prokka
prokka copied to clipboard
tseemann
Issue calling Hmmer when running Prokka
Hello Prokka Team,
I am trying to run prokka on an Ubuntu 20.04 LTS laptop using a fresh install (installed 20FEB2022) of Prokka via conda (minconda3) and I'm not sure how to troubleshoot this issue. This error is repeatable and hoappens when I use a snakemake pipeline or when I try running one sample via the command line. According to the conda env hmmr is there.
I installed prokka via conda in its own environment and then activated the environment in order to do the analysis.
Any help in resolving this error will be greatly appreciated.
Cheers, Sean
[17:50:50] Will use hmmer3 to search against /home/sean/miniconda3/envs/prokka/db/hmm/HAMAP.hmm with 4 CPUs
[17:50:50] Running: cat 3\-P2131619\-Ery_prokka\/3\-P2131619\-Ery\.HAMAP\.hmm\.tmp\.27952\.faa | parallel --gnu --plain -j 4 --block 30247 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /home/sean/miniconda3/envs/prokka/db/hmm/HAMAP.hmm /dev/stdin > 3\-P2131619\-Ery_prokka\/3\-P2131619\-Ery\.HAMAP\.hmm\.tmp\.27952\.hmmer3 2> /dev/null
Bio::SearchIO: hmmer3 cannot be found
Exception
------------- EXCEPTION -------------
MSG: Failed to load module Bio::SearchIO::hmmer3. Can't locate Bio/SearchIO/hmmer3.pm in @INC (you may need to install the Bio::SearchIO::hmmer3 module) (@INC contains: /home/sean/miniconda3/envs/prokka/lib/perl5/5.32/site_perl /home/sean/miniconda3/envs/prokka/lib/perl5/site_perl /home/sean/miniconda3/envs/prokka/lib/perl5/5.32/vendor_perl /home/sean/miniconda3/envs/prokka/lib/perl5/vendor_perl /home/sean/miniconda3/envs/prokka/lib/perl5/5.32/core_perl /home/sean/miniconda3/envs/prokka/lib/perl5/core_perl .) at /home/sean/miniconda3/envs/prokka/lib/perl5/site_perl/Bio/Root/Root.pm line 520.
STACK Bio::Root::Root::_load_module /home/sean/miniconda3/envs/prokka/lib/perl5/site_perl/Bio/Root/Root.pm:522
STACK (eval) /home/sean/miniconda3/envs/prokka/lib/perl5/site_perl/Bio/SearchIO.pm:620
STACK Bio::SearchIO::_load_format_module /home/sean/miniconda3/envs/prokka/lib/perl5/site_perl/Bio/SearchIO.pm:619
STACK Bio::SearchIO::new /home/sean/miniconda3/envs/prokka/lib/perl5/site_perl/Bio/SearchIO.pm:217
STACK toplevel /home/sean/miniconda3/envs/prokka/bin/prokka:1113
-------------------------------------
# packages in environment at /home/sean/miniconda3/envs/prokka:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
aragorn 1.2.38 h779adbc_4 bioconda
barrnap 0.9 hdfd78af_4 bioconda
bedtools 2.30.0 h7d7f7ad_2 bioconda
blast 2.12.0 h3289130_3 bioconda
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
clustalw 2.1 h7d875b9_6 bioconda
curl 7.81.0 h2574ce0_0 conda-forge
entrez-direct 16.2 he881be0_0 bioconda
expat 2.4.4 h9c3ff4c_0 conda-forge
hmmer 3.3.2 h1b792b2_1 bioconda
infernal 1.1.4 h779adbc_0 bioconda
krb5 1.19.2 hcc1bbae_3 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libcurl 7.81.0 h2574ce0_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 11.2.0 h1d223b6_12 conda-forge
libgomp 11.2.0 h1d223b6_12 conda-forge
libiconv 1.16 h516909a_0 conda-forge
libidn11 1.34 h1cef754_0 conda-forge
libnghttp2 1.46.0 h812cca2_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_12 conda-forge
libzlib 1.2.11 h36c2ea0_1013 conda-forge
minced 0.4.2 hdfd78af_1 bioconda
ncurses 6.3 h9c3ff4c_0 conda-forge
openjdk 11.0.1 h516909a_1016 conda-forge
