver
Error:
undefined method empty?' for nil:NilClass /data/seqserv2rc8/lib/sequenceserver.rb:251:in assert_blast_installed_and_compatible’
/data/seqserv2rc8/lib/sequenceserver.rb:192:in init_binaries' /data/seqserv2rc8/lib/sequenceserver.rb:81:in init’
bin/sequenceserver:180:in block (2 levels) in <top (required)>' /var/lib/gems/2.7.0/gems/slop-3.6.0/lib/slop.rb:260:in parse!’
/var/lib/gems/2.7.0/gems/slop-3.6.0/lib/slop.rb:65:in parse!' bin/sequenceserver:48:in <top (required)>’
/var/lib/gems/2.7.0/gems/bundler-2.2.30/lib/bundler/cli/exec.rb:58:in load' /var/lib/gems/2.7.0/gems/bundler-2.2.30/lib/bundler/cli/exec.rb:58:in kernel_load’
…
???
In the past, I had never seen this problem, then all of a sudden, today, it started happening.
Later, it just magically started working after changing the debug code a little (seemingly inconsequential change).
[2022-02-01 07:23:54] INFO Reading configuration file: /data/seqserv2rc8/sequenceserver.conf.
output: version
2
blastdbcmd: 2.12.0+ <---- surprise!!! started working! why???
Package: blast 2.12.0, build Jun 4 2021 03:22:54
…
Running sequenceserver 2 rc8