having error during running the "Trinonate"

usegalaxy.org support
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Error, no gene_id for trans: [TRINITY_DN76711_c0_g1_i1] at /mnt/tools/tool_dependencies/_conda/envs/mulled-v1-0534adab201f5820009b76442004c506252b49a190f1c3ca55d89fa4eb5bd895/bin/TrinotateSeqLoader.pl line 132, <$filehandle> line 1.
Error, cmd: TrinotateSeqLoader.pl --sqlite Trinotate.sqlite --gene_trans_map /mnt/user-data-volA/data16/e/e/0/dataset_ee0c8c35-1a2f-4a43-85b4-f097c7aa23fc.dat --transcript_fasta /mnt/user-data-volA/data14/9/a/d/dataset_9ade07cc-26ee-4573-9b0f-c3dcfa55aecb.dat --transdecoder_pep /mnt/user-data-volA/data14/2/d/a/dataset_2da597d4-56bf-4375-9a01-41c24086767c.dat --bulk_load died with ret 6400 at /mnt/tools/tool_dependencies/_conda/envs/mulled-v1-0534adab201f5820009b76442004c506252b49a190f1c3ca55d89fa4eb5bd895/bin/Trinotate line 126

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Hi @Ravita_Tadiya

You’ll need to check if that transcript_id is associated with a gene_id, or whether all transcript_ids don’t have a gene_id. Why? Sometimes tools just report the first time they hit a problem and quit out.

Now, that identifier is for a gene_id (unless I am mixing things up?) which makes this more confusing, and points to some larger data organization problem. Double check your inputs versus the labels on the tool form.

Examples:

  • If an input area is referring to a transcript, make sure the files are transcript based.
  • Do the same for any inputs labeled as gene based.
  • Remember that tools are usually picky about how important data keys are formatted, so make sure your data files are super-clean.

What does “super-clean” mean?? :mechanic: It means no stray characters, same caPitalization between files, the right number of data columns, and similar.

  • This FAQ covers different tools but the general formatting guidelines are good for nearly all Bioinformatics tools. FAQ: Extended Help for Differential Expression Analysis Tools
  • Now, some tools might not need data as strictly formatted as that, but none of this can harm inputs to those other tools either.
  • The exception would be if a tool explicitly states that it wants some alternative format. That would be captured on the tool form, or any user guide link outs on the form, or tutorials linked on the form (author hosted or in the GTN).
  • Once you get familiar with a tool, you’ll learn how tolerant it is about variations in formats. Before that, using clean formats avoids weird errors, or poor scientific results (not always so easy to detect).

So, please give that a review and try to solve the problem. If you get stuck, we’ll need to see the complete run with the parameters and inputs to troubleshoot this here. See the banner at this site for how to share your work, or see directly here:

Let’s start there, thanks! :slight_smile: