error running RaFAH
Issue #42
closed
Hi Simon,
As mentioned via Twitter, I have met this error when running the RaFAH step. Please help. Thank you.
Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /home/linking/miniconda3/envs/iphop_env/lib/perl5/site_perl/5.22.2/x86_64-linux-thread-multi /home/linking/miniconda3/envs/iphop_env/lib/perl5/site_perl/5.22.2 /home/linking/miniconda3/envs/iphop_env/lib/perl5/5.22.2/x86_64-linux-thread-multi /home/linking/miniconda3/envs/iphop_env/lib/perl5/5.22.2 .) at /home/linking/miniconda3/envs/iphop_env/lib/python3.8/site-packages/iphop/utils/RaFAH_v0.3.pl line 5.
BEGIN failed--compilation aborted at /home/linking/miniconda3/envs/iphop_env/lib/python3.8/site-packages/iphop/utils/RaFAH_v0.3.pl line 5.
Best,
LINXING
Comments (13)
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repo owner
-
reporter
Hi Simon,
Thanks for your reply.
(1) I got this list for
$ conda list -n iphop_env# packages in environment at /home/linking/miniconda3/envs/iphop_env: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge abseil-cpp 20210324.2 h9c3ff4c_0 conda-forge absl-py 1.4.0 pyhd8ed1ab_0 conda-forge aiohttp 3.8.4 py38h01eb140_1 conda-forge aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge alsa-lib 1.2.8 h166bdaf_0 conda-forge astunparse 1.6.3 pyhd8ed1ab_0 conda-forge async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge attrs 23.1.0 pyh71513ae_1 conda-forge binutils_impl_linux-64 2.40 hf600244_0 conda-forge biopython 1.79 py38h0a891b7_3 conda-forge blast 2.12.0 hf3cf87c_4 bioconda blinker 1.6.2 pyhd8ed1ab_0 conda-forge boltons 23.0.0 pyhd8ed1ab_0 conda-forge boost-cpp 1.74.0 h75c5d50_8 conda-forge bottleneck 1.3.7 py38h7e4f40d_0 conda-forge brotli-python 1.0.9 py38hfa26641_9 conda-forge bwidget 1.9.14 ha770c72_1 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.19.1 hd590300_0 conda-forge ca-certificates 2023.5.7 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 4.2.4 pyhd8ed1ab_0 conda-forge cairo 1.16.0 ha61ee94_1014 conda-forge certifi 2023.5.7 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py38h4a40e3a_3 conda-forge charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge click 8.0.4 py38h578d9bd_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge conda 23.5.0 py38h578d9bd_1 conda-forge conda-package-handling 2.0.2 pyh38be061_0 conda-forge conda-package-streaming 0.8.0 pyhd8ed1ab_0 conda-forge crisper_recognition_tool 1.2 hdfd78af_2 bioconda cryptography 39.0.0 py38h1724139_0 conda-forge cuda-version 11.1 hdbd7af8_2 conda-forge cudatoolkit 11.1.1 ha002fc5_11 conda-forge cudnn 8.8.0.121 h0800d71_1 conda-forge curl 7.86.0 h7bff187_1 conda-forge diamond 2.0.15 hb97b32f_1 bioconda entrez-direct 16.2 he881be0_1 bioconda expat 2.5.0 hcb278e6_1 conda-forge fmt 9.1.0 h924138e_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge frozenlist 1.3.3 py38h0a891b7_0 conda-forge gast 0.4.0 pyh9f0ad1d_0 conda-forge gcc_impl_linux-64 13.1.0 hc4be1a9_0 conda-forge gettext 0.21.1 h27087fc_0 conda-forge gfortran_impl_linux-64 13.1.0 hd511a9b_0 conda-forge giflib 5.2.1 h0b41bf4_3 conda-forge google-auth 1.35.0 pyh6c4a22f_0 conda-forge google-auth-oauthlib 0.4.6 pyhd8ed1ab_0 conda-forge google-pasta 0.2.0 pyh8c360ce_0 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge grpc-cpp 1.43.2 h9e046d8_3 conda-forge grpcio 1.43.0 py38hdd6454d_0 conda-forge gsl 2.7 he838d99_0 conda-forge gxx_impl_linux-64 13.1.0 hc4be1a9_0 conda-forge h5py 3.8.0 nompi_py38hd5fa8ee_100 conda-forge harfbuzz 6.0.0 h8e241bc_0 conda-forge hdf5 1.12.2 nompi_h2386368_100 conda-forge hmmer 3.3.2 hdbdd923_4 bioconda icu 70.1 h27087fc_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge importlib-metadata 6.7.0 pyha770c72_0 conda-forge iphop 1.3.2 pyhdfd78af_0 bioconda joblib 1.0.1 pyhd8ed1ab_0 conda-forge jpeg 9e h0b41bf4_3 conda-forge jsonpatch 1.32 pyhd8ed1ab_0 conda-forge jsonpointer 2.0 py_0 conda-forge keras 2.7.0 pyhd8ed1ab_0 conda-forge keras-preprocessing 1.1.2 pyhd8ed1ab_0 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.19.3 h3790be6_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 libarchive 3.5.2 hb890918_3 conda-forge libblas 3.9.0 17_linux64_openblas conda-forge libcblas 3.9.0 17_linux64_openblas conda-forge libcups 2.3.3 h3e49a29_2 conda-forge libcurl 7.86.0 h7bff187_1 conda-forge libdeflate 1.14 h166bdaf_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-devel_linux-64 13.1.0 he3cc6c4_0 conda-forge libgcc-ng 13.1.0 he5830b7_0 conda-forge libgfortran-ng 13.1.0 h69a702a_0 conda-forge libgfortran5 13.1.0 h15d22d2_0 conda-forge libglib 2.76.3 hebfc3b9_0 conda-forge libgomp 13.1.0 he5830b7_0 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libidn2 2.3.4 h166bdaf_0 conda-forge liblapack 3.9.0 17_linux64_openblas conda-forge libmamba 0.24.0 hd8a31e3_1 conda-forge libmambapy 0.24.0 py38h923e62a_1 conda-forge libnghttp2 1.51.0 hdcd2b5c_0 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libopenblas 0.3.23 pthreads_h80387f5_0 conda-forge libpng 1.6.39 h753d276_0 conda-forge libprotobuf 3.19.6 h3eb15da_0 conda-forge libsanitizer 13.1.0 hfd8a6a1_0 conda-forge libsolv 0.7.24 hfc55251_1 conda-forge libsqlite 3.42.0 h2797004_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-devel_linux-64 13.1.0 he3cc6c4_0 conda-forge libstdcxx-ng 13.1.0 hfd8a6a1_0 conda-forge libtiff 4.4.0 h82bc61c_5 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.3.1 hd590300_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxml2 2.10.3 hca2bb57_4 conda-forge libzlib 1.2.13 hd590300_5 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge lzo 2.10 h516909a_1000 conda-forge make 4.3 hd18ef5c_1 conda-forge mamba 0.24.0 py38h1abaa86_1 conda-forge markdown 3.4.3 pyhd8ed1ab_0 conda-forge markupsafe 2.1.3 py38h01eb140_0 conda-forge multidict 6.0.4 py38h1de0b5d_0 conda-forge nccl 2.18.3.1 h12f7317_0 conda-forge ncurses 6.4 hcb278e6_0 conda-forge nomkl 1.0 h5ca1d4c_0 conda-forge numexpr 2.8.4 py38h69a160b_100 conda-forge numpy 1.23.5 py38h7042d01_0 conda-forge oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge openjdk 17.0.3 h58dac75_5 conda-forge openssl 1.1.1u hd590300_0 conda-forge opt_einsum 3.3.0 pyhd8ed1ab_1 conda-forge packaging 23.1 pyhd8ed1ab_0 conda-forge pandas 1.3.5 py38h8c16a72_0 pango 1.50.14 hd33c08f_0 conda-forge pcre 8.45 h9c3ff4c_0 conda-forge pcre2 10.40 hc3806b6_0 conda-forge perl 5.22.2.1 0 conda-forge perl-archive-tar 2.18 1 bioconda perl-bioperl 1.6.924 4 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-yaml 1.24 pl522_1 bioconda piler-cr 1.06 h4ac6f70_4 bioconda pip 23.1.2 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge platformdirs 3.8.0 pyhd8ed1ab_0 conda-forge pluggy 1.2.0 pyhd8ed1ab_0 conda-forge pooch 1.7.0 pyha770c72_3 conda-forge prodigal 2.6.3 