Hi all,
I am trying to run metagenomic profiling on one read (the fwd one) from paired end shot gun sequencing. Everything seems to work- I ran a tutorial with the Supragingival_plaque.fasta and it worked great. When I tried to use my own files I don’t get any error messages but I get this result:
the bowtie output file looks like this:
Here is the code I used for the run:
And if it helps, here’s all the code from downloading MetaPhlAn and its databases:
(base) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % conda config --add channels defaults
Warning: ‘defaults’ already in ‘channels’ list, moving to the top
(base) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % conda config --add channels bioconda
Warning: ‘bioconda’ already in ‘channels’ list, moving to the top
(base) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % conda config --add channels conda-forge
Warning: ‘conda-forge’ already in ‘channels’ list, moving to the top
(base) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % conda create --name mpa -c bioconda python=3.7 metaphlan
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 4.13.0
Please update conda by running
$ conda update -n base conda
Package Plan
environment location: /Users/stephaniegetto/opt/anaconda3/envs/mpa
added / updated specs:
- metaphlan
- python=3.7
The following packages will be downloaded:
package | build
---------------------------|-----------------
biom-format-2.1.12 | py37h49e79e5_1 10.4 MB conda-forge
biopython-1.79 | py37h271585c_1 2.6 MB conda-forge
bowtie2-2.4.5 | py37h0f016ca_2 1.4 MB bioconda
brotlipy-0.7.0 |py37h69ee0a8_1004 366 KB conda-forge
bx-python-0.8.13 | py37h2b10027_1 931 KB bioconda
certifi-2022.5.18.1 | py37hf985489_0 150 KB conda-forge
cffi-1.15.0 | py37h446072c_0 218 KB conda-forge
click-8.1.3 | py37hf985489_0 145 KB conda-forge
cryptography-37.0.2 | py37h0169fcd_0 1.2 MB conda-forge
fonttools-4.33.3 | py37h994c40b_0 1.6 MB conda-forge
future-0.18.2 | py37hf985489_5 709 KB conda-forge
h5py-3.6.0 |nompi_py37h0ac0de7_100 1.1 MB conda-forge
importlib-metadata-4.11.4 | py37hf985489_0 33 KB conda-forge
kiwisolver-1.4.2 | py37h18621fa_1 61 KB conda-forge
matplotlib-base-3.5.2 | py37h80cb303_0 7.4 MB conda-forge
metaphlan-3.0.14 | pyhb7b1952_0 237 KB bioconda
numpy-1.21.6 | py37h345d48f_0 6.0 MB conda-forge
pandas-1.3.4 | py37h5b83a90_1 11.3 MB conda-forge
pillow-9.1.1 | py37h1eb1bbc_1 44.5 MB conda-forge
pysam-0.19.1 | py37h64e44a1_0 2.3 MB bioconda
pysocks-1.7.1 | py37hf985489_5 28 KB conda-forge
python-3.7.12 |haf480d7_100_cpython 24.3 MB conda-forge
python-lzo-1.14 | py37h1c4811e_1 18 KB conda-forge
python_abi-3.7 | 2_cp37m 4 KB conda-forge
scipy-1.7.3 | py37h4e3cf02_0 19.7 MB conda-forge
setuptools-59.8.0 | py37hf985489_1 1.0 MB conda-forge
statsmodels-0.13.2 | py37h032687b_0 10.6 MB conda-forge
typing-extensions-4.2.0 | hd8ed1ab_1 8 KB conda-forge
typing_extensions-4.2.0 | pyha770c72_1 27 KB conda-forge
unicodedata2-14.0.0 | py37h69ee0a8_1 497 KB conda-forge
zipp-3.8.0 | pyhd8ed1ab_0 12 KB conda-forge
------------------------------------------------------------
Total: 148.8 MB
The following NEW packages will be INSTALLED:
bcbio-gff bioconda/noarch::bcbio-gff-0.6.9-pyh5e36f6f_0
biom-format conda-forge/osx-64::biom-format-2.1.12-py37h49e79e5_1
biopython conda-forge/osx-64::biopython-1.79-py37h271585c_1
blast bioconda/osx-64::blast-2.6.0-boost1.64_2
boost-cpp conda-forge/osx-64::boost-cpp-1.74.0-h8b082ac_8
bowtie2 bioconda/osx-64::bowtie2-2.4.5-py37h0f016ca_2
brotli conda-forge/osx-64::brotli-1.0.9-h5eb16cf_7
brotli-bin conda-forge/osx-64::brotli-bin-1.0.9-h5eb16cf_7
brotlipy conda-forge/osx-64::brotlipy-0.7.0-py37h69ee0a8_1004
bx-python bioconda/osx-64::bx-python-0.8.13-py37h2b10027_1
bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4
c-ares conda-forge/osx-64::c-ares-1.18.1-h0d85af4_0
ca-certificates conda-forge/osx-64::ca-certificates-2022.5.18.1-h033912b_0
cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1
cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1
capnproto conda-forge/osx-64::capnproto-0.9.1-h45c0eea_5
certifi conda-forge/osx-64::certifi-2022.5.18.1-py37hf985489_0
cffi conda-forge/osx-64::cffi-1.15.0-py37h446072c_0
charset-normalizer conda-forge/noarch::charset-normalizer-2.0.12-pyhd8ed1ab_0
click conda-forge/osx-64::click-8.1.3-py37hf985489_0
cmseq bioconda/noarch::cmseq-1.0.4-pyhb7b1952_0
cryptography conda-forge/osx-64::cryptography-37.0.2-py37h0169fcd_0
cycler conda-forge/noarch::cycler-0.11.0-pyhd8ed1ab_0
dendropy bioconda/noarch::dendropy-4.5.2-pyh3252c3a_0
diamond bioconda/osx-64::diamond-2.0.15-h9d1909e_0
fasttree bioconda/osx-64::fasttree-2.1.11-hdcdfbac_1
fonttools conda-forge/osx-64::fonttools-4.33.3-py37h994c40b_0
freetype conda-forge/osx-64::freetype-2.10.4-h4cff582_1
future conda-forge/osx-64::future-0.18.2-py37hf985489_5
giflib conda-forge/osx-64::giflib-5.2.1-hbcb3906_2
gsl conda-forge/osx-64::gsl-2.7-h93259b0_0
h5py conda-forge/osx-64::h5py-3.6.0-nompi_py37h0ac0de7_100
hdf5 conda-forge/osx-64::hdf5-1.12.1-nompi_ha60fbc9_104
htslib bioconda/osx-64::htslib-1.15.1-hc057d7f_0
icu conda-forge/osx-64::icu-70.1-h96cf925_0
idna conda-forge/noarch::idna-3.3-pyhd8ed1ab_0
importlib-metadata conda-forge/osx-64::importlib-metadata-4.11.4-py37hf985489_0
iqtree bioconda/osx-64::iqtree-2.2.0.3-h135ad0d_0
jpeg conda-forge/osx-64::jpeg-9e-h5eb16cf_1
kiwisolver conda-forge/osx-64::kiwisolver-1.4.2-py37h18621fa_1
krb5 conda-forge/osx-64::krb5-1.19.3-hb49756b_0
lcms2 conda-forge/osx-64::lcms2-2.12-h577c468_0
lerc conda-forge/osx-64::lerc-3.0-he49afe7_0
libblas conda-forge/osx-64::libblas-3.9.0-14_osx64_openblas
libbrotlicommon conda-forge/osx-64::libbrotlicommon-1.0.9-h5eb16cf_7
libbrotlidec conda-forge/osx-64::libbrotlidec-1.0.9-h5eb16cf_7
libbrotlienc conda-forge/osx-64::libbrotlienc-1.0.9-h5eb16cf_7
libcblas conda-forge/osx-64::libcblas-3.9.0-14_osx64_openblas
libcurl conda-forge/osx-64::libcurl-7.83.1-h372c54d_0
libcxx conda-forge/osx-64::libcxx-14.0.4-hc203e6f_0
libdeflate conda-forge/osx-64::libdeflate-1.10-h0d85af4_0
libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2
libev conda-forge/osx-64::libev-4.33-haf1e3a3_1
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libgfortran conda-forge/osx-64::libgfortran-5.0.0-9_3_0_h6c81a4c_23
libgfortran5 conda-forge/osx-64::libgfortran5-9.3.0-h6c81a4c_23
liblapack conda-forge/osx-64::liblapack-3.9.0-14_osx64_openblas
libnghttp2 conda-forge/osx-64::libnghttp2-1.47.0-h942079c_0
libopenblas conda-forge/osx-64::libopenblas-0.3.20-openmp_hb3cd9ec_0
libpng conda-forge/osx-64::libpng-1.6.37-h7cec526_2
libssh2 conda-forge/osx-64::libssh2-1.10.0-h52ee1ee_2
libtiff conda-forge/osx-64::libtiff-4.4.0-hfca7e8f_0
libwebp conda-forge/osx-64::libwebp-1.2.2-h28dabe5_0
libwebp-base conda-forge/osx-64::libwebp-base-1.2.2-h0d85af4_1
libxcb conda-forge/osx-64::libxcb-1.13-h0d85af4_1004
libzlib conda-forge/osx-64::libzlib-1.2.12-h6c3fc93_0
llvm-openmp conda-forge/osx-64::llvm-openmp-14.0.4-ha654fa7_0
lz4-c conda-forge/osx-64::lz4-c-1.9.3-he49afe7_1
lzo conda-forge/osx-64::lzo-2.10-haf1e3a3_1000
mafft bioconda/osx-64::mafft-7.505-ha5712d3_0
mash bioconda/osx-64::mash-2.3-hf785b45_2
matplotlib-base conda-forge/osx-64::matplotlib-base-3.5.2-py37h80cb303_0
metaphlan bioconda/noarch::metaphlan-3.0.14-pyhb7b1952_0
munkres bioconda/noarch::munkres-1.0.7-py_1
muscle bioconda/osx-64::muscle-5.1-hb339e23_1
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
numpy conda-forge/osx-64::numpy-1.21.6-py37h345d48f_0
openjpeg conda-forge/osx-64::openjpeg-2.4.0-h6e7aa92_1
