Prokka: ubuntu安装的时候出现错误

2024-01-08 22:48:02

[14:10:57] Running: cat /app/prokka_result/ref_file/ref_file.HAMAP.hmm.tmp.77.faa | parallel --gnu --plain -j 2 --block 108208 --recstart ‘>’ --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /opt/prokka/db/hmm/HAMAP.hmm /dev/stdin > /app/prokka_result/ref_file/ref_file.HAMAP.hmm.tmp.77.hmmer3 2> /dev/null
Bio::SearchIO: hmmer3 cannot be found
Exception
------------- EXCEPTION: Bio::Root::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: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/share/perl5/Bio/Root/Root.pm line 520.

sudo apt-get install libbio-searchio-hmmer-perl # Ubuntu系统上，可以使用该命令安装

Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y ‘Annotated using prokka 1.14.6 from https://github.com/tseemann/prokka’ -Z output_directory/PROKKA_01082024.err -i output_directory/PROKKA_01082024.fsa 2> /dev/null
[08:45:22] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y ‘Annotated using prokka 1.14.6 from https://github.com/tseemann/prokka’ -Z output_directory/PROKKA_01082024.err -i output_directory/PROKKA_01082024.fsa 2> /dev/null

sudo apt-get install ncbi-tools-bin # Ubuntu系统上，可以使用该命令安装

文章来源:https://blog.csdn.net/weixin_44750594/article/details/135464036
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