h031d066_6 bioconda protobuf 3.19.6 py38h8dc9893_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pyasn1 0.4.8 py_0 conda-forge pyasn1-modules 0.2.7 py_0 conda-forge pybind11-abi 4 hd8ed1ab_3 conda-forge pycosat 0.6.4 py38h0a891b7_1 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pyjwt 2.7.0 pyhd8ed1ab_0 conda-forge pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge python 3.8.15 h257c98d_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-flatbuffers 2.0 pyhd8ed1ab_0 conda-forge python_abi 3.8 3_cp38 conda-forge pytz 2023.3 pyhd8ed1ab_0 conda-forge pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge r-base 4.0.5 hb87df5d_8 conda-forge r-lattice 0.20_45 r40hcfec24a_0 conda-forge r-matrix 1.4_1 r40h0154571_0 conda-forge r-ranger 0.13.1 r40h03ef668_0 conda-forge r-rcpp 1.0.9 r40h7525677_1 conda-forge r-rcppeigen 0.3.3.9.2 r40h43535f1_0 conda-forge re2 2022.02.01 h9c3ff4c_0 conda-forge readline 8.2 h8228510_1 conda-forge reproc 14.2.4 h0b41bf4_0 conda-forge reproc-cpp 14.2.4 hcb278e6_0 conda-forge requests 2.31.0 pyhd8ed1ab_0 conda-forge requests-oauthlib 1.3.1 pyhd8ed1ab_0 conda-forge rsa 4.9 pyhd8ed1ab_0 conda-forge ruamel.yaml 0.17.32 py38h01eb140_0 conda-forge ruamel.yaml.clib 0.2.7 py38h1de0b5d_1 conda-forge scikit-learn 0.22.2.post1 py38hcdab131_0 conda-forge scipy 1.10.1 py38h59b608b_3 conda-forge sed 4.8 he412f7d_0 conda-forge setuptools 68.0.0 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.1.10 h9fff704_0 conda-forge sqlite 3.42.0 h2c6b66d_0 conda-forge sysroot_linux-64 2.12 he073ed8_15 conda-forge tensorboard 2.6.0 pyhd8ed1ab_1 conda-forge tensorboard-data-server 0.6.1 py38h2b5fc30_4 conda-forge tensorboard-plugin-wit 1.8.1 pyhd8ed1ab_0 conda-forge tensorflow 2.7.0 pypi_0 pypi tensorflow-base 2.7.1 cuda111py38h13b88b6_0 conda-forge tensorflow-decision-forests 0.2.2 pypi_0 pypi tensorflow-estimator 2.7.1 cuda111py38h6353a60_0 conda-forge termcolor 2.3.0 pyhd8ed1ab_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge tktable 2.10 hb7b940f_3 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge tqdm 4.65.0 pyhd8ed1ab_1 conda-forge typing-extensions 4.7.1 hd8ed1ab_0 conda-forge typing_extensions 4.7.1 pyha770c72_0 conda-forge urllib3 2.0.3 pyhd8ed1ab_1 conda-forge werkzeug 2.3.6 pyhd8ed1ab_0 conda-forge wget 1.20.3 ha56f1ee_1 conda-forge wheel 0.40.0 pyhd8ed1ab_0 conda-forge wrapt 1.15.0 py38h1de0b5d_0 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-inputproto 2.3.2 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.8.4 h0b41bf4_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxi 1.7.10 h7f98852_0 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-libxt 1.3.0 hd590300_0 conda-forge xorg-libxtst 1.2.3 h7f98852_1002 conda-forge xorg-recordproto 1.14.2 h7f98852_1002 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml-cpp 0.7.0 h27087fc_2 conda-forge yarl 1.9.2 py38h01eb140_0 conda-forge zipp 3.15.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstandard 0.19.0 py38ha98ab4e_2 conda-forge zstd 1.5.2 h3eb15da_6 conda-forge(2) and got this list for
$ find /home/linking/miniconda3/envs/iphop_env/lib/perl5/site_perl/ -name "*SeqIO*"/home/linking/miniconda3/envs/iphop_env/lib/perl5/site_perl/5.22.0/Bio/SeqIO.pm /home/linking/miniconda3/envs/iphop_env/lib/perl5/site_perl/5.22.0/Bio/SeqIOPlease let me know what should I do next to fix the issue. Thank you.
