This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Fasta_reader isn't working.

Dear all,

When I try to use the script, fasta_seq_length.pl in Trinity, it outputed the following error message.

fasta_seq_length.pl fasta > fasta.seq_lens

Can't locate fasta_reader.pm in @INC (you may need to install the fasta_reader module) (@INC contains: /Users/tomitariku/Bioinformatics/Aphelenchoididae/scripts/../../PerlLib /opt/anaconda3/envs/trinity/lib/perl5/5.32/site_perl /opt/anaconda3/envs/trinity/lib/perl5/site_perl /opt/anaconda3/envs/trinity/lib/perl5/5.32/vendor_perl /opt/anaconda3/envs/trinity/lib/perl5/vendor_perl /opt/anaconda3/envs/trinity/lib/perl5/5.32/core_perl /opt/anaconda3/envs/trinity/lib/perl5/core_perl .) at scripts/fasta_seq_length.pl line 8.

It seemed that there is similar problems before, so I have installed Fasta_reader as same way. But it has outputed the same error.

pip install Fasta_reader

What's a problem? Could you please give me a help.

Thanks.

fasta_reader fasta_seq_length.pl ngs rnaseq trinity
• 2,861 views • link
updated by Pilar • Pilar • written by Riku • Riku

1 answer

fasta_reader.pm refers to a perl module, not python. I think it is part of Trinity installation in the PerlLib directory:

https://github.com/genome-vendor/trinity/blob/master/PerlLib/Fasta_reader.pm

There should be an explanation in Trinity documentation how to install the program so this directory is visible to perl scripts.

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

I found out that pm is perl module. But I didn't know how to install the program, because I wasn't able to find an explanetion as you say. And I'm beginner at bioinformatics, so could you please tell me in details if you are okay?

Many thanks to your help.

• 0 views • link
written by Riku • Riku

I solved this problem. I made a path to my environment in anaconda.

Specifically, I changed the first line of the script to my path in anaconda as following. I used vim command, but any means should be fine.

#!/opt/anaconda3/envs/trinity/bin/perl

I'm not an expert so I'm just speculating, I guess I was able to become using fasta-reader of anaconda by the change. However this environment need to have fasta-reader, so you havo to install it in your environment as following if you haven't.

pip install Fasta_reader

I hope this question helps someone!

• 0 views • link
written by Riku • Riku

hi! in which script have you made changes? I don't have permissions in Fasta_reader.pm

• 0 views • link
written by Pilar • Pilar

Log in to answer this question.

More posts like this
  • error to run rnammer
    written by microorganism_001 • microorganism_001
    I have installed rnammer software to extract 16s rRNA gene and dependencies (hammer) but I am getting errors when run it. I have followed many …
  • I'm not being able to use TransDecoder because of URI::Escape module, but it's already installed
    written by Vinícius • Vinícius
    I'm trying to use TransDecoder, but I'm getting this error: TransDecoder.LongOrfs -h Can't locate URI/Escape.pm in @INC (you may need to install the URI::Escape module) …
  • Can't install Transdecoder -
    written by Pedro • Pedro
    I was trying to install TransDecoder to do Transcriptome annotation, but when I run make test, this shows up. I've tried to install the module …
  • Failing to compile kent utilities due to openSSL dependencies
    written by 4galaxy77 4galaxy77
    I would like to use the LOFTEE plugin for VEP on a cluster with no root permissions, but it fails with this error: ``` WARNING: …
  • Conda environment perl issue
    written by Paulo • Paulo
    Greetings. I'm trying to use the program "https://github.com/rhysf/Synima" using a conda environment. I've created a new environment and used conda to download the needed depenencies …
  • perl can't see path problem
    written by Xylanaser Xylanaser
    Hi I'm trying to run `pfam_scan.pl`. I'm using conda but there's perl from ubuntu system. It conflicts with another? Or script can't see modules? $ …
  • Fasta_reader.pm Trinity fails
    written by Pilar • Pilar
    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 …
  • abricate perl module not found
    written by zhichusun • zhichusun
    abricate Can't locate Path/Tiny.pm in @INC (@INC contains: /root/miniconda3/envs/abricate/lib/site_perl/5.26.2/Path/Tiny.pm /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /root/miniconda3/envs/abricate/bin/abricate line 7. BEGIN failed--compilation aborted at /root/miniconda3/envs/abricate/bin/abricate …
  • The problems when i install the miRDeep2
    written by 51203903042 • 51203903042
    I am trying to install mirdeep2. I tested make_html.pl and error appeared as following: Can't locate PDF/API2.pm in @inc (@inc contains: /home/students/anaconda3/lib/site_perl/5.26.2/PDF/API2.pm /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl …
  • DE analysis using trinity
    written by sukesh1411 • sukesh1411
    Hi I am new to RNA-Seq data analysis. I am using example files, which is given in trinity to perform denovo assembly of rna-seq data. …