openssl 1.1.1l h7f98852_0 conda-forge
paml 4.9 h779adbc_6 bioconda
parallel 20211222 ha770c72_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
perl-algorithm-diff 1.201 pl5321hd8ed1ab_0 conda-forge
perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda
perl-base 2.23 pl5321hdfd78af_2 bioconda
perl-bio-asn1-entrezgene 1.73 pl5321hdfd78af_3 bioconda
perl-bio-coordinate 1.007001 pl5321hdfd78af_3 bioconda
perl-bio-featureio 1.6.905 pl5321hdfd78af_4 bioconda
perl-bio-samtools 1.43 pl5321h5bf99c6_2 bioconda
perl-bio-tools-phylo-paml 1.7.3 pl5321hdfd78af_3 bioconda
perl-bio-tools-run-alignment-clustalw 1.7.4 pl5321hdfd78af_3 bioconda
perl-bio-tools-run-alignment-tcoffee 1.7.4 pl5321hdfd78af_4 bioconda
perl-bioperl 1.7.8 hdfd78af_0 bioconda
perl-bioperl-core 1.7.8 pl5321h9ee0642_0 bioconda
perl-bioperl-run 1.007003 pl5321hdfd78af_0 bioconda
perl-business-isbn 3.007 pl5321hdfd78af_0 bioconda
perl-business-isbn-data 20210112.006 pl5321hdfd78af_0 bioconda
perl-capture-tiny 0.48 pl5321ha770c72_1 conda-forge
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-class-data-inheritable 0.09 pl5321hdfd78af_0 bioconda
perl-common-sense 3.75 pl5321hdfd78af_0 bioconda
perl-compress-raw-bzip2 2.101 pl5321h1b792b2_0 bioconda
perl-compress-raw-zlib 2.101 pl5321h1b792b2_1 bioconda
perl-constant 1.33 pl5321hd8ed1ab_0 conda-forge
perl-data-dumper 2.183 pl5321h779adbc_0 bioconda
perl-devel-stacktrace 2.04 pl5321hdfd78af_1 bioconda
perl-digest-hmac 1.04 pl5321hdfd78af_0 bioconda
perl-digest-md5 2.58 pl5321h779adbc_0 bioconda
perl-encode 3.16 pl5321h779adbc_0 bioconda
perl-encode-locale 1.05 pl5321hdfd78af_7 bioconda
perl-exception-class 1.45 pl5321hdfd78af_0 bioconda
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-exporter-tiny 1.002002 pl5321hdfd78af_0 bioconda
perl-extutils-makemaker 7.64 pl5321hd8ed1ab_0 conda-forge
perl-file-listing 6.14 pl5321hdfd78af_0 bioconda
perl-file-path 2.18 pl5321hd8ed1ab_0 conda-forge
perl-file-slurp-tiny 0.004 pl5321hdfd78af_2 bioconda
perl-file-sort 1.01 pl5321hdfd78af_3 bioconda
perl-file-spec 3.48_01 pl5321hdfd78af_2 bioconda
perl-file-temp 0.2304 pl5321hd8ed1ab_0 conda-forge
perl-getopt-long 2.52 pl5321hdfd78af_0 bioconda
perl-html-parser 3.72 pl5321h7d875b9_7 bioconda
perl-html-tagset 3.20 pl5321hdfd78af_4 bioconda
perl-http-cookies 6.10 pl5321hdfd78af_0 bioconda
perl-http-daemon 6.13 pl5321hdfd78af_0 bioconda
perl-http-date 6.05 pl5321hdfd78af_0 bioconda
perl-http-message 6.36 pl5321hdfd78af_0 bioconda
perl-http-negotiate 6.01 pl5321hdfd78af_4 bioconda
perl-io-compress 2.102 pl5321h1b792b2_0 bioconda
perl-io-html 1.004 pl5321hdfd78af_0 bioconda
perl-io-socket-ssl 2.074 pl5321hdfd78af_0 bioconda
perl-io-string 1.08 pl5321hdfd78af_4 bioconda
perl-io-tty 1.16 pl5321h779adbc_0 bioconda
perl-io-zlib 1.11 pl5321hdfd78af_0 bioconda
perl-ipc-run 20200505.0 pl5321hdfd78af_0 bioconda
perl-json 4.05 pl5321hdfd78af_0 bioconda
perl-json-xs 2.34 pl5321h7d875b9_4 bioconda
perl-libwww-perl 6.61 pl5321hdfd78af_0 bioconda
perl-libxml-perl 0.08 pl5321hdfd78af_3 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h779adbc_0 bioconda
perl-lwp-mediatypes 6.04 pl5321hdfd78af_1 bioconda
perl-mime-base64 3.16 pl5321h779adbc_1 bioconda
perl-net-http 6.22 pl5321hdfd78af_0 bioconda
perl-net-ssleay 1.92 pl5321he7163dc_0 bioconda
perl-ntlm 1.09 pl5321hdfd78af_5 bioconda
