Error in filter_sequences_by_length.pl

[Timmywang1]

When I run the command ‘perl filter_sequences_by_length.pl -input /data/Timmy/metagenome_test/ERR1051325.fa -output /data/Timmy/plasflow/filtered_ERR1051325.fa -thresh sequence_length_threshold’

Error: “(plasflow) [wangbh@tc6000 Plasflow]$ perl filter_sequences_by_length.pl -input /data/Timmy/metagenome_test/ERR1051325.fa -output /data/Timmy/plasflow/filtered_ERR1051325.fa -thresh sequence_length_threshold Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /usr/lib/perl5/site_perl /data2/wangbh/perl5/lib/perl5/x86_64-linux-thread-multi /data2/wangbh/perl5/lib/perl5 /public/home/bma/miniconda2/envs/plasflow/lib/site_perl/5.32.0/x86_64-linux-thread-multi /public/home/bma/miniconda2/envs/plasflow/lib/site_perl/5.32.0 /public/home/bma/miniconda2/envs/plasflow/lib/5.32.0/x86_64-linux-thread-multi /public/home/bma/miniconda2/envs/plasflow/lib/5.32.0 .) at filter_sequences_by_length.pl line 24. BEGIN failed--compilation aborted at filter_sequences_by_length.pl line 24.” It seems that Bio::SeqIO is not installed, And when I run the command ‘conda install -c bioconda perl -bioperl perl-getopt-long’; Error : “usage: conda [-h] [-V] command ... conda: error: unrecognized arguments: -bioperl perl-getopt-long”;

when I run the command ‘cpan -i Bio::Perl Getopt::longer’, Error : “(error): Skipping Getopt::longer because I couldn't find a matching namespace.”

[smaegol]

Hi, you had accidentally put a dash (-) before bioperl in your command.

Try this: conda install -c bioconda perl bioperl perl-getopt-long

[vincenzopennone]

Hi, I have exactly the same issue, however, I'm sure I have Bio::SeqIO installed. For some reason filter_sequences_by_length.pl doesn't find it. How can this be fixed? Thanks