Miseq RTA crashed

[CMG_seq]

Hello all,

We are running a 300v2 run on our miseq. Sadly, rta crashed during the first cycle. We tried restarting rta, but the process crashed over and over. Meanwhile, miseq continued to sequence and pile up raw data untill the D drive was completely full (200+ GB of raw data). Obviously the run stopped (at cycle 145) untill more space is cleared from d drive.

As the machine stopped sequencing, awaiting space on d drive, the internal computer has become more responsive and re launching rta at this point does not seem to crash it. However rta does not process the data that is waiting in the queue, instead it pops out error messages.

Does anyone know how we can continue the run? The first priority should be processing the data that is in the queueu now. As rta has crahed during cycle 1, no cluster densities have been reported ...

Any help would be appreciated !

[sklages]

The first priority should be contacting Illumina's Tech support IMHO.

[kcchan]

How are you restarting RTA? Are you just clicking on the .bat file in the run folder or are you making a new .bat file?

[kodbeeck]

@ sklages: illlumina's tech support is not available during the weekend

@ kcchan: just clicking the bat file indeed.

this is my home account, from which i'm posting now

[kcchan]

Can you double check the Windows task manager to make sure that RTA isn't open multiple times? If so you should close them all, then re-start a new instance.

Edit: also, if you get RTA back up and running, pause the MiSeq for at least 15 minutes to give it a chance to process some the images. When the drive frees up a bit you can resume normal cycling.

[kodbeeck]

There is just one RTA running.

I've tried the 15 minute tip, but rta remains idle.

Thanks anyway. Will contact Illumina tech support tomorrow.

[MadsAlbertsen]

Seems like we just got the same problem. Huge amounts of raw data filling up the drives without being processed.

Did it work to just restart the RTA?

rgds
Mads Albertsen

[kodbeeck]

We were not able to recover the run.

On monday, following the weekend where we had the problem, I contacted tech support, after I tried restarting RTA for countless times which -for us- did not work.

They took a look at the run, but in the end, miseq software terminated the run and we were directed to a post run wash.
Illumina compensated all reagents for this run.


Maybe you can try restarting RTA, it might help. In our case, the problem was that another RTA process from a previous run was still running in the background, corrupting the current run. This process was invisible for windows, so we could not shut it down. The simple fix was to restart miseq between each run.

Good luck.

[MadsAlbertsen]

OK. Thanks for the fast answer - we'll give it a go.

rgds
Mads

[MadsAlbertsen]

It seem to have been a tile failing that caused the processing of the images to stop. The Illumina tech support was able to disable the specific tile and after a restart of RTA we seem to be up and running again.

rgds
Mads Albertsen

[kerryp]

my RTA failed less than 50 cycles into a 600 cycle MiSeq run. I've been in contact with tech support and they've agreed to replace reagents. BUT because it stopped so early on, could I re-use the reagent cartridge and/or flow cell using the same pooled library? The flow cell will be clustered - if I bypass the barcode recognition, is there any way of skipping ahead to avoid upsetting the software, or could I just start from the start and see what happens? I've got nothing to lose but breaking the instrument (I don't want to do that).