Open Mewgia opened 9 months ago
update kaiju to the latest version from GitHub. The URL for the progenomes download changed since release v1.9.2.
I should make a new release including this fix..
Thanks, done. But now there's a new error: Downloading proGenomes database progenomes3.proteins.representatives.f 100%[=========================================================================>] 23.78G 21.1MB/s in 17m 45s 2023-11-27 10:53:36 URL:https://progenomes.embl.de/data/repGenomes/progenomes3.proteins.representatives.fasta.bz2 [25536098227/25536098227] -> "progenomes/source/progenomes3.proteins.representatives.fasta.bz2" [1] Downloading virus genomes from RefSeq Extracting protein sequences from downloaded files xargs: warning: options --max-args and --replace/-I/-i are mutually exclusive, ignoring previous --max-args value Creating Borrows-Wheeler transform infilename= progenomes/kaiju_db_progenomes.faa outfilename= progenomes/kaiju_db_progenomes Alphabet= ACDEFGHIKLMNPQRSTVWY nThreads= 5 length= 0.000000 checkpoint= 3 caseSens=OFF revComp=OFF term= revsort=OFF help=OFF Sequences read time = 2346.803643s SLEN 46856907323 NSEQ 141847069 ALPH ACDEFGHIKLMNPQRSTVWY Killed
96Gb RAM, Debian GNU/Linux 11 (bullseye) Previously, I've used kaiju with progenomes on debian jessie without any problems.
Have a look at the table in the README for the memory requirements for building the kaiju index for each available reference database. For proGenomes v3 it is 120GB of RAM.
update kaiju to the latest version from GitHub. The URL for the progenomes download changed since release v1.9.2.
I should make a new release including this fix..
I would like to install the latest version because of the same issue , but unfortunately the conda version I downloaded is still recording v1.9.2 despite bioconda page saying its 1.10.0 and the kaiju-makedb -s progenomes
still gets the same not found error. can you please check since I cant install the github way because I am working in a cluster and I don't have the sudo permissions which means I have to wait until they resolve my installation ticket which takes days sometimes.
conda create -n kaiju2 -y -c bioconda kaiju=1.10.0
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/maloo/.conda/envs/kaiju2
added / updated specs:
- kaiju=1.10.0
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-hd590300_5
c-ares conda-forge/linux-64::c-ares-1.23.0-hd590300_0
ca-certificates conda-forge/linux-64::ca-certificates-2023.11.17-hbcca054_0
curl conda-forge/linux-64::curl-8.4.0-hca28451_0
gettext conda-forge/linux-64::gettext-0.21.1-h27087fc_0
kaiju bioconda/linux-64::kaiju-1.10.0-h43eeafb_0
keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
krb5 conda-forge/linux-64::krb5-1.21.2-h659d440_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0
libcurl conda-forge/linux-64::libcurl-8.4.0-hca28451_0
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-h516909a_1
libexpat conda-forge/linux-64::libexpat-2.5.0-hcb278e6_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h807b86a_3
libgomp conda-forge/linux-64::libgomp-13.2.0-h807b86a_3
libidn2 conda-forge/linux-64::libidn2-2.3.4-h166bdaf_0
libnghttp2 conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_0
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.44.2-h2797004_0
libssh2 conda-forge/linux-64::libssh2-1.11.0-h0841786_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.2.0-h7e041cc_3
libunistring conda-forge/linux-64::libunistring-0.9.10-h7f98852_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.2.13-hd590300_5
ncurses conda-forge/linux-64::ncurses-6.4-h59595ed_2
openssl conda-forge/linux-64::openssl-3.2.0-hd590300_1
perl conda-forge/linux-64::perl-5.32.1-4_hd590300_perl5
pip conda-forge/noarch::pip-23.3.1-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.12.0-hab00c5b_0_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-68.2.2-pyhd8ed1ab_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2023c-h71feb2d_0
wget conda-forge/linux-64::wget-1.20.3-ha35d2d1_1
wheel conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
zlib conda-forge/linux-64::zlib-1.2.13-hd590300_5
zstd conda-forge/linux-64::zstd-1.5.5-hfc55251_0
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate kaiju2
#
# To deactivate an active environment, use
#
# $ conda deactivate
conda activate kaiju2
kaiju
Error: Please specify the location of the nodes.dmp file, using the -t option.
Kaiju 1.9.2
Copyright 2015-2022 Peter Menzel, Anders Krogh
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
Just tried to install v1.10.0 via conda and got the correct version. You can also just compile it from source and run it without need for root.
I have encountered the same problem:
\033[0;32mExtracting taxdump.tar.gz\033[0m Creating Borrows-Wheeler transform
Sequences read time = 339.643674s SLEN 50636639214 NSEQ 155772604 ALPH *ACDEFGHIKLMNPQRSTVWY /home/Public/Anaconda3/ENTER/envs/kaiju/bin/kaiju-makedb: line 261: 1817838 Killed kaiju-mkbwt -n $threadsBWT -e $exponentSA -a ACDEFGHIKLMNPQRSTVWY -o $DB/kaijudb$DB $DB/kaijudb$DB.faa
Is this the problem with RAM?
Probably. See the README for required RAM for each reference database. You can also download premade indexes.
but the indexes offered on kaiju website is a little outdatetd, is there a way to locally make the index with out this much RAM? the server i work on has about 115gb of free RAM, just short to build the current refseq index
You won't loose much when using the index file from last year. The memory requirements cannot be reduced..
Hello! I'm trying to download progenomes database and see that: Downloading taxdump.tar.gz .listing [ <=> ] 1.85K --.-KB/s in 0.01s
2023-11-23 13:11:56 URL: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz [1890] -> ".listing" [1] taxdump.tar.gz 100%[=========================================================================>] 60.88M 13.6MB/s in 5.5s
2023-11-23 13:12:03 URL: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz [63835104] -> "taxdump.tar.gz" [1] Extracting taxdump.tar.gz Downloading proGenomes database https://progenomes.embl.de/data/repGenomes/freeze12.proteins.representatives.fasta.gz: 2023-11-23 13:12:16 ERROR 404: Not Found.
What should I do? Thanks.