Best,
LINXING -
repo owner
This is interesting, BioPerl was correctly installed, and is found in the expected folder. Can you try the following:
$ conda activate iphop_env $ ls /home/linking/miniconda3/envs/iphop_env/etc/conda/activate.d/ $ cat /home/linking/miniconda3/envs/iphop_env/etc/conda/activate.d/iphop_activate.shWhat seems to be happening here is that BioPerl is in folder “lib/perl5/site_perl/5.22.0”, and that’s where iPHoP expects it, but for a reason I can’t understand yet, Perl seems to look for this module in the folder “lib/perl5/site_perl/5.22.2” (based on the first error message you shared). This “activate.d” is where usually these different library folders are indicated, so hopefully we can narrow down which file is problematic here, and fix this !
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reporter
Hi Simon,
This is what I got,
ls /home/linking/miniconda3/envs/iphop_env/etc/conda/activate.d/ activate-r-base.sh iphop_activate.sh libglib_activate.sh libxml2_activate.sh openjdk_activate.sh cat /home/linking/miniconda3/envs/iphop_env/etc/conda/activate.d/iphop_activate.sh export OLD_PERL5LIB=$PERL5LIB export PERL5LIB=${CONDA_PREFIX}/lib/perl5/site_perl/5.22.0:${CONDA_PREFIX}/lib/perl5/site_perl/:${PERL5LIB}What do you think?
Thank you.
Best,
LINXING
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repo owner
Looks like something re-writes your PERL5LIB variable later, and/or PERL5LIB is not the right variable in your case. Let’s try the following:
$ conda activate iphop_env $ export PERL5LIB=/home/linking/miniconda3/envs/iphop_env/lib/perl5/site_perl/5.22.0:/home/linking/miniconda3/envs/iphop_env/lib/perl5/site_perl/:${PERL5LIB} $ echo $PERL5LIB $ perl -e “use Bio::SeqIO;”
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reporter
Hi Simon,
Looks like the issue has been fixed, right?
perl -e "use Bio::SeqIO;" -h Usage: perl [switches] [--] [programfile] [arguments] -0[octal] specify record separator (\0, if no argument) -a autosplit mode with -n or -p (splits $_ into @F) -C[number/list] enables the listed Unicode features -c check syntax only (runs BEGIN and CHECK blocks) -d[:debugger] run program under debugger -D[number/list] set debugging flags (argument is a bit mask or alphabets) -e program one line of program (several -e's allowed, omit programfile) -E program like -e, but enables all optional features -f don't do $sitelib/sitecustomize.pl at startup -F/pattern/ split() pattern for -a switch (//'s are optional) -i[extension] edit <> files in place (makes backup if extension supplied) -Idirectory specify @INC/#include directory (several -I's allowed) -l[octal] enable line ending processing, specifies line terminator -[mM][-]module execute "use/no module..." before executing program -n assume "while (<>) { ... }" loop around program -p assume loop like -n but print line also, like sed -s enable rudimentary parsing for switches after programfile -S look for programfile using PATH environment variable -t enable tainting warnings -T enable tainting checks -u dump core after parsing program -U allow unsafe operations -v print version, patchlevel and license -V[:variable] print configuration summary (or a single Config.pm variable) -w enable many useful warnings -W enable all warnings -x[directory] ignore text before #!perl line (optionally cd to directory) -X disable all warnings Run 'perldoc perl' for more help with Perl.
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repo owner
possibly, if you remove the “-h” it should not give you any output, but also no error, that would be what I expected. Then if that’s the case, we can try to run iPHoP again in the same session (or if in a new session / terminal, use “export PERL5LIB=/home/linking/miniconda3/envs/iphop_env/lib/perl5/site_perl/5.22.0:/home/linking/miniconda3/envs/iphop_env/lib/perl5/site_perl/:${PERL5LIB}” after loading the conda environment and before running iphop).
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reporter
Right, nothing out without “-h“. Great. I will run iPHoP again, and see what will happen.
Thank you so much for your help. :)
Best,
LINXING
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repo owner
Fingers crossed !
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reporter
Hi Simon, just want to let you know it goes well. Thanks again for your patience and help. Have a good day.
Best,
LINXING
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repo owner
Glad to hear ! I’ll close this issue, but let me know if you have any other issues
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repo owner
- changed status to closed
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reporter
Yes. will do. thank you.
- Log in to comment
Hi Lin-Xing,
I think I know where things might have gone wrong, most likely BioPerl got installed in a location different from the one iPHoP expected. A few things we can do to verify this:
We are especially looking for perl-bioperl to be in this list
This should help us figure out where Bio::SeqIO is in this environment, then we can try to point perl to it.
Thanks,
Best,
Simon