Kata-Pa
commented
5 years ago I have the same problem. I found this https://github.com/CompSynBioLab-KoreaUniv/FunGAP/issues/11 but unfortunately didnt work for me. Any luck for you?
Closed reslp closed 5 years ago
Kata-Pa
commented
5 years ago I have the same problem. I found this https://github.com/CompSynBioLab-KoreaUniv/FunGAP/issues/11 but unfortunately didnt work for me. Any luck for you?
mbnmbn00
commented
5 years ago Could you show me the output of:
conda listIt should look like below. Note that all the channels end with /label/cf201901. Hope it helps.
> conda list
# packages in environment at /home/mbnmbn00/anaconda2/envs/maker:
#
# Name Version Build Channel
augustus 3.3 pl526hcfae127_4 bioconda/label/cf201901
bamtools 2.4.1 1 bioconda/label/cf201901
binutils_impl_linux-64 2.28.1 had2808c_3
binutils_linux-64 7.2.0 had2808c_27
blas 1.0 mkl
blast 2.7.1 h4422958_6 bioconda/label/cf201901
boost 1.67.0 py27h3e44d54_0 conda-forge/label/cf201901
boost-cpp 1.67.0 h3a22d5f_0 conda-forge/label/cf201901
bowtie 1.2.2 py27h2d50403_1 bioconda/label/cf201901
bzip2 1.0.6 h470a237_2 conda-forge/label/cf201901
ca-certificates 2018.11.29 ha4d7672_0 conda-forge/label/cf201901
cairo 1.14.12 h276e583_5 conda-forge/label/cf201901
certifi 2018.11.29 py27_1000 conda-forge/label/cf201901
clustalw 2.1 h2d50403_2 bioconda/label/cf201901
curl 7.63.0 h74213dd_0 conda-forge/label/cf201901
exonerate 2.4.0 0 bioconda/label/cf201901
expat 2.2.5 hfc679d8_2 conda-forge/label/cf201901
fontconfig 2.13.1 h65d0f4c_0 conda-forge/label/cf201901
freetype 2.9.1 h6debe1e_4 conda-forge/label/cf201901I did the conda list, but none except one has the /label/cf201901.
packages in environment at /home/katerina87/miniconda3: Name Version Build Channel asn1crypto 0.24.0 py37_0 binutils_impl_linux-64 2.31.1 h6176602_1 conda-forge binutils_linux-64 2.31.1 h6176602_6 bz2file 0.98 py_0 conda-forge bzip2 1.0.6 h14c3975_1002 conda-forge ca-certificates 2018.11.29 ha4d7672_0 conda-forge certifi 2018.11.29 py37_1000 conda-forge cffi 1.11.5 py37he75722e_1 chardet 3.0.4 py37_1 conda 4.6.8 py37_0 conda-forge conda-env 2.6.0 1 cryptography 2.4.2 py37h1ba5d50_0 cutadapt 1.18 py37h14c3975_1 bioconda cycler 0.10.0 pypi_0 pypi exonerate 2.4.0 hb9387b2_1 bioconda fastqc 0.11.8 1 bioconda font-ttf-dejavu-sans-mono 2.37 h6964260_0 fontconfig 2.13.1 h2176d3f_1000 conda-forge freetype 2.9.1 h94bbf69_1005 conda-forge gcc_impl_linux-64 7.3.0 habb00fd_1 conda-forge gcc_linux-64 7.3.0 h553295d_6 conda-forge gettext 0.19.8.1 h9745a5d_1001 conda-forge glib 2.55.0 h464dc38_2 conda-forge gxx_impl_linux-64 7.3.0 hdf63c60_1 conda-forge gxx_linux-64 7.3.0 h553295d_6 icu 58.2 hf484d3e_1000 conda-forge idna 2.8 py37_0 kiwisolver 1.0.1 pypi_0 pypi krb5 1.16.1 h173b8e3_7 libedit 3.1.20170329 h6b74fdf_2 libffi 3.2.1 hd88cf55_4 libgcc-ng 8.2.0 hdf63c60_1 libiconv 1.15 h14c3975_1004 conda-forge libpng 1.6.36 h84994c4_1000 conda-forge libpq 11.1 h20c2e04_0 libstdcxx-ng 8.2.0 hdf63c60_1 libuuid 2.32.1 h14c3975_1000 conda-forge libxml2 2.9.8 h143f9aa_1005 conda-forge matplotlib 3.0.2 pypi_0 pypi ncurses 6.1 he6710b0_1 numpy 1.16.1 pypi_0 pypi openjdk 11.0.1 h14c3975_1014 conda-forge openssl 1.1.1b h14c3975_1 conda-forge pcre 8.41 hf484d3e_1003 conda-forge perl 5.26.2 h14c3975_1002 conda-forge perl-acme-damn 0.08 pl526h2d50403_2 bioconda perl-apache-test 1.40 pl526_1 bioconda perl-app-cpanminus 1.7044 pl526_1 bioconda perl-attribute-handlers 0.96 pl526_1 bioconda perl-base 2.23 pl526_1 bioconda perl-bit-vector 7.4 pl526_2 bioconda perl-carp 1.38 pl526_1 bioconda perl-class-load 0.25 pl526_0 bioconda perl-class-load-xs 0.10 pl526h2d50403_0 bioconda perl-class-method-modifiers 2.12 pl526_0 bioconda perl-constant 1.33 pl526_1 bioconda perl-data-dumper 2.173 pl526_0 bioconda perl-data-optlist 0.110 pl526_2 bioconda perl-dbd-pg 3.5.3 pl526_1 bioconda perl-dbd-sqlite 1.60 pl526h470a237_0 bioconda perl-dbi 1.642 pl526_0 bioconda perl-devel-globaldestruction 0.14 pl526_0 bioconda perl-devel-overloadinfo 0.005 pl526_0 bioconda perl-devel-stacktrace 2.03 pl526_1 bioconda perl-devel-symdump 2.18 pl526_1 bioconda perl-dist-checkconflicts 0.11 pl526_2 bioconda perl-eval-closure 0.14 pl526h2d50403_3 bioconda perl-exporter 5.72 pl526_1 bioconda perl-exporter-tiny 1.002001 pl526_0 bioconda perl-extutils-makemaker 7.34 pl526_3 bioconda perl-file-homedir 1.00 pl526_2 bioconda perl-file-path 2.15 pl526_0 bioconda perl-file-temp 0.2304 pl526_2 bioconda perl-file-which 1.23 pl526_0 bioconda perl-forks 0.36 pl526_4 bioconda perl-getopt-long 2.50 pl526_1 bioconda perl-importer 0.025 pl526_0 bioconda perl-list-moreutils 0.428 pl526_1 bioconda perl-list-moreutils-xs 0.428 pl526_0 bioconda perl-module-implementation 0.09 pl526_2 bioconda perl-module-pluggable 5.2 pl526_0 bioconda perl-module-runtime 0.016 pl526_0 bioconda perl-module-runtime-conflicts 0.003 pl526_0 bioconda perl-moo 2.003004 pl526_0 bioconda perl-moose 2.2011 pl526h2d50403_0 bioconda perl-mro-compat 0.13 pl526_0 bioconda perl-package-deprecationmanager 0.17 pl526_0 bioconda perl-package-stash 0.38 pl526hfc679d8_0 bioconda perl-package-stash-xs 0.28 pl526hfc679d8_0 bioconda perl-parallel-forkmanager 2.02 pl526_0 bioconda perl-params-util 1.07 pl526h2d50403_3 bioconda perl-parent 0.236 pl526_1 bioconda perl-pathtools 3.73 h470a237_2 bioconda perl-perl-unsafe-signals 0.03 pl526h2d50403_2 bioconda perl-role-tiny 2.000006 pl526_0 bioconda perl-scalar-list-utils 1.45 pl526h470a237_3 bioconda perl-scalar-util-numeric 0.40 pl526_1 bioconda/label/cf201901 perl-scope-guard 0.21 pl526_2 bioconda perl-storable 3.11 pl526_0 bioconda perl-sub-exporter 0.987 pl526_2 bioconda perl-sub-exporter-progressive 0.001013 pl526_0 bioconda perl-sub-identify 0.12 pl526_1 bioconda perl-sub-info 0.002 pl526_0 bioconda perl-sub-install 0.928 pl526_2 bioconda perl-sub-name 0.21 pl526_1 bioconda perl-sub-quote 2.005001 pl526_0 bioconda perl-sys-sigaction 0.23 pl526_1 bioconda perl-term-table 0.013 pl526_0 bioconda perl-test-more 1.001002 pl526_1 bioconda perl-test2-suite 0.000117 pl526_0 bioconda perl-text-soundex 3.05 pl526_1000 conda-forge perl-threaded 5.22.0 13 bioconda perl-time-hires 1.9758 pl526_0 bioconda perl-try-tiny 0.30 pl526_0 bioconda perl-want 0.29 pl526_1 bioconda perl-xsloader 0.24 pl526_0 bioconda pigz 2.3.4 0 conda-forge pip 19.0.2 pypi_0 pypi postgresql 11.1 h20c2e04_0 pycosat 0.6.3 py37h14c3975_0 pycparser 2.19 py37_0 pyopenssl 18.0.0 py37_0 pyparsing 2.3.1 pypi_0 pypi pysocks 1.6.8 py37_0 python 3.7.1 h381d211_1002 conda-forge python-dateutil 2.8.0 pypi_0 pypi readline 7.0 h7b6447c_5 requests 2.21.0 py37_0 ruamel_yaml 0.15.46 py37h14c3975_0 setuptools 40.6.3 py37_0 six 1.12.0 py37_0 sqlite 3.26.0 h7b6447c_0 tk 8.6.9 h84994c4_1000 conda-forge trim-galore 0.5.0 0 bioconda urllib3 1.24.1 py37_0 wheel 0.32.3 py37_0 xopen 0.5.0 py_0 bioconda xz 5.2.4 h14c3975_4 yaml 0.1.7 had09818_2 zlib 1.2.11 h7b6447c_3
So I guess I did something wrong or I missed something. I will try to figure out what later today but meanwhile if you have an idea and you would like to give me a hint, I would be glad :)
Kata-Pa
commented
5 years ago I had to uninstall and reinstall perl and all modules needed, always with the label /label/cf201901. Now it works! Thank you for the help!