openssl conda-forge/osx-64::openssl-1.1.1o-hfe4f2af_0
packaging conda-forge/noarch::packaging-21.3-pyhd8ed1ab_0
pandas conda-forge/osx-64::pandas-1.3.4-py37h5b83a90_1
patsy conda-forge/noarch::patsy-0.5.2-pyhd8ed1ab_0
perl conda-forge/osx-64::perl-5.32.1-2_h0d85af4_perl5
phylophlan bioconda/noarch::phylophlan-3.0.2-py_0
pillow conda-forge/osx-64::pillow-9.1.1-py37h1eb1bbc_1
pip conda-forge/noarch::pip-22.1.2-pyhd8ed1ab_0
pthread-stubs conda-forge/osx-64::pthread-stubs-0.4-hc929b4f_1001
pycparser conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
pyopenssl conda-forge/noarch::pyopenssl-22.0.0-pyhd8ed1ab_0
pyparsing conda-forge/noarch::pyparsing-3.0.9-pyhd8ed1ab_0
pysam bioconda/osx-64::pysam-0.19.1-py37h64e44a1_0
pysocks conda-forge/osx-64::pysocks-1.7.1-py37hf985489_5
python conda-forge/osx-64::python-3.7.12-haf480d7_100_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python-lzo conda-forge/osx-64::python-lzo-1.14-py37h1c4811e_1
python_abi conda-forge/osx-64::python_abi-3.7-2_cp37m
pytz conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
raxml bioconda/osx-64::raxml-8.2.12-ha5712d3_4
readline conda-forge/osx-64::readline-8.1-h05e3726_0
requests conda-forge/noarch::requests-2.27.1-pyhd8ed1ab_0
samtools bioconda/osx-64::samtools-1.15.1-h9f30945_0
scipy conda-forge/osx-64::scipy-1.7.3-py37h4e3cf02_0
seaborn conda-forge/noarch::seaborn-0.11.2-hd8ed1ab_0
seaborn-base conda-forge/noarch::seaborn-base-0.11.2-pyhd8ed1ab_0
setuptools conda-forge/osx-64::setuptools-59.8.0-py37hf985489_1
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
sqlite conda-forge/osx-64::sqlite-3.38.5-hd9f0692_0
statsmodels conda-forge/osx-64::statsmodels-0.13.2-py37h032687b_0
tbb conda-forge/osx-64::tbb-2020.2-h940c156_4
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
trimal bioconda/osx-64::trimal-1.4.1-hcd10b59_6
typing-extensions conda-forge/noarch::typing-extensions-4.2.0-hd8ed1ab_1
typing_extensions conda-forge/noarch::typing_extensions-4.2.0-pyha770c72_1
unicodedata2 conda-forge/osx-64::unicodedata2-14.0.0-py37h69ee0a8_1
urllib3 conda-forge/noarch::urllib3-1.26.9-pyhd8ed1ab_0
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xorg-libxau conda-forge/osx-64::xorg-libxau-1.0.9-h35c211d_0
xorg-libxdmcp conda-forge/osx-64::xorg-libxdmcp-1.1.3-h35c211d_0
xz conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
zipp conda-forge/noarch::zipp-3.8.0-pyhd8ed1ab_0
zlib conda-forge/osx-64::zlib-1.2.12-h6c3fc93_0
zstd conda-forge/osx-64::zstd-1.5.2-ha9df2e0_1
Proceed ([y]/n)? y
Downloading and Extracting Packages
pandas-1.3.4 | 11.3 MB | ##################################### | 100%
typing-extensions-4. | 8 KB | ##################################### | 100%
statsmodels-0.13.2 | 10.6 MB | ##################################### | 100%
fonttools-4.33.3 | 1.6 MB | ##################################### | 100%
pysam-0.19.1 | 2.3 MB | ##################################### | 100%
python-3.7.12 | 24.3 MB | ##################################### | 100%
unicodedata2-14.0.0 | 497 KB | ##################################### | 100%
brotlipy-0.7.0 | 366 KB | ##################################### | 100%
cryptography-37.0.2 | 1.2 MB | ##################################### | 100%
importlib-metadata-4 | 33 KB | ##################################### | 100%
bx-python-0.8.13 | 931 KB | ##################################### | 100%
future-0.18.2 | 709 KB | ##################################### | 100%
biopython-1.79 | 2.6 MB | ##################################### | 100%
h5py-3.6.0 | 1.1 MB | ##################################### | 100%
typing_extensions-4. | 27 KB | ##################################### | 100%
biom-format-2.1.12 | 10.4 MB | ##################################### | 100%
certifi-2022.5.18.1 | 150 KB | ##################################### | 100%
