Unintended saving of images on HiSeq

[kmcarr]

We seem to have encountered a bug in the HiSeq Control Software (HCS v1.4.8) and I was wondering if any others have had a similar experience and if so is there a solution or workaround.

When configuring a run the technician will select "Save All Thumbnails" from the popup menu under Advanced on the Scan page of Run Configuration. However on two occasions thus far the configuration gets set to "Save All Images" which obviously has a disastrous impact on the run. Both the HiSeq control computer and the network storage location become filled with image files. We have confirmed that the software appears to be altering the selection on its own. We will select "Save All Thumbnails" (which is the default selection), clicked "Next" to move forward with the configuration then immediately clicked "Back" to return to the Scan setup page. It now displays "Save All Images" for the 'Save Images' option. We have repeated this but did not explicitly set this option ("Save All Thumbnails" is supposed to be the default) but got the same results. Even though "Save All Thumbnails" was selected when moving forward from the 'Scan' page to the 'Recipe' page, if you then go back it will show "Save All Images" being selected.

Tech support has not provided any possible cause or solution other than try reinstalling the software.

Has anybody else had a similar experience with the HiSeq Control Software?

[pmiguel]

We deliberately save our image files. Which doesn't help you.

But, recently our FAS asked if it would be okay to have an engineer change our settings so that image files could not be saved. I did not want this, but it sounds like a good solution in your case.

(We have a HiScanSQ, not a HiSeq, but we do use HiSeq Control Software.)

--
Phillip

[kmcarr]

Update

So after contacting our FAS he remotely changed the configuration of the instrument so that it could no longer save images. Apparently the option is enabled in some config file. The only reason it exists is to allow FSE's to save images if needed when installing/troubleshooting instruments which makes sense I guess. But it seems to me that a normal part of the installation process should be disabling that option before releasing the instrument to the customer.

Phillip, thanks for your input. But I have to ask, what is the total size of the image files for a HiScan run of 2x100bp and how long do you keep them after the run. On a HiSeq 2000 the size is easily > 10TB. RTA on the instrument computer can not keep up with copying those images in addition to analyzing the data hence the run was repeatedly paused while it was waiting for disk space to free up. I also had to manually delete images from the network storage location several times during the run because it was getting full.

[MRSeq]

What are the "disastrous effects"?

Hello,

I am actually interested in saving images intentionally - our samples have very low initial nucleotide composition diversity, so we wanted to try alternative image analysis to improve data quality. My question is, what is the worst that can happen when we would choose to save all the images? Does the machine simply stops and wait for the disk space to be freed, as you reported? Does such stopping has any adverse effects on the sequencing quality? Is there a risk of image file being over written before the image analysis is completed?

[Tom Barker]

If the D: and E: fill up during a run it will pause the run as mentioned above but it can also slow down the performance of the computer. We've had runs where RTA for whatever reason has not been processing the cif files and as a result the hard drives filled up and either HCS or both HCS and the computer cease to respond, in which case the computer may need to be forced to shutdown, restarted, and some space cleared on the drives. This can be time consuming and means the run takes longer to complete which can result in lower quality. If paused intentionally for a day or so, when a run is restarted the intensities drop a bit. However overall the quality of the run doesn't seem to be affected too badly. I guess it depends on how much space is on the drives and the length of the run. We don't save images and try to keep the drives as clear as possible at the start of a run.

[MRSeq]

Hello Tom,

Thank you very much for your answer. Can you also tell me what HCS version you were using? He have 1.5.15 and it seems to be more difficult to save images with that version. We have seen Delete Threads log file obtained from a Hiseq run, January this year , and they do not contain a trace of deleting tif files. The tif images were not saved on disk either.

Does anyone know how to save or salvage images while using HCS 1.5.15?

[Tom Barker]

Hi MRSeq,

We are currently using HCS version 1.4.8 as our engineer said there were some bugs with the newer version and it was probably best to wait until they're fixed so i'm afraid i can't help you with your question about version 1.5.15.