Perhaps CONS-Dfam_3.2 missing from container? about tetools HOT 3 CLOSED

Not sure, but maybe the RepeatMasker Libraries directory is missing a file/dir like CONS-Dfam_3.2? Should this work, or is it misguided?

It's not missing! The directory should be generated on an as-needed basis, by default in Libraries/ if it is writable, or in a directory under $HOME if Libraries is readonly.

Building general libraries in: /projects/hpcrcf/mcolema5/mcurrey-repeatmasker/Libraries/CONS-Dfam_3.2/general
RepeatMasker::createLib(): Error invoking /opt/rmblast/bin/makeblastdb on file /projects/hpcrcf/mcolema5/mcurrey-repeatmasker/Libraries/CONS-Dfam_3.2/general
/is.lib.

From around this time there should be a log file named rmblast.log, in that general/ directory. Could you paste or attach the contents of that file? It might have a more specific or informative error.

from tetools.

Thanks, that was very helpful. Here was what was in that log:

New DB name:   /projects/hpcrcf/mcolema5/mcurrey-repeatmasker/Libraries/CONS-Dfam_3.2/general/is.lib
New DB title:  /projects/hpcrcf/mcolema5/mcurrey-repeatmasker/Libraries/CONS-Dfam_3.2/general/is.lib
Sequence type: Nucleotide
Deleted existing Nucleotide BLAST database named /projects/hpcrcf/mcolema5/mcurrey-repeatmasker/Libraries/CONS-Dfam_3.2/general/is.lib
Keep MBits: T
Maximum file size: 1000000000B

No volumes were created.

Error: mdb_env_open: Cannot allocate memory

Looking around, this appears to be similar to this: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960756
In particular, it seems plausible that this is an mmap call failing. The 'ulimit -v' was set to about 48GB, but apparently that wasn't enough. Retrying with 'unlimited' seemed to get it working.

Appreciate your help!

P.S. Would be handy to have strace in that container, for debugging.

from tetools.

Glad to hear you found the cause - and thanks for that link. Apparently -blastdb_version 4 is a potential workaround for this issue in the debian bug report, which I'll consider adding to RepeatMasker itself - we have seen other issues with the version 5 databases in other contexts as well.

I have also added strace to the container starting in 1.3-beta-1, so I'm closing this issue. Thanks for the report!

from tetools.