[d00b]

we used exactly same PAL (stopped running) for next new running and it works well. This indicates the PAL is not a problem. it is fluidics.. illumina techsupport said "Miseq should have alert before start running, if there is flow cell problem."

But I don't think, the fluid is delivered from sample load tube by sipper 17 (miseq cartridge in position 17) for flow rate testing. if the fluid tube or sipper has air bubble or dust, the PAL sample won't be able to deliver to the flow cell chamber. It will lead to stop the premature running.

[Yepler]

Hmmm, one other thing to check is whether the flow cell is all snapped together. I had the same issue (unable to focus - probably because there was nothing to focus on), and the flow cell housing was loose. I get kits about 20 at a time, and about 2/3rds of the flowcells in that batch had plastic housings that weren't fully snapped together.

Sometimes these will just throw the pre-check error, but other times it will go through the precheck and then fail at focusing.

Illumina did replace my kit when the run failed; I just check the housing carefully now.

This may have nothing to do with what you're seeing, but it's something to check.

Cheers-
Deb

[GA-J]

I had a stopped miseq run, 2x300, it stopped at 546 cycle. Run completed with error message: best focus is too near edge to the range.So no fastq files generated. Anyone knows what cause this stopping? The cluster density is 1156k/mm^2,Q30 and pass filter both good. I did the miseq system check, everything passed, I started a rerun, almost same. But I worry it may stop again. Should I worry??

[nucacidhunter]

It could be due to overclustering. Look at page 3 for details in the following doc:

http://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdf

[bunce]

Hi GA-J, Are you sequencing amplicons? - you can attempt to salvage the data by altering the sample sheet to do 300 in read 1 and then~240 for R2 (you do this in MiSeq reporter - http://localhost:8042). And then re-queue the run analysis.It may output the fast files you are after. The quality issues in R2 for 600 cycle kits are well documented - you might want to let Illumina know - your kit may be in the batch that they will replace? good luck....

[GA-J]

Yes,we got replacement kit. My problem is there is no name appear at my Miseq reporter, how can I work it out?
Thank you!

[GenoMax]

Yes,we got replacement kit. My problem is there is no name appear at my Miseq reporter, how can I work it out?
Thank you!

Since the run "failed" you may have to process the data using CASAVA/bcl2fastq outside of MiSeq reporter. It also will require using appropriate --use-bases-mask.

You may be able to "trick" MiSeq reporter into displaying the run name by creating a "Run/analysis complete" file in the flowcell folder. Someone more familiar with MiSeq reporter will have to tell you how to do that.

[GA-J]

Thank you very much! I will try to work it out!

[bunce]

You might want to call Illumina and get some formal help. On the two occasions that we have had a premature run termination (primarily when the run hits the 'end of a amplicon' and the signal falls away to much') then MiSeq reporter always had the run present (as a reagent carriage ID).

I am not sure of the root cause of what you are describing - but it could be amplicon 'cliff edge' effects (that are exacerbated by lower R2 quality?) coupled with a low % PhiX spike in? Hard to guess without more info. Cheers Mike.

[GA-J]

I would like to share some information from the stopped run. Thanks for any words.

Newest update: the rerun passed without error! Quality looks OK.