Common Errors & Solutions

Introduction

The goal of this page is to provide some troubleshooting guidance for commonly reported user errors. Although Semblans primarily utilizes local versions of its dependencies to maximize compatibility across machines, certain issues may arise, particularly during the Trinity step, that warrant some extra troubleshooting by the user. The following page documents common problems while running Semblans and their solutions.

If you experience any issues not addressed on this page, please post an issue with a screenshot of the error, as well as data, command(s) that produced it. Thanks!

List of Errors, Solutions

'...failed updating X targets... Error at line: Y' or 'fatal error: rapidxml/rapidxml.hpp: No such file or directory' and other from-source installation issues

This error has been reported to occur during a from-scratch Semblans installation, and indicates a failure to install a dependency. First, try running ./install.sh again, as this can sometimes be a one-off error stemming from a bad download of the dependency. If this does not solve the problem, try downloading Semblans from one of the pre-compiled releases on this repository.

'Can't locate URI/Escape.pm in @INC (you may need to install the URI::Escape module) ...'

This error sometimes occurs in Semblans' postprocessing phase, during the final prediction of coding regions and peptides. It arises when the program TransDecoder is unable to locate a non-standard Perl library called URI::Escape. Per the TransDecoder installation instructions, the user can enter the following into their terminal to install the library:

curl -L https://cpanmin.us | perl - App::cpanminus
cpanm install DB_File
cpanm install URI::Escape

Issues at Trinity stage

Issues are known to occasionally arise during the Trinity stage of Semblans. If your assembly run fails at this stage, we first recommend installing Trinity on your system via a package manager such as apt or homebrew:

apt install trinityrnaseq

Generally, this also installs Trinity's dependencies, but make sure you have working installations of:

• bowtie2
• jellyfish
• salmon
• samtools
• numpy

This fixes most issues. Further errors/solutions are listed below:

Trinity unable to locate 'samtools', 'bowtie', or 'jellyfish', etc (CLUSTERS)

This error is known to occasionally occur on clusters, and typically results from the node not having access to these programs' binaries. This can usually be fixed by including the following lines in whatever script or bash interface used to submit the job to the cluster:

module load samtools
module load bowtie
module load jellyfish
...

If your issue is not addressed by this list, we urge you to post an issue to this repository's page containing your error message so that we can help you troubleshoot.