Problem with Trinotate runMe.sh script

Question

[lidanqing1990]

Dear all, I would like to learn how to use Trinotate in my supercompute account. There is already Trinotate installed in the supercompute. Firstly, I module load Trinotate and then try to run runMe.sh script to see how Trinotate works. But there is always the error:

line 49 ../Trinotate ${sqlite_db} init --gene_trans_map Trinity.fasta.gene_trans_map --transcript_fasta Trinity.fasta --transdecoder_pep Trinity.fasta.transdecoder.pep No such file or directory

I think the error might be caused by my failure in module load Trinotate, but I don't know what else should I do, I used the same method to module load other softwares and they alway work well.

Could anyone give me some suggestions? Thank you!

[GenoMax]

It is useful to include the original command you used since the error on its own may not always be informative (like in this case).

[lidanqing1990]

Thank you for reminding.

Answer 1

[h.mon]

Trinotate module did load successfully, otherwise the error would be:

bash: runMe.sh: command not found

or something similar.

There are two runMe.sh on latest Trinotate (version 3.0.2), but they are just testing scripts. The Trinotate web page has detailed instructions on how to run Trinotate, please read them carefully.

[lidanqing1990]

Ok, thank you so much.