Error:
CRITICAL ERROR: Error executing: /revan/scratch/projects/2023/envs/biobakery3/bin/diamond blastx --query /revan/scratch/projects/2023/data/humann_output_veba_db_v3/SRR5788015_humann_temp_f65f3csv/SRR5788015_bowtie2_unaligned.fa --evalue 1.0 --threads 50 --top 1 --sensitive --outfmt 6 --db /revan/scratch/projects/2023/data/dmnd_db/uniref50_201901b_full --out /revan/scratch/projects/2023/data/humann_output_veba_db_v3/SRR5788015_humann_temp_f65f3csv/tmp93e56v68/diamond_m8_ejh7pvsv --tmpdir /revan/scratch/projects/2023/data/humann_output_veba_db_v3/SRR5788015_humann_temp_f65f3csv/tmp93e56v68
Error message returned from diamond :
diamond v2.0.15.153 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)
#CPU threads: 50
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /revan/scratch/projects/2023/data/humann_output_veba_db_v3/SRR5788015_humann_temp_f65f3csv/tmp93e56v68
Percentage range of top alignment score to report hits: 1
Opening the database... [0.179s]
Database: /revan/scratch/projects/2023/data/dmnd_db/uniref50_201901b_full.dmnd (type: Diamond database, sequences: 32474829, letters: 9843106304)
Here’s the linux version:
NAME="Red Hat Enterprise Linux"
VERSION="8.4 (Ootpa)"
ID="rhel"
ID_LIKE="fedora"
VERSION_ID="8.4"
PLATFORM_ID="platform:el8"
PRETTY_NAME="Red Hat Enterprise Linux 8.4 (Ootpa)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:redhat:enterprise_linux:8.4:GA"
HOME_URL="https://www.redhat.com/"
DOCUMENTATION_URL="https://access.redhat.com/documentation/red_hat_enterprise_linux/8/"
BUG_REPORT_URL="https://bugzilla.redhat.com/"
REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 8"
REDHAT_BUGZILLA_PRODUCT_VERSION=8.4
REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="8.4"
Uploaded the conda environment:
name: biobakery3
channels:
- plotly
- biobakery
- conda-forge
- bioconda
- defaults
- revan
- qiime2
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_kmp_llvm
- _r-mutex=1.0.1=anacondar_1
- alsa-lib=1.2.8=h166bdaf_0
- attr=2.5.1=h166bdaf_1
- bcbio-gff=0.7.0=pyh7cba7a3_0
- binutils_impl_linux-64=2.36.1=h193b22a_2
- binutils_linux-64=2.36=hf3e587d_10
- biom-format=2.1.12=py37hda87dfa_1
- blas=2.116=openblas
- blas-devel=3.9.0=16_linux64_openblas
- blast=2.13.0=hf3cf87c_0
- boost-cpp=1.74.0=h75c5d50_8
- bowtie2=2.4.5=py37h1840d8f_3
- brotli=1.0.9=h166bdaf_8
- brotli-bin=1.0.9=h166bdaf_8
- brotlipy=0.7.0=py37h540881e_1004
- bwidget=1.9.14=ha770c72_1
- bx-python=0.9.0=py37hfa8f21c_0
- bzip2=1.0.8=h7f98852_4
- c-ares=1.18.1=h7f98852_0
- ca-certificates=2022.12.7=ha878542_0
- cached-property=1.5.2=hd8ed1ab_1
- cached_property=1.5.2=pyha770c72_1
- cairo=1.16.0=ha61ee94_1014
- capnproto=0.10.2=h6239696_0
- certifi=2022.12.7=pyhd8ed1ab_0