perl-parent 0.238 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321h779adbc_2 bioconda
perl-scalar-list-utils 1.61 pl5321h779adbc_0 bioconda
perl-socket 2.027 pl5321h779adbc_2 bioconda
perl-sub-uplevel 0.2800 pl5321h779adbc_3 bioconda
perl-test-deep 1.130 pl5321hdfd78af_0 bioconda
perl-test-differences 0.69 pl5321hdfd78af_0 bioconda
perl-test-exception 0.43 pl5321hdfd78af_3 bioconda
perl-test-most 0.37 pl5321hdfd78af_0 bioconda
perl-test-warn 0.36 pl5321hdfd78af_2 bioconda
perl-text-diff 1.45 pl5321hdfd78af_1 bioconda
perl-time-local 1.30 pl5321hdfd78af_0 bioconda
perl-timedate 2.33 pl5321hdfd78af_2 bioconda
perl-tree-dag_node 1.32 pl5321hdfd78af_0 bioconda
perl-try-tiny 0.31 pl5321hdfd78af_0 bioconda
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
perl-uri 5.10 pl5321hdfd78af_0 bioconda
perl-url-encode 0.03 pl5321h9ee0642_0 bioconda
perl-www-robotrules 6.02 pl5321hdfd78af_4 bioconda
perl-xml-dom 1.46 pl5321hdfd78af_1 bioconda
perl-xml-dom-xpath 0.14 pl5321hdfd78af_2 bioconda
perl-xml-namespacesupport 1.12 pl5321hdfd78af_1 bioconda
perl-xml-parser 2.44_01 pl5321hc3e0081_1003 conda-forge
perl-xml-regexp 0.04 pl5321hdfd78af_3 bioconda
perl-xml-sax 1.02 pl5321hdfd78af_1 bioconda
perl-xml-sax-base 1.09 pl5321hdfd78af_1 bioconda
perl-xml-sax-expat 0.51 pl5321hdfd78af_4 bioconda
perl-xml-simple 2.25 pl5321hdfd78af_2 bioconda
perl-xml-xpathengine 0.14 pl5321hdfd78af_3 bioconda
pip 22.0.3 pyhd8ed1ab_0 conda-forge
prodigal 2.6.3 h779adbc_3 bioconda
prokka 1.14.6 pl5321hdfd78af_2 bioconda
python 3.7.12 hb7a2778_100_cpython conda-forge
python_abi 3.7 2_cp37m conda-forge
readline 8.1 h46c0cb4_0 conda-forge
setuptools 60.9.3 py37h89c1867_0 conda-forge
sqlite 3.37.0 h9cd32fc_0 conda-forge
t_coffee 11.0.8 py37hea885bf_8 bioconda
tbl2asn-forever 25.7.2f h779adbc_1 bioconda
tk 8.6.12 h27826a3_0 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
I did figure out a work around that appears to be helping.
First I tried the advice in this post https://github.com/tseemann/prokka/issues/598 by simply installing the missing module with the following command. sudo cpan Bio::SearchIO::hmmer3
This seemed to install the module, no errors, however when I the workflow again it failed at the same spot. This made me think that I installed the module into the system's perl instance and not the environment. So I googled how to install perl modules install a specific conda environment and found this blog post.
In that post he says to install this package conda install perl-app-cpanminus and then use cpanm <package> to install in that environment. So I did cpanm Bio::SearchIO::hmmer3 and it failed, but it said I could force the install so I did.
cpanm Bio::SearchIO::hmmer3 --force
The install was successful and now the analysis is working.
I am posting this here for other people who may run into this problem until a permanent fix can be made.
This became a problem since the Bioperl team decided to take Bio::SearchIO::hmmer3 (and a bunch of other things) out of the core distribution in v1.7.3 (https://metacpan.org/dist/BioPerl/changes).
Suffering from this problem myself, I decided to shave the yak and got this module added to bioconda. Now you can conda install perl-bio-searchio-hmmer.
This problem should go away in the future since future conda installations of bioperl will pull this in automatically.
