refseq_microbial: archaea-chromosome_level is not a valid domain about centrifuge HOT 4 CLOSED

I guess the definition for refseq_microbial should be adapted to this:

refseq_microbial: export COMPLETE_GENOMES:=archaea bacteria fungi protozoa viral
##refseq_microbial: export CHROMOSOME_LEVEL_GENOMES:=$(COMPLETE_GENOMES)
##refseq_microbial: export SMALL_GENOMES:=mitochondrion plasmid plastid # TODO
##refseq_microbial: export MAMMALIAN_TAXIDS:=9606 10090
##refseq_microbial: export INCLUDE_CONTAMINANTS:=1
refseq_microbial: export IDX_NAME:=refseq_microbial
refseq_microbial: export CF_BUILD_OPTS+=--ftabchars 14

from centrifuge.

It works for me. Are you using the latest GitHub version? Probably its due to different platform / make / bash version. It's really a pain. What's you platform and bash/make versions?

The archaea-chromosome_level.fna should be captured by the following make target:

$(REFERENCE_SEQUENCES_DIR)/all-%-chromosome_level.fna: | $(REFERENCE_SEQUENCES_DIR) .dustmasker-ok
   ...

The refseq_microbial target downloads all 'Complete' plus all 'Chromosome level' microbial genomes. If you comment the second line, then you only get the complete assemblies.

By the way, you can adjust any of the variables also on the command line. E.g.

make refseq_microbial MAMMALIAN_TAXIDS="" COMPLETE_GENOMES="archaea bacteria viral" CHROMOSOME_LEVEL_GENOMES=""

Note that you may want to go into a new directory for index building, and refer to the Makefile with -f to avoid interferences with previously partially downloaded files.

from centrifuge.

Very strange; it works correctly if I move the all-%-chromosome_level rule in front of the all-%.fna one.

GNU Make 3.81, bash 4.3.11(1)-release on Ubuntu 14.04 LTS.

from centrifuge.

Hi @sjaenick , please feel free to reopen if the problem still is present.

from centrifuge.