- cffi=1.15.1=py37h43b0acd_1
- charset-normalizer=3.1.0=pyhd8ed1ab_0
- click=7.1.2=pyh9f0ad1d_0
- cmseq=1.0.4=pyhb7b1952_0
- colorama=0.4.6=pyhd8ed1ab_0
- conda=4.14.0=py37h89c1867_0
- conda-package-handling=1.9.0=py37h540881e_0
- cryptography=37.0.4=py37h38fbfac_0
- curl=7.83.1=h7bff187_0
- cycler=0.11.0=pyhd8ed1ab_0
- dbus=1.13.6=h5008d03_3
- dendropy=4.5.2=pyh3252c3a_0
- entrez-direct=16.2=he881be0_1
- ete3=3.1.2=pyh9f0ad1d_0
- expat=2.5.0=hcb278e6_1
- fasttree=2.1.11=hec16e2b_1
- fftw=3.3.10=nompi_hc118613_107
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=hab24e00_0
- fontconfig=2.14.2=h14ed4e7_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- fonttools=4.34.4=py37h540881e_0
- freetype=2.12.1=hca18f0e_1
- fribidi=1.0.10=h36c2ea0_0
- future=0.18.2=py37h89c1867_5
- gcc_impl_linux-64=11.2.0=h82a94d6_16
- gcc_linux-64=11.2.0=h39a9532_10
- gettext=0.21.1=h27087fc_0
- gfortran_impl_linux-64=11.2.0=h7a446d4_16
- gfortran_linux-64=11.2.0=h777b47f_10
- giflib=5.2.1=h0b41bf4_3
- glib=2.74.1=h6239696_0
- glib-tools=2.74.1=h6239696_0
- glpk=5.0=h445213a_0
- gmp=6.2.1=h58526e2_0
- graphite2=1.3.13=h58526e2_1001
- gsl=2.7=he838d99_0
- gst-plugins-base=1.21.3=h4243ec0_1
- gstreamer=1.21.3=h25f0c4b_1
- gstreamer-orc=0.4.33=h166bdaf_0
- gxx_impl_linux-64=11.2.0=h82a94d6_16
- gxx_linux-64=11.2.0=hacbe6df_10
- h5py=3.7.0=nompi_py37hf1ce037_101
- harfbuzz=6.0.0=h8e241bc_0
- hdf5=1.12.2=nompi_h2386368_100
- htslib=1.15.1=h9753748_0
- humann=3.0.1=pyh5e36f6f_0
- icu=70.1=h27087fc_0
- idna=3.4=pyhd8ed1ab_0
- iqtree=2.2.0.3=hb97b32f_1
- jack=1.9.22=h11f4161_0
- jpeg=9e=h0b41bf4_3
- kernel-headers_linux-64=2.6.32=he073ed8_15
- keyutils=1.6.1=h166bdaf_0
- kiwisolver=1.4.4=py37h7cecad7_0
- krb5=1.19.3=h3790be6_0
- lame=3.100=h166bdaf_1003
- lcms2=2.12=hddcbb42_0
- ld_impl_linux-64=2.36.1=hea4e1c9_2
- lerc=3.0=h9c3ff4c_0
- libarchive=3.5.2=hb890918_3
- libblas=3.9.0=16_linux64_openblas
- libbrotlicommon=1.0.9=h166bdaf_8
- libbrotlidec=1.0.9=h166bdaf_8
- libbrotlienc=1.0.9=h166bdaf_8
- libcap=2.66=ha37c62d_0
- libcblas=3.9.0=16_linux64_openblas
- libclang=15.0.7=default_had23c3d_1
- libclang13=15.0.7=default_h3e3d535_1
- libcups=2.3.3=h3e49a29_2
- libcurl=7.83.1=h7bff187_0
- libdb=6.2.32=h9c3ff4c_0
- libdeflate=1.10=h7f98852_0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libevent=2.1.10=h9b69904_4
- libexpat=2.5.0=hcb278e6_1
- libffi=3.4.2=h7f98852_5
- libflac=1.4.2=h27087fc_0
- libgcc-devel_linux-64=11.2.0=h0952999_16
- libgcc-ng=12.2.0=h65d4601_19
- libgcrypt=1.10.1=h166bdaf_0
- libgfortran-ng=12.2.0=h69a702a_19
- libgfortran5=12.2.0=h337968e_19
- libglib=2.74.1=h7a41b64_0
- libgomp=12.2.0=h65d4601_19
- libgpg-error=1.46=h620e276_0
- libiconv=1.17=h166bdaf_0