scipy-1.7.3 | 19.7 MB | ##################################### | 100%
click-8.1.3 | 145 KB | ##################################### | 100%
numpy-1.21.6 | 6.0 MB | ##################################### | 100%
bowtie2-2.4.5 | 1.4 MB | ##################################### | 100%
cffi-1.15.0 | 218 KB | ##################################### | 100%
kiwisolver-1.4.2 | 61 KB | ##################################### | 100%
metaphlan-3.0.14 | 237 KB | ##################################### | 100%
setuptools-59.8.0 | 1.0 MB | ##################################### | 100%
matplotlib-base-3.5. | 7.4 MB | ##################################### | 100%
zipp-3.8.0 | 12 KB | ##################################### | 100%
python-lzo-1.14 | 18 KB | ##################################### | 100%
pillow-9.1.1 | 44.5 MB | ##################################### | 100%
pysocks-1.7.1 | 28 KB | ##################################### | 100%
python_abi-3.7 | 4 KB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
To activate this environment, use
$ conda activate mpa
To deactivate an active environment, use
$ conda deactivate
(base) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % cd
(base) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % mkdir -p db/metaphlan_databases
(base) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % conda activate mpa
(mpa) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % metaphlan --install --bowtie2db ~/db/metaphlan_databases
Downloading http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_latest
Downloading file of size: 0.00 MB
0.01 MB 31507.69 % 53.19 MB/sec 0 min -0 sec
Downloading MetaPhlAn database
Please note due to the size this might take a few minutes
Downloading http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.tar
Downloading file of size: 366.62 MB
366.62 MB 100.00 % 7.71 MB/sec 0 min -0 sec
Downloading http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.md5
Downloading file of size: 0.00 MB
0.01 MB 12800.00 % 35.01 MB/sec 0 min -0 sec
Decompressing /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.fna.bz2 into /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.fna
Building Bowtie2 indexes
Renaming /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.3.bt2.tmp to /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.3.bt2
Renaming /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.4.bt2.tmp to /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.4.bt2
Renaming /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.1.bt2.tmp to /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.1.bt2
Renaming /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.2.bt2.tmp to /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.2.bt2
Renaming /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.rev.1.bt2.tmp to /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.rev.1.bt2
Renaming /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.rev.2.bt2.tmp to /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.rev.2.bt2
Removing uncompress database /Users/stephaniegetto/db/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.fna
Download complete
The database is installed
(mpa) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % mkdir metaphlan_analysis
(mpa) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % cd metaphlan_analysis
(mpa) stephaniegetto@Stephanies-MacBook-Pro-3 metaphlan_analysis % curl -LO https://github.com/biobakery/biobakery/raw/master/demos/biobakery_demos/data/metaphlan3/input/SRS014476-Supragingival_plaque.fasta.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 192k 0 192k 0 0 360k 0 --:–:-- --:–:-- --:–:-- 365k
I have run this sample in other programs and gotten some results, so I don’t think it’s bad data… any ideas?