Error in RNA STAR - wrong read ID line format

jennaj · April 1, 2026, 6:11pm

Thanks for sending in the bug report as @wm75 suggested!

I replied to your report with the message below. In short, when a tool reports an issue with fastq data content, starting with content checks is where to start. This is how I replied to your email.

However, after taking a closer look at your most recent reruns (and QA), the reads themselves seem fine now, and I can see that different samples may fail with your exact reruns on the full collection. This was an important clue!

The jobs are likely failing for a technical issue. We had some cluster hiccups over the last week or so but this can happen at any time (thousands of jobs are processing, constantly!). Some jobs will fail by chance and produce an unreliable error message.

What to do

Try a rerun! You won’t want to rerun the entire collection. Instead, only rerun the failed job(s).

Workflows: job queues and managing partial failures with Resume and Replace!

Then, the advice I would have for larger batches of work at the public servers. 1. start up the processing for an entire batch. 2. Later, if some fail, click into the collection and use the rerun icon (FAQ: Different dataset icons and their usage) on each failed dataset. This brings up the original tool form and you can run it again for just that single sample.

Bonus: If the failed job was run as part of a workflow, right above the Run Tool button (on the tool form) will be two new extra options. This is useful when running longer, complicated workflows, but also shorter ones. The result is indistinguishable from runs where everything worked perfectly to start with.

Replace elements – this sorts the new output back into the original collection output nesting (with the already successful inputs).

Resume dependencies – this starts up any downstream tools that were paused because of these upstream failures (assuming the new job works!)

Full details with screenshots are here (including the Planemo option for bunk reruns!). → Rerunning only failed jobs in a workflow: Replace and Resume functions - #2 by jennaj