Problem building DB with metacache-build-refseq about metacache HOT 6 CLOSED

Hi,

thanks for pointing out the issue with the assembly_summery.txt files. We'll update our scripts.

Regarding the other problem - I think we have to try to reproduce it in order to diagnose what's wrong. Could you maybe try to build again, but with option -verbose. This will list the currently processed genomes. Maybe that could indicate at what point / processed sequence it goes wrong. Other than that we'll also (try to) build the latest RefSeq.

from metacache.

We also ran into the same problem when trying to build the latest RefSeq. I don't think it has anything to do with the input files. We'll investigate and let you know as soon as we find something.

from metacache.

Great - thank you for the quick response and for looking into the issue.

from metacache.

Turns out the problem is rather mundane: the latest RefSeq releases contain so many complete genomes that our default data type for storing reference sequence ids is not sufficient anymore. The current defaults only support up to 65536 reference sequences. This should have triggered an error message during the build, but the error handling for this case seems to be broken and the build just paused.

We'll change the default from 16bit to 32bit and fix the error handling.
In the meantime you can compile with:
make MACROS="-DMC_TARGET_ID_TYPE=uint32_t"

Note that this will increase the memory footprint of the databases slightly.

from metacache.

The latest release contains a fixed download script, the new data type defaults and an updated documentation.
https://github.com/muellan/metacache/releases/tag/v2.2.0

from metacache.

Excellent - that you for the quick response and fix.

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