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Error in filter_sequences_by_length.pl #36

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Timmywang1 opened this issue Apr 28, 2021 · 2 comments
Open

Error in filter_sequences_by_length.pl #36

Timmywang1 opened this issue Apr 28, 2021 · 2 comments

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@Timmywang1
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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
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smaegol commented Apr 29, 2021

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

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

@vincenzopennone
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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

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