AME package 在 CONDA 環境下找不到模板

Question

我在 SLURM 服務器上的 Conda (4.5.4) 下使用 MEME-Suite package 中的 AME 軟件。 使用 AME 時，我收到以下錯誤消息：

Bad file name.  
Bad file name.  
Bad file name.  
Bad file name.  
Bad file name.  
Bad file name.  
Bad file name.  
Bad file name.  
Bad file name.  
Bad file name.  
Bad file name.  
Bad file name.  
FATAL: Template does not contain data section.  

看起來 AME 無法為 output 生產檢索其模板文件我嘗試了以下解決方案：

• conda install meme=5.0.2
• conda install meme=5.3.0
• conda install -c bioconda/label/cf201901 meme
• 此處提出的解決方案： https://github.com/bioconda/bioconda-recipes/issues/22909和此處： https://www.biostars.org/p/401084/

不幸的是，沒有什么能解決我的問題。 我必須維護 Python 3.X 版本，因此不能使用 Python 2.X 的 MEME 版本。

知道如何在這種情況下安裝 MEME 嗎？

以下是來自 Conda 環境的依賴項：

dependencies:
  - bioconductor-seqlogo=1.56.0=r40_0
  - blast=2.10.1=pl526he19e7b1_3
  - clustalo=1.2.4=he1b5a44_3
  - entrez-direct=13.9=pl526h375a9b1_1
  - logomaker=0.8=pyh864c0ab_1
  - meme=5.3.0=py37pl526h072abfd_0
  - perl-app-cpanminus=1.7044=pl526_1
  - perl-archive-tar=2.32=pl526_0
  - perl-base=2.23=pl526_1
  - perl-business-isbn=3.004=pl526_0
  - perl-business-isbn-data=20140910.003=pl526_0
  - perl-carp=1.38=pl526_3
  - perl-cgi=4.44=pl526h14c3975_1
  - perl-common-sense=3.74=pl526_2
  - perl-compress-raw-bzip2=2.087=pl526he1b5a44_0
  - perl-compress-raw-zlib=2.087=pl526hc9558a2_0
  - perl-constant=1.33=pl526_1
  - perl-data-dumper=2.173=pl526_0
  - perl-dbi=1.642=pl526_0
  - perl-digest-hmac=1.03=pl526_3
  - perl-digest-md5=2.55=pl526_0
  - perl-encode=2.88=pl526_1
  - perl-encode-locale=1.05=pl526_6
  - perl-exporter=5.72=pl526_1
  - perl-exporter-tiny=1.002001=pl526_0
  - perl-extutils-makemaker=7.36=pl526_1
  - perl-file-listing=6.04=pl526_1
  - perl-file-path=2.16=pl526_0
  - perl-file-temp=0.2304=pl526_2
  - perl-file-which=1.23=pl526_0
  - perl-html-parser=3.72=pl526h6bb024c_5
  - perl-html-tagset=3.20=pl526_3
  - perl-html-template=2.97=pl526_1
  - perl-html-tree=5.07=pl526_1
  - perl-http-cookies=6.04=pl526_0
  - perl-http-daemon=6.01=pl526_1
  - perl-http-date=6.02=pl526_3
  - perl-http-message=6.18=pl526_0
  - perl-http-negotiate=6.01=pl526_3
  - perl-io-compress=2.087=pl526he1b5a44_0
  - perl-io-html=1.001=pl526_2
  - perl-io-socket-ssl=2.066=pl526_0
  - perl-io-zlib=1.10=pl526_2
  - perl-json=4.02=pl526_0
  - perl-json-xs=2.34=pl526h6bb024c_3
  - perl-libwww-perl=6.39=pl526_0
  - perl-list-moreutils=0.428=pl526_1
  - perl-list-moreutils-xs=0.428=pl526_0
  - perl-log-log4perl=1.49=pl526_0
  - perl-lwp-mediatypes=6.04=pl526_0
  - perl-lwp-protocol-https=6.07=pl526_4
  - perl-math-cdf=0.1=pl526h14c3975_5
