Error: differential expression -- Issues with older Trinity tools and tutorials

For RNA assembly I am following the following link (on
Followed all steps as mentioned in the above link, for abundance estimation to matrix tool I have used two samples and the output files are TMM EXPR and counts matrix. Further used edgeR tool where I have to give inputs of counts matrix and trinity assembled transcripts. Here I have doubt which assembled transcript I need to give as input. my sample one’s or two’s because the resulted file from edger is combination of two samples.
I have run edgeR once with sample one’s and second time with other sample’s assembled transcript. In both cases I have got output without any error. Followed by I have run differential expression where I have got error like below.

I have rerun the jobs and checked all other outputs(have multiple pairs per sample so checked with all the outputs) but the result is same error. what does this error mean and how to rectify it?

Can anyone suggest the way out please?

Thank you

1 Like

Hello @YKV

Please review this server’s learning resources and contact information in this prior post:

The information posted is not enough to diagnose the problem. Try reviewing the Job details (“i” icon) report, including the stderr and stdout reports linked from it. Often these tools will report what is going wrong in those reports, but near the end. Right now all that is visible is the very top of the stderr report, and it almost looks as if the environment used to execute the tool failed to build – but that is just a guess. IF that is the actual problem, someone who has administrative access to the server would need to help with that.

The server you are working on hosts custom versions of these tools. There may be a known issue server-side, or they may be able to help in other ways.

Hi @jennaj,



Hope this will help.

Thank you

1 Like

thanks @YKV, the extra error information helps

In the simplest terms, the process was unable to locate a file. This appears to be a technical error unrelated to usage/inputs.

You may want to switch to using the more recently updated suite of Trinity tools. Resources below, plus review the tool forms for usage help: inputs and outputs, upstream and downstream tools – all are described. To avoid unexpected problems, avoid mixing tools from different tool suites/authors. The usegalaxy.* servers host the tools below:,, and Other public Galaxy servers may as well, you’ll need to check.