Documentation PlantQTLdb Assistant Troubleshooting and Limitations
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Getting Started with Assistant Gene Structure and Sequence Extraction Variant Annotation and Local QTL Evidence Functional Enrichment with g:Profiler Network Analysis with STRING Finding Sequencing Data with ENA Sequence Similarity Search with BLAST Plant Motif Analysis with JASPAR and FIMO DNA Analysis with Evo2 External Biological Evidence Sources Troubleshooting and Limitations

PlantQTLdb Assistant

Troubleshooting and Limitations

resolve missing cards, unsupported inputs, pending jobs and incomplete results

Check the selected mode and returned status

Open PlantQTLdb Assistant

A tool question returned only literature

For the six new scientific tools, check that the composer says Research before sending. Standard and Quick do not execute that analysis workflow. Resend after changing the mode; an existing completed answer is not automatically rerun.

Use the complete example, including species, identifiers or actual sequence. Questions such as 'What is STRING?' ask for an explanation rather than a network analysis.

Retry an explicit analysis in Research

ask
Use STRING to analyze the functional association network of Arabidopsis genes AT1G01010 and AT1G01020

what you receive

A named STRING result and, on success, its network card. If the service fails, read the returned reason instead of interpreting an ordinary literature answer as a successful network search.

A species or transcript is unavailable

Cotton enrichment
g:Profiler is disabled for G. hirsutum and G. arboreum; no different cotton species is silently substituted.
Sorghum and tomato references
Sequence extraction and the dependent gene-structure/variant-window workflow are paused pending reference compatibility checks. This does not disable every external tool for those species.
Multiple transcripts
Structure displays all returned transcripts. For a single extracted CDS, cDNA, protein or promoter, supply a transcript_id from the returned list.
Mixed species or ambiguous IDs
Separate species into different messages and resolve ambiguous mappings before interpreting results.

Pending, busy and failed are different

BLAST pending/running
A remote job exists. Wait for the indicated interval and use Check job status, then send the composed query.
FIMO busy
No queued job has been created for you. Retry the request later when the single worker is available.
Provider unavailable
The external service did not provide a usable result. Do not read this as a biological negative.
Card loading failure
Use Reload result when shown, or reload the conversation. A completed immutable result can be fetched without resubmitting the scientific analysis.

Empty or truncated output

A successful empty result may reflect identifier coverage, thresholds or a real lack of matching records. It is not equivalent to 'not supported' or a timeout.

Preview tables can show fewer rows than downloads. Truncation limits the data returned by the analysis itself; downloading CSV does not bypass that limit. In particular, gene-window QTL counts can be lower bounds and the associated plot can be partial.

What to include in a problem report

  • The exact question, selected mode, species, gene/transcript or reference version, and the displayed error/status.
  • The time of the request and a screenshot of the relevant answer/card. Avoid sharing session cookies, passwords or private sequences in a public report.