Hello Biobakery team!
In short, i am unable to use metaphlan4.0.6/humann3.8 because I cannot get metaphlan to silence this interactive message:
Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_latest
Downloading file of size: 0.00 MB
A newer version of the database (mpa_vJan25_CHOCOPhlAnSGB_202503) is available. Do you want to download it and replace the current one (mpa_vOct22_CHOCOPhlAnSGB_202212)? [Y/N]
I have successfully ran many samples with this conda environment/program version pair before, and am attempting to on new samples to add to my existing dataset, therefore do not want to change any versions of databases or programs. However I cannot run this on our HPCs slurm queue because metaphlan continually throws this interactive message, even though i am specifying my bowtie2 database location. this happens in metaphlan inside and outside of humann. Of note, I did open an interactive node on our HPC and ran metaphlan outside of humann, specifying N on the download question, and allowed it to complete. After a successful run, it still prompted me to download the database when i tried to run a different sample.
The command im running:
humann --input ./raw/${PREFIX}.fq.gz \
--output ./humann/${PREFIX} \
-v --memory-use maximum --threads 48 \
--metaphlan-options "--bowtie2db /home/hhallow1/shared_databases/metaphlan/" \
--remove-temp-output
any help on getting this message permanently silenced would be appreciated! Thanks!
Conda environment:
# packages in environment at /home/hhallow1/.conda/envs/biobakery:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bcbio-gff 0.7.0 pyh7cba7a3_1 bioconda
biom-format 2.1.12 py37hda87dfa_1 conda-forge
biopython 1.79 py37h540881e_2 conda-forge
blast 2.15.0 pl5321h6f7f691_1 bioconda
bottleneck 1.3.5 py37hda87dfa_0 conda-forge
bowtie2 2.5.1 py37hb24965f_1 bioconda
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.0.9 py37hd23a5d3_7 conda-forge
bx-python 0.9.0 py37hfa8f21c_1 bioconda
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.25.0 hd590300_0 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
capnproto 0.10.2 h6239696_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.3 py37h89c1867_0 conda-forge
cmseq 1.0.4 pyhb7b1952_0 bioconda
curl 7.87.0 h6312ad2_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
dendropy 4.6.1 pyhdfd78af_0 bioconda
diamond 2.1.8 h43eeafb_0 bioconda
entrez-direct 16.2 he881be0_1 bioconda
fasttree 2.1.11 h031d066_2 bioconda
fonttools 4.38.0 py37h540881e_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
future 0.18.2 py37h89c1867_5 conda-forge
gawk 5.3.0 ha916aea_0 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
glpk 5.0 h445213a_0 conda-forge
gmp 6.3.0 h59595ed_0 conda-forge
gsl 2.7 he838d99_0 conda-forge
h5py 3.7.0 nompi_py37hf1ce037_101 conda-forge
hdf5 1.12.2 nompi_h2386368_101 conda-forge
htslib 1.17 h6bc39ce_1 bioconda
humann 3.8 pyh7cba7a3_0 bioconda
icu 73.2 h59595ed_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
importlib-metadata 4.11.4 py37h89c1867_0 conda-forge
iqtree 2.2.6 h21ec9f0_0 bioconda
jpeg 9e h0b41bf4_3 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 py37h7cecad7_0 conda-forge
krb5 1.20.1 hf9c8cef_0 conda-forge
lcms2 2.14 h6ed2654_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libaec 1.1.2 h59595ed_1 conda-forge
libblas 3.9.0 20_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcblas 3.9.0 20_linux64_openblas conda-forge
libcurl 7.87.0 h6312ad2_0 conda-forge
libdeflate 1.13 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h807b86a_3 conda-forge
libgfortran-ng 13.2.0 h69a702a_3 conda-forge
libgfortran5 13.2.0 ha4646dd_3 conda-forge
libgomp 13.2.0 h807b86a_3 conda-forge
libhwloc 2.9.3 default_h554bfaf_1009 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libidn2 2.3.4 h166bdaf_0 conda-forge
liblapack 3.9.0 20_linux64_openblas conda-forge