- libidn2=2.3.4=h166bdaf_0
- liblapack=3.9.0=16_linux64_openblas
- liblapacke=3.9.0=16_linux64_openblas
- libllvm15=15.0.7=hadd5161_1
- libmamba=0.25.0=hd8a31e3_2
- libmambapy=0.25.0=py37h1ee4b26_2
- libnghttp2=1.47.0=h727a467_0
- libnsl=2.0.0=h7f98852_0
- libogg=1.3.4=h7f98852_1
- libopenblas=0.3.21=pthreads_h78a6416_3
- libopus=1.3.1=h7f98852_1
- libpng=1.6.39=h753d276_0
- libpq=15.1=hf695f80_1
- libsanitizer=11.2.0=he4da1e4_16
- libsndfile=1.2.0=hb75c966_0
- libsolv=0.7.23=h3eb15da_0
- libsqlite=3.40.0=h753d276_0
- libssh2=1.10.0=haa6b8db_3
- libstdcxx-devel_linux-64=11.2.0=h0952999_16
- libstdcxx-ng=12.2.0=h46fd767_19
- libsystemd0=252=h2a991cd_0
- libtiff=4.4.0=h0fcbabc_0
- libtool=2.4.7=h27087fc_0
- libudev1=253=h0b41bf4_0
- libunistring=0.9.10=h7f98852_0
- libuuid=2.38.1=h0b41bf4_0
- libvorbis=1.3.7=h9c3ff4c_0
- libwebp=1.2.4=h522a892_0
- libwebp-base=1.2.4=h166bdaf_0
- libxcb=1.13=h7f98852_1004
- libxkbcommon=1.5.0=h79f4944_1
- libxml2=2.10.3=hca2bb57_4
- libxslt=1.1.37=h873f0b0_0
- libzlib=1.2.13=h166bdaf_4
- llvm-openmp=16.0.1=h417c0b6_0
- lxml=4.9.1=py37h540881e_0
- lz4-c=1.9.4=hcb278e6_0
- lzo=2.10=h516909a_1000
- mafft=7.520=hec16e2b_0
- make=4.3=hd18ef5c_1
- mamba=0.25.0=py37h6dacc13_2
- mash=2.3=hd3113c8_4
- matplotlib-base=3.5.3=py37hf395dca_2
- metaphlan=3.0.14=pyhb7b1952_0
- mpg123=1.31.3=hcb278e6_0
- munkres=1.1.4=pyh9f0ad1d_0
- muscle=5.1=h9f5acd7_1
- mysql-common=8.0.32=h14678bc_0
- mysql-libs=8.0.32=h54cf53e_0
- ncurses=6.3=h27087fc_1
- nspr=4.35=h27087fc_0
- nss=3.89=he45b914_0
- numpy=1.21.6=py37h976b520_0
- openblas=0.3.21=pthreads_h320a7e8_3
- openjpeg=2.5.0=h7d73246_1
- openssl=1.1.1t=h0b41bf4_0
- packaging=23.0=pyhd8ed1ab_0
- pandas=1.2.3=py37hdc94413_0
- pango=1.50.14=hd33c08f_0
- patsy=0.5.3=pyhd8ed1ab_0
- pcre=8.45=h9c3ff4c_0
- pcre2=10.37=hc3806b6_1
- perl=5.32.1=2_h7f98852_perl5
- perl-archive-tar=2.40=pl5321hdfd78af_0
- perl-carp=1.50=pl5321hd8ed1ab_0
- perl-common-sense=3.75=pl5321hd8ed1ab_0
- perl-compress-raw-bzip2=2.201=pl5321h166bdaf_0
- perl-compress-raw-zlib=2.202=pl5321h166bdaf_0
- perl-encode=3.19=pl5321h166bdaf_0
- perl-exporter=5.74=pl5321hd8ed1ab_0
- perl-exporter-tiny=1.002002=pl5321hd8ed1ab_0
- perl-extutils-makemaker=7.70=pl5321hd8ed1ab_0
- perl-io-compress=2.201=pl5321h87f3376_0
- perl-io-zlib=1.14=pl5321hdfd78af_0
- perl-json=4.10=pl5321hdfd78af_0
- perl-json-xs=2.34=pl5321h9f5acd7_5
- perl-list-moreutils=0.430=pl5321hdfd78af_0
- perl-list-moreutils-xs=0.430=pl5321hec16e2b_1
- perl-parent=0.241=pl5321hd8ed1ab_0
- perl-pathtools=3.75=pl5321h166bdaf_0
- perl-scalar-list-utils=1.63=pl5321h166bdaf_0
- perl-storable=3.15=pl5321h166bdaf_0
- perl-types-serialiser=1.01=pl5321hdfd78af_0
- phylophlan=3.0.3=pyhdfd78af_0
