Hi all,
I am using Bentobox (v3), and get the error message below when running the peak detection script using centWave.
'Error in checkForRemoteErrors(val) :
89 nodes produced errors; first error: m/z sort assumption violated ! (scan 618, p 7536, current 951.7201 (I=35.00), last 951.7378)'
traceback()
4: stop(count, " nodes produced errors; first error: ", firstmsg)
3: checkForRemoteErrors(val)
2: xcmsClusterApply(cl = snowclust, x = argList, fun = findPeaksPar,
msgfun = msgfun.featureDetection)
1: xcmsSet(method = "centWave", peakwidth = c(CPWmin, CPWmax), ppm = ppm,
snthresh = xsnthresh, lock = LM, integrate = integrate, nSlaves = nSlaves,
prefilter = c(5, 1000), noise = (300), scanrange = c(30,1363))
I have seen that many people have had this problem due to conversion software. This data was originally converted using DataBridge (Data was acquired on Waters Synapt G2). I reconverted using databridge on another computer is case it was a system issue, with no success.
As suggested in other feeds, I then converted the raw files to the mzXML format using Proteowizard, and get the following error message:
'89 nodes produced errors; first error: Time for scan 1499 (1319.56) greater than scan 1500 (1.225)'
> traceback()
4: stop(count, " nodes produced errors; first error: ", firstmsg)
3: checkForRemoteErrors(val)
2: xcmsClusterApply(cl = snowclust, x = argList, fun = findPeaksPar,
msgfun = msgfun.featureDetection)
1: xcmsSet(method = "centWave", peakwidth = c(CPWmin, CPWmax), ppm = ppm,
snthresh = xsnthresh, lock = LM, integrate = integrate, nSlaves = nSlaves,
prefilter = c(5, 1000), noise = (300), scanrange = c(30,
50))
My run time is 22 mins, so (from my naive eye) it looks like its either replacing the last scan with the first, or looping. I have tried playing with the scan range used (30-1363 is default), but it all seems redundant as I get the same error every time.
Does anyone know a successful way of fixing this issue? I know this issue has been posted a few times before, but none of the current suggestions have worked when applied.
Thanks in advance,
Kallie
Tried this: viewtopic.php?t=144&p=274 (http://www.metabolomics-forum.com/viewtopic.php?t=144&p=274) ?
Hi Jan,
Yes, I've tried this with no success
Kallie
Perhaps try masswolf then: viewtopic.php?f=26&t=359&p=1694 (http://www.metabolomics-forum.com/viewtopic.php?f=26&t=359&p=1694)