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Fasta_reader.pm Trinity fails

Hi, I was trying to execute perl script TrinityStats.pl with the command:

perl TrinityStats.pl Trinity.fasta > tr.log

But there is an error:

Can't locate Fasta_reader.pm in @INC (you may need to install the Fasta_reader module) (@INC contains: /home/pilofer/Escritorio/TRINITY/all_sequences/../PerlLib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.32.1 /usr/local/share/perl/5.32.1 /usr/lib/x86_64-linux-gnu/perl5/5.32 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.32 /usr/share/perl/5.32 /usr/local/lib/site_perl) at TrinityStats.pl line 8.
BEGIN failed--compilation aborted at TrinityStats.pl line 8.

I've already tried to upgrade my Trinity version, install Fasta_reader module, etc, but anything works.
Thank you in advance

perl fasta_reader trinityrnaseq trinity
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written by Pilar • Pilar

Have you tried the solution suggested here ? I had the same issue some months ago and it worked for me.

Ah, I also modified the line #!/usr/bin/env perl in TrinityStats.pl to be able to locate the Fasta_reader module.

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written by iraun iraun

Yes. When i do pip install Fasta_Reader, the output is:

Requirement already satisfied: Fasta_reader in /home/pilofer/.local/lib/python3.9/site-packages (1.0.0)
Requirement already satisfied: importlib-resources>=1.4.0 in /home/pilofer/.local/lib/python3.9/site-packages (from Fasta_reader) (5.4.0)
Requirement already satisfied: pytest>=5.4.3 in /usr/lib/python3/dist-packages (from Fasta_reader) (6.0.2)
Requirement already satisfied: click>=7.1.2 in /usr/lib/python3/dist-packages (from Fasta_reader) (7.1.2)
Requirement already satisfied: xopen>=1.0.1 in /usr/lib/python3/dist-packages (from Fasta_reader) (1.1.0)
Requirement already satisfied: more-itertools>=8.4.0 in /home/pilofer/.local/lib/python3.9/site-packages (from Fasta_reader) (8.12.0)
Requirement already satisfied: zipp>=3.1.0 in /home/pilofer/.local/lib/python3.9/site-packages (from importlib-resources>=1.4.0->Fasta_reader) (3.7.0)
Requirement already satisfied: isal>=0.3.0 in /home/pilofer/.local/lib/python3.9/site-packages (from xopen>=1.0.1->Fasta_reader) (0.11.1)

So I modified the line #!/usr/bin/env perl in TrinityStats.pl for: #!/home/pilofer/.local/lib/python3.9/site-packages perl

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updated by GenoMax GenoMax • written by Pilar • Pilar

okey I don't know why, but it works without writing "perl" at the beginning in command

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written by Pilar • Pilar

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