Comments (2)
I think we might have fixed this issue, and the fix is incorporated in the master branch. Would it be possible for you to try the GitHub version?
from centrifuge.
Hi there,
I would like to receive some help. Our system administrator tried to install centrifuge and got Error 1 and Error 2. Please see the details of the errors below:
/xxx/xxx/centrifuge/indices@node12> make p+h+v
Making: p+h+v: p+h+v
make -f Makefile IDX_NAME=p+h+v
make[1]: Entering directory /misc/xxx/software/centrifuge/indices' mkdir -p reference-sequences [[ -d tmp_p+h+v ]] && rm -rf tmp_p+h+v; mkdir -p tmp_p+h+v Downloading and dust-masking archaea centrifuge-download -o tmp_p+h+v -m -d "archaea" -P 1 refseq > \ tmp_p+h+v/all-archaea.map Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/assembly_summary.txt ... Downloading 224 archaea genomes at assembly level Complete Genome ... (will take a while) Progress : [####------------------------------------] 12% 28/224 Progress : [########################################] 100% 224/224 cat tmp_p+h+v/archaea/*.fna > reference-sequences/all-archaea.fna.tmp && mv reference-sequences/all-archaea.fna.tmp reference-sequences/all-archaea.fna mv tmp_p+h+v/all-archaea.map reference-sequences/all-archaea.map rm -rf tmp_p+h+v [[ -d tmp_p+h+v ]] && rm -rf tmp_p+h+v; mkdir -p tmp_p+h+v Downloading and dust-masking bacteria centrifuge-download -o tmp_p+h+v -m -d "bacteria" -P 1 refseq > \ tmp_p+h+v/all-bacteria.map Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt ... Downloading 6498 bacteria genomes at assembly level Complete Genome ... (will take a while) Progress : [----------------------------------------] 0% 64/6498 Progress : [########################################] 100% 6498/6498 cat tmp_p+h+v/bacteria/*.fna > reference-sequences/all-bacteria.fna.tmp && mv reference-sequences/all-bacteria.fna.tmp reference-sequences/all-bacteria.fna mv tmp_p+h+v/all-bacteria.map reference-sequences/all-bacteria.map rm -rf tmp_p+h+v [[ -d tmp_p+h+v ]] && rm -rf tmp_p+h+v; mkdir -p tmp_p+h+v Downloading and dust-masking viral-any_level centrifuge-download -o tmp_p+h+v -m -d "viral-any_level" -P 1 refseq > \ tmp_p+h+v/all-viral-any_level.map viral-any_level is not a valid domain - use one of the following: archaea bacteria fungi invertebrate plant protozoa unknown vertebrate_mammalian vertebrate_other viral make[1]: *** [reference-sequences/all-viral-any_level.fna] Error 1 make[1]: Leaving directory
/misc/xxx/software/centrifuge/indices'
make: *** [p+h+v] Error 2
from centrifuge.
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from centrifuge.