- pillow=9.2.0=py37h850a105_2
- pip=23.0.1=pyhd8ed1ab_0
- pixman=0.40.0=h36c2ea0_0
- ply=3.11=py_1
- pthread-stubs=0.4=h36c2ea0_1001
- pulseaudio=16.1=h4ab2085_1
- pybind11-abi=4=hd8ed1ab_3
- pycosat=0.6.4=py37h540881e_0
- pycparser=2.21=pyhd8ed1ab_0
- pyopenssl=22.0.0=pyhd8ed1ab_1
- pyparsing=3.0.9=pyhd8ed1ab_0
- pyqt=5.15.7=py37hf30b843_1
- pyqt5-sip=12.11.0=py37hd23a5d3_1
- pysam=0.19.1=py37h8fe4cdf_0
- pysocks=1.7.1=py37h89c1867_5
- python=3.7.12=hb7a2778_100_cpython
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python-kaleido=0.0.3=py37_0
- python-lzo=1.14=py37hd06c622_1
- python_abi=3.7=3_cp37m
- pytz=2023.3=pyhd8ed1ab_0
- qt=5.15.6=hf11cfaa_0
- qt-main=5.15.6=h25460bb_4
- qt-webengine=5.15.4=h325cec9_3
- r-base=4.2.1=ha8c3e7c_1
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- readline=8.2=h8228510_1
- reproc=14.2.4=h0b41bf4_0
- reproc-cpp=14.2.4=hcb278e6_0
- requests=2.28.2=pyhd8ed1ab_1
- ruamel_yaml=0.15.80=py37h540881e_1007
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- scipy=1.7.3=py37hf2a6cf1_0
- seaborn=0.12.2=hd8ed1ab_0
- seaborn-base=0.12.2=pyhd8ed1ab_0
- sed=4.8=he412f7d_0
- seqkit=2.3.1=h9ee0642_0
- seqtk=1.3=h7132678_4
- setuptools=59.8.0=py37h89c1867_1
- sip=6.7.2=py37hd23a5d3_0
- six=1.16.0=pyh6c4a22f_0
- sqlite=3.40.0=h4ff8645_0
- statsmodels=0.13.2=py37hda87dfa_0
- sysroot_linux-64=2.12=he073ed8_15
- taxonomy_ranks=0.0.10=py_0
- tbb=2020.2=h4bd325d_4
- tk=8.6.12=h27826a3_0
- tktable=2.10=hb7b940f_3
- toml=0.10.2=pyhd8ed1ab_0
- toolz=0.12.0=pyhd8ed1ab_0
- trimal=1.4.1=h9f5acd7_6
- typing-extensions=4.5.0=hd8ed1ab_0
- typing_extensions=4.5.0=pyha770c72_0
- unicodedata2=14.0.0=py37h540881e_1
- urllib3=1.26.15=pyhd8ed1ab_0
- wget=1.20.3=ha56f1ee_1
- wheel=0.40.0=pyhd8ed1ab_0
- xcb-util=0.4.0=h516909a_0
- xcb-util-image=0.4.0=h166bdaf_0
- xcb-util-keysyms=0.4.0=h516909a_0
- xcb-util-renderutil=0.3.9=h166bdaf_0
- xcb-util-wm=0.4.1=h516909a_0
- xkeyboard-config=2.38=h0b41bf4_0
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.0.10=h7f98852_0
- xorg-libsm=1.2.3=hd9c2040_1000
- xorg-libx11=1.8.4=h0b41bf4_0
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- xorg-libxdmcp=1.1.3=h7f98852_0
- xorg-libxext=1.3.4=h0b41bf4_2
- xorg-libxrender=0.9.10=h7f98852_1003
- xorg-libxt=1.2.1=h7f98852_2
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- xz=5.2.6=h166bdaf_0
- yaml=0.2.5=h7f98852_2
- yaml-cpp=0.7.0=h27087fc_2
- zlib=1.2.13=h166bdaf_4
- zstd=1.5.2=h3eb15da_6
- pip:
- bio==1.5.3
- biopython==1.80
- biothings-client==0.2.6
- configobj==5.0.8
- diamond==4.0.515
- joblib==1.2.0
- mygene==3.2.2
- psutil==5.9.4
- pydiffmap==0.2.0.1
- scikit-learn==1.0.2
- threadpoolctl==3.1.0
- tqdm==4.64.1
prefix: /revan/scratch/projects/2023/envs/biobakery3