  - perl-mime-base64=3.15=pl526_1
  - perl-mozilla-ca=20180117=pl526_1
  - perl-net-http=6.19=pl526_0
  - perl-net-ssleay=1.88=pl526h90d6eec_0
  - perl-ntlm=1.09=pl526_4
  - perl-parent=0.236=pl526_1
  - perl-pathtools=3.75=pl526h14c3975_1
  - perl-scalar-list-utils=1.52=pl526h516909a_0
  - perl-socket=2.027=pl526_1
  - perl-storable=3.15=pl526h14c3975_0
  - perl-test-requiresinternet=0.05=pl526_0
  - perl-time-local=1.28=pl526_1
  - perl-try-tiny=0.30=pl526_1
  - perl-types-serialiser=1.0=pl526_2
  - perl-uri=1.76=pl526_0
  - perl-www-robotrules=6.02=pl526_3
  - perl-xml-namespacesupport=1.12=pl526_0
  - perl-xml-sax=1.02=pl526_0
  - perl-xml-sax-base=1.09=pl526_0
  - perl-xml-sax-expat=0.51=pl526_3
  - perl-xml-simple=2.25=pl526_1
  - perl-xsloader=0.24=pl526_0
  - perl-yaml=1.29=pl526_0
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=1_gnu
  - _r-mutex=1.0.1=anacondar_1
  - argtable2=2.13=h14c3975_1001
  - binutils_impl_linux-64=2.35.1=h193b22a_2
  - binutils_linux-64=2.35=h67ddf6f_30
  - biopython=1.78=py37h5e8e339_1
  - bwidget=1.9.14=ha770c72_0
  - bzip2=1.0.8=h7f98852_4
  - c-ares=1.17.1=h36c2ea0_0
  - ca-certificates=2020.12.5=ha878542_0
  - cairo=1.16.0=hcf35c78_1003
  - certifi=2020.12.5=py37h89c1867_1
  - curl=7.71.1=he644dc0_8
  - cycler=0.10.0=py_2
  - dbus=1.13.6=he372182_0
  - expat=2.2.10=h9c3ff4c_0
  - fontconfig=2.13.1=hba837de_1004
  - freetype=2.10.4=h0708190_1
  - fribidi=1.0.10=h36c2ea0_0
  - gcc_impl_linux-64=7.5.0=hda68d29_13
  - gcc_linux-64=7.5.0=h47867f9_30
  - gettext=0.19.8.1=hf34092f_1004
  - gfortran_impl_linux-64=7.5.0=h56cb351_18
  - gfortran_linux-64=7.5.0=h78c8a43_30
  - ghostscript=9.53.3=h58526e2_2
  - glib=2.66.1=h680cd38_0
  - graphite2=1.3.13=h58526e2_1001
  - gsl=2.6=he838d99_2
  - gst-plugins-base=1.14.5=h0935bb2_2
  - gstreamer=1.14.5=h36ae1b5_2
  - gxx_impl_linux-64=7.5.0=h64c220c_13
  - gxx_linux-64=7.5.0=h555fc39_30
  - harfbuzz=2.4.0=h9f30f68_3
  - icu=64.2=he1b5a44_1
  - jpeg=9d=h36c2ea0_0
  - kernel-headers_linux-64=2.6.32=h77966d4_13
  - kiwisolver=1.3.1=py37h2527ec5_1
  - krb5=1.17.2=h926e7f8_0
  - lcms2=2.12=hddcbb42_0
  - ld_impl_linux-64=2.35.1=hea4e1c9_2
  - libblas=3.9.0=8_openblas
  - libcblas=3.9.0=8_openblas
  - libclang=9.0.1=default_hde54327_0
  - libcurl=7.71.1=hcdd3856_8
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=h516909a_1
  - libffi=3.2.1=he1b5a44_1007
  - libgcc-ng=9.3.0=h2828fa1_18
  - libgfortran-ng=7.5.0=h14aa051_18
  - libgfortran4=7.5.0=h14aa051_18
  - libgomp=9.3.0=h2828fa1_18
  - libiconv=1.16=h516909a_0
  - liblapack=3.9.0=8_openblas
  - libllvm9=9.0.1=hf817b99_2
  - libnghttp2=1.43.0=h812cca2_0
  - libopenblas=0.3.12=pthreads_hb3c22a3_1
  - libpng=1.6.37=h21135ba_2
  - libssh2=1.9.0=hab1572f_5
  - libstdcxx-ng=9.3.0=h6de172a_18
  - libtiff=4.2.0=hdc55705_0
  - libuuid=2.32.1=h7f98852_1000
  - libwebp-base=1.2.0=h7f98852_0
  - libxcb=1.13=h7f98852_1003
  - libxkbcommon=0.10.0=he1b5a44_0
  - libxml2=2.9.10=hee79883_0
  - libxslt=1.1.33=h31b3aaa_0
  - lz4-c=1.9.3=h9c3ff4c_0
  - make=4.3=hd18ef5c_1
  - matplotlib=3.3.4=py37h89c1867_0
  - matplotlib-base=3.3.4=py37h0c9df89_0
  - mpi=1.0=openmpi
  - ncurses=6.2=h58526e2_4
  - nspr=4.29=h9c3ff4c_1
  - nss=3.61=hb5efdd6_0
  - numpy=1.20.1=py37haa41c4c_0
  - olefile=0.46=pyh9f0ad1d_1
  - openmpi=4.0.5=ha4a8674_4
  - openssl=1.1.1j=h7f98852_0
  - pandas=1.1.2=py37h3340039_0
  - pango=1.42.4=h7062337_4
  - pcre=8.44=he1b5a44_0
  - pcre2=10.35=h032f7d1_2
  - perl=5.26.2=h36c2ea0_1008
  - perl-xml-parser=2.44_01=pl526ha1d75be_1002
  - pillow=8.1.0=py37h4600e1f_2
  - pip=21.0.1=pyhd8ed1ab_0
  - pixman=0.38.0=h516909a_1003
  - pthread-stubs=0.4=h36c2ea0_1001
  - pyparsing=2.4.7=pyh9f0ad1d_0
  - pypdf2=1.26.0=py_2
  - pyqt=5.12.3=py37h8685d9f_3
  - python=3.7.8=h8bdb77d_2_cpython
  - python-dateutil=2.8.1=py_0
  - python_abi=3.7=1_cp37m
  - pytz=2021.1=pyhd8ed1ab_0
  - qt=5.12.5=hd8c4c69_1
  - r-base=4.0.2=h95c6c4b_0
  - readline=8.0=he28a2e2_2
  - reportlab=3.5.60=py37h69800bb_0
  - scipy=1.5.3=py37h8911b10_0
  - sed=4.8=he412f7d_0
  - setuptools=49.6.0=py37h89c1867_3
  - six=1.15.0=pyh9f0ad1d_0
  - sqlite=3.34.0=h74cdb3f_0
  - sysroot_linux-64=2.12=h77966d4_13
  - tk=8.6.10=h21135ba_1
  - tktable=2.10=hb7b940f_3
  - tornado=6.1=py37h5e8e339_1
  - wheel=0.36.2=pyhd3deb0d_0
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.0.10=h516909a_0
  - xorg-libsm=1.2.3=h84519dc_1000
  - xorg-libx11=1.6.12=h516909a_0
  - xorg-libxau=1.0.9=h7f98852_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h516909a_0
  - xorg-libxrender=0.9.10=h516909a_1002
  - xorg-renderproto=0.11.1=h14c3975_1002
  - xorg-xextproto=7.3.0=h7f98852_1002
  - xorg-xproto=7.0.31=h7f98852_1007
  - xz=5.2.5=h516909a_1
  - yaml=0.2.5=h516909a_0
  - zlib=1.2.11=h516909a_1010
  - zstd=1.4.8=ha95c52a_1

Answer 1

不太確定 SO 用戶可以在這里提供什么幫助。 鏈接的 repo 問題清楚地描述了這個問題，唯一的解決方法是使用舊版本，但該解決方法需要 Python <=3.6，這與當前環境中 OP 的 Python 3.7 沖突。

如果真的只需要 Python 3，而沒有專門的 3.7，則使用 Python 3.6 和 MEME 的解決方法版本創建一個新環境¹ ：

conda create -n meme -c conda-forge -c bioconda python=3 bioconda/label/cf201901::meme

否則，您需要征求原料維護者來解決問題，即，為問題添加您的聲音。

---

_{[1] ：在當前環境中也可以嘗試降級到 Python 3.6，但在現有環境中更改 Python 版本總是需要更改大量軟件包，因此不會節省任何空間。 此外，Conda 可以比改變現有環境更快地解決新環境的創建問題。}