AME包在CONDA环境下找不到模板

如何解决AME包在CONDA环境下找不到模板

我在 SLURM 服务器上使用 Conda (4.5.4) 下 MEME-Suite 包中的 AME 软件。使用 AME 时，我收到以下错误消息：

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.

似乎 AME 无法检索其输出产品的模板文件我尝试了以下解决方案：

conda install meme=5.0.2
conda install meme=5.3.0
conda install -c bioconda/label/cf201901 meme
此处提出的解决方案：https://github.com/bioconda/bioconda-recipes/issues/22909 和此处：https://www.biostars.org/p/401084/

不幸的是没有解决我的问题。我必须维护 Python 3.X 版本，所以不能使用 Python 2.X 的 MEME 版本。

知道如何在这种情况下安装 MEME 吗？

以下是 Conda 环境的依赖项：

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

解决方法

不太确定 SO 用户可以在这里提供什么帮助。 The linked repo Issue 清楚地描述了这个问题，唯一的解决方法是使用旧版本，但该解决方法需要 Python

如果真的只需要 Python 3，没有特别需要 3.7，那么创建一个新环境¹ 使用 Python 3.6 和 MEME 的变通版本：

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

否则，您需要请求原料维护人员解决该问题，即 add your voice to the issue。

_{[1]：在当前环境中也可以尝试降级到 Python 3.6，但是在现有环境中改变 Python 版本总是需要更改过多的包，所以它赢了不节省任何空间。此外，与改变现有环境相比，Conda 可以更快地解决新环境的创建问题。}

AME包在CONDA环境下找不到模板

如何解决AME包在CONDA环境下找不到模板

解决方法

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