libnghttp2 1.51.0 hdcd2b5c_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libsqlite 3.44.2 h2797004_0 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge
libtiff 4.4.0 h0e0dad5_3 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.11.6 h232c23b_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lzo 2.10 h516909a_1000 conda-forge
mafft 7.520 h031d066_3 bioconda
mash 2.3 hd3113c8_6 bioconda
matplotlib-base 3.5.3 py37hf395dca_2 conda-forge
metaphlan 4.0.6 pyhca03a8a_0 bioconda
mpfr 4.2.1 h9458935_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
muscle 5.1 h4ac6f70_3 bioconda
ncbi-vdb 3.0.10 hdbdd923_0 bioconda
ncurses 6.4 h59595ed_2 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
numexpr 2.8.3 py37h85a3170_100 conda-forge
numpy 1.21.6 py37h976b520_0 conda-forge
openjpeg 2.5.0 h7d73246_1 conda-forge
openssl 1.1.1w hd590300_0 conda-forge
ossuuid 1.6.2 hf484d3e_1000 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pandas 1.3.5 py37h8c16a72_0
patsy 0.5.6 pyhd8ed1ab_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
perl 5.22.2.1 0 conda-forge
perl-archive-tar 2.18 1 bioconda
perl-common-sense 3.74 0 bioconda
perl-exporter-tiny 0.042 1 bioconda
perl-json 2.90 1 bioconda
perl-json-xs 2.34 0 bioconda
perl-list-moreutils 0.413 1 bioconda
perl-threaded 5.32.1 hdfd78af_1 bioconda
perl-uri 1.71 0 bioconda
perl-xml-libxml 2.0124 0 bioconda
perl-xml-namespacesupport 1.11 0 bioconda
perl-xml-sax 0.99 0 bioconda
perl-xml-sax-base 1.08 0 bioconda
phylophlan 3.0.3 pyhdfd78af_0 bioconda
pillow 9.2.0 py37h850a105_2 conda-forge
pip 23.3.2 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge
pysam 0.21.0 py37hee149a5_0 bioconda
pysocks 1.7.1 py37h89c1867_5 conda-forge
python 3.7.12 hb7a2778_100_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-lzo 1.14 py37hd06c622_1 conda-forge
python_abi 3.7 4_cp37m conda-forge
pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge
raxml 8.2.13 h031d066_0 bioconda
readline 8.2 h8228510_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
samtools 1.18 hd87286a_0 bioconda
scipy 1.7.3 py37hf2a6cf1_0 conda-forge
seaborn 0.12.2 hd8ed1ab_0 conda-forge
seaborn-base 0.12.2 pyhd8ed1ab_0 conda-forge
setuptools 69.0.3 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.44.2 h2c6b66d_0 conda-forge
statsmodels 0.13.2 py37hda87dfa_0 conda-forge
tbb 2021.11.0 h00ab1b0_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
trimal 1.4.1 h4ac6f70_8 bioconda
typing-extensions 4.7.1 hd8ed1ab_0 conda-forge
typing_extensions 4.7.1 pyha770c72_0 conda-forge
unicodedata2 14.0.0 py37h540881e_1 conda-forge
urllib3 2.1.0 pyhd8ed1ab_0 conda-forge
wget 1.20.3 ha56f1ee_1 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zipp 3.15.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
conda info:
active environment : biobakery
active env location : /home/hhallow1/.conda/envs/biobakery
shell level : 1
user config file : /home/hhallow1/.condarc
populated config files : /home/hhallow1/.condarc
conda version : 4.8.3
conda-build version : 3.18.11
python version : 3.8.3.final.0
virtual packages : __glibc=2.28
base environment : /data/apps/linux-centos8-cascadelake/gcc-9.3.0/anaconda3-2020.07-i7qavhiohb2uwqs4eqjeefzx3kp5jqdu (read only)
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/biobakery/linux-64
https://conda.anaconda.org/biobakery/noarch
https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /data/apps/linux-centos8-cascadelake/gcc-9.3.0/anaconda3-2020.07-i7qavhiohb2uwqs4eqjeefzx3kp5jqdu/pkgs
/home/hhallow1/.conda/pkgs
envs directories : /home/hhallow1/.conda/envs
/data/apps/linux-centos8-cascadelake/gcc-9.3.0/anaconda3-2020.07-i7qavhiohb2uwqs4eqjeefzx3kp5jqdu/envs
platform : linux-64
user-agent : conda/4.8.3 requests/2.24.0 CPython/3.8.3 Linux/4.18.0-477.21.1.el8_8.x86_64 rocky/8.8 glibc/2.28
UID:GID : 2072:1272
netrc file : None
offline mode : False