mbnmbn00
commented
5 years ago Glad it helped! Please close the Issue.
Kata-Pa
commented
5 years ago Sorry for asking but I am a bit new in Github. I dont think I can close the issue, I guess @reslp should do it, (if his problem was solved) since he is the one who opened it?
reslp
commented
5 years ago Hi, thanks for the answers. I have not had time to test using the different conda channel. I will close the issue now. I will test with /label/cf201901 as soon as I have time and will reopen in case it does not work.
nathanweeks
commented
5 years ago I'm still seeing this issue with maker 2.31.10--pl526_12, at least when using a Singularity image of the biocontainers version on one of the sample data sets (see below), but I imagine it still affects the conda version as well. The apparent source of the issue is in Bio::DB::IndexedBase, described at:
https://github.com/bioperl/bioperl-live/issues/305
It should be fixed in the next bioperl release. But maker is still broken for now.
$ singularity pull maker_2.31.10--pl526_12.sif docker://quay.io/biocontainers/maker:2.31.10--pl526_12
$ singularity exec --cleanenv maker_2.31.10--pl526_12.sif maker -C
$ mv maker_opts.ctl maker_opts.ctl.orig && mv maker_opts.ctl.new maker_opts.ctl
$ diff maker_opts.ctl.orig maker_opts.ctl
$ diff maker_opts.ctl.orig maker_opts.ctl
2c2
< genome= #genome sequence (fasta file or fasta embeded in GFF3 file)
---
> genome=dpp_contig.fasta #genome sequence (fasta file or fasta embeded in GFF3 file)
16c16
< est= #set of ESTs or assembled mRNA-seq in fasta format
---
> est=dpp_est.fasta #set of ESTs or assembled mRNA-seq in fasta format
22c22
< protein= #protein sequence file in fasta format (i.e. from mutiple oransisms)
---
> protein=dpp_protein.fasta #protein sequence file in fasta format (i.e. from mutiple oransisms)
26c26
< model_org=all #select a model organism for RepBase masking in RepeatMasker
---
> model_org= #select a model organism for RepBase masking in RepeatMasker
$ singularity exec --contain --cleanenv --bind $PWD --pwd $PWD maker_2.31.10--pl526_12.sif maker
...
Running Mkbootstrap for IndexedBase_14e0 ()
chmod 644 "IndexedBase_14e0.bs"
"/usr/local/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- IndexedBase_14e0.bs blib/arch/auto/Bio/DB/IndexedBase_14e0/IndexedBase_14e0.bs 644
"/usr/local/bin/perl" "/usr/local/lib/site_perl/5.26.2/ExtUtils/xsubpp" -typemap "/usr/local/lib/5.26.2/ExtUtils/typemap" IndexedBase_14e0.xs > IndexedBase_14e0.xsc
mv IndexedBase_14e0.xsc IndexedBase_14e0.c
/bin/x86_64-conda_cos6-linux-gnu-gcc -c -I"/usr/local/bin" -D_REENTRANT -D_GNU_SOURCE --sysroot=/x86_64-conda_cos6-linux-gnu/sysroot -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2 -DVERSION=\"0.00\" -DXS_VERSION=\"0.00\" -fPIC --sysroot=/x86_64-conda_cos6-linux-gnu/sysroot "-I/usr/local/lib/5.26.2/x86_64-linux-thread-multi/CORE" IndexedBase_14e0.c
/bin/sh: /bin/x86_64-conda_cos6-linux-gnu-gcc: not found
make: *** [Makefile:330: IndexedBase_14e0.o] Error 127
Hi,
I am having troubles getting maker to run inside my conda environment. Everything seemed to have installed correctly. I had to make some changes to link RepBase correctly but I got it to work. Now when I run maker I get errors like this:
maker keeps running but the contigs are not processed correctly. It seems that while trying to compile inline C code, maker can't find the compiler because it is pointed to the wrong location:
I am not running maker as MPI.
Is there a way to fix this?
Many thanks,
Philipp
Here is my environment info from conda list: