Pipeline failure

Support Questions
1

Hello,
I have a pipeline failure during data processing that does not go beyond step 5 (so apparently fails during data integration). I checked that I don’t have a sample without enough cells, but the smaller one at the end of step 5 has more than 300 so that shouldn’t be a problem according to the user guide.
The indicated reason is States.Timeout.

Is there anything I should do with the data for the integration to succeed?
Many thanks

2

In case this is of any help, here is the data processing settings:
[1-classifier.copd152b]
FDR = 0.01

[1-classifier.copd8]
FDR = 0.01

[1-classifier.copd137]
FDR = 0.01

[1-classifier.copd153b]
FDR = 0.01

[1-classifier.ctrl1]
FDR = 0.01

[1-classifier.ctrl84]
FDR = 0.01

[1-classifier.ctrl92b]
FDR = 0.01

[1-classifier.ctrl81]
FDR = 0.01

[1-classifier.ctrl2]
FDR = 0.01

[1-classifier.ctrl388]
FDR = 0.01

[1-classifier.ctrl137]
FDR = 0.01

[1-classifier.ctrl65]
FDR = 0.01

[1-classifier.ctrl208]
FDR = 0.01

[1-classifier.ctrl454]
FDR = 0.01

[1-classifier.ctrl218b]
FDR = 0.01

[1-classifier.ctrl244]
FDR = 0.01

[1-classifier.ctrl484]
FDR = 0.01

[1-classifier.ctrl34]
FDR = 0.01

[1-classifier.ctrl92]
FDR = 0.01

[1-classifier.copd23]
FDR = 0.01

[1-classifier.ctrl253]
FDR = 0.01

[1-classifier.ctrl219b]
FDR = 0.01

[1-classifier.ctrl396]
FDR = 0.01

[1-classifier.copd56]
FDR = 0.01

[1-classifier.copd184a]
FDR = 0.01

[1-classifier.copd186]
FDR = 0.01

[1-classifier.copd153a]
FDR = 0.01

[1-classifier.copd184b]
FDR = 0.01

[1-classifier.copd192b]
FDR = 0.01

[1-classifier.copd192]
FDR = 0.01

[1-classifier.copd192a]
FDR = 0.01

[1-classifier.copd193b]
FDR = 0.01

[1-classifier.ctrl160]
FDR = 0.01

[1-classifier.copd194]
FDR = 0.01

[1-classifier.copd237]
FDR = 0.01

[1-classifier.ctrl3]
FDR = 0.01

[1-classifier.ctrl439a]
FDR = 0.01

[1-classifier.ctrl439b]
FDR = 0.01

[1-classifier.ctrl483]
FDR = 0.01

[1-classifier.copd217]
FDR = 0.01

[1-classifier.ctrl137a]
FDR = 0.01

[1-classifier.ctrl22b]
FDR = 0.01

[1-classifier.ctrl219a]
FDR = 0.01

[1-classifier.copd235]
FDR = 0.01

[1-classifier.ctrl222]
FDR = 0.01

[1-classifier.copd207]
FDR = 0.01

[1-classifier.ctrl296]
FDR = 0.01

[1-classifier.ctrl226b]
FDR = 0.01

[1-classifier.copd193a]
FDR = 0.01

[1-classifier.copd178]
FDR = 0.01

[1-classifier.ctrl98a]
FDR = 0.01

[1-classifier.ctrl465]
FDR = 0.01

[1-classifier.copd152a]
FDR = 0.01

[1-classifier.ctrl133]
FDR = 0.01

[1-classifier.copd238]
FDR = 0.01

[1-classifier.ctrl192]
FDR = 0.01

[1-classifier.ctrl226a]
FDR = 0.01

[1-classifier.ctrl218a]
FDR = 0.01

[1-classifier.ctrl22a]
FDR = 0.01

[1-classifier.ctrl137b]
FDR = 0.01

[1-classifier.ctrl98b]
FDR = 0.01

[1-classifier.copd52]
FDR = 0.01

[2-cellSizeDistribution.copd152b]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd8]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd137]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd153b]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl1]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl84]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl92b]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl81]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl2]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl388]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl137]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl65]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl208]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl454]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl218b]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl244]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl484]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl34]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl92]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd23]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl253]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl219b]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl396]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd56]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd184a]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd186]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd153a]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd184b]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd192b]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd192]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd192a]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd193b]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl160]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd194]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd237]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl3]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl439a]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl439b]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl483]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd217]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl137a]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl22b]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl219a]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd235]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl222]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd207]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl296]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl226b]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd193a]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd178]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl98a]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl465]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd152a]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl133]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd238]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl192]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl226a]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl218a]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl22a]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl137b]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.ctrl98b]
binStep = 200
minCellSize = 100

[2-cellSizeDistribution.copd52]
binStep = 200
minCellSize = 100

[3-mitochondrialContent.copd152b]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd8]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd137]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd153b]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl1]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl84]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl92b]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl81]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl2]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl388]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl137]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl65]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl208]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl454]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl218b]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl244]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl484]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl34]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl92]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd23]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl253]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl219b]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl396]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd56]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd184a]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd186]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd153a]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd184b]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd192b]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd192]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd192a]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd193b]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl160]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd194]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd237]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl3]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl439a]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl439b]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl483]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd217]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl137a]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl22b]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl219a]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd235]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl222]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd207]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl296]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl226b]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd193a]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd178]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl98a]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl465]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd152a]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl133]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd238]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl192]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl226a]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl218a]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl22a]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl137b]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.ctrl98b]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[3-mitochondrialContent.copd52]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0.4

[4-numGenesVsNumUmis.copd152b]
regressionType = linear
p.level = 0.001

[4-numGenesVsNumUmis.copd8]
regressionType = linear
p.level = 0.0003998401

[4-numGenesVsNumUmis.copd137]
regressionType = linear
p.level = 0.0004528986

[4-numGenesVsNumUmis.copd153b]
regressionType = linear
p.level = 0.0003888025

[4-numGenesVsNumUmis.ctrl1]
regressionType = linear
p.level = 0.0003427005

[4-numGenesVsNumUmis.ctrl84]
regressionType = linear
p.level = 0.001

[4-numGenesVsNumUmis.ctrl92b]
regressionType = linear
p.level = 0.0001824152

[4-numGenesVsNumUmis.ctrl81]
regressionType = linear
p.level = 0.0005476451

[4-numGenesVsNumUmis.ctrl2]
regressionType = linear
p.level = 0.0009182736

[4-numGenesVsNumUmis.ctrl388]
regressionType = linear
p.level = 0.0001924928

[4-numGenesVsNumUmis.ctrl137]
regressionType = linear
p.level = 0.0001601025

[4-numGenesVsNumUmis.ctrl65]
regressionType = linear
p.level = 0.0003888025

[4-numGenesVsNumUmis.ctrl208]
regressionType = linear
p.level = 0.000295858

[4-numGenesVsNumUmis.ctrl454]
regressionType = linear
p.level = 0.0004955401

[4-numGenesVsNumUmis.ctrl218b]
regressionType = linear
p.level = 0.0005773672

[4-numGenesVsNumUmis.ctrl244]
regressionType = linear
p.level = 0.001

[4-numGenesVsNumUmis.ctrl484]
regressionType = linear
p.level = 0.0003775009

[4-numGenesVsNumUmis.ctrl34]
regressionType = linear
p.level = 0.0001352631

[4-numGenesVsNumUmis.ctrl92]
regressionType = linear
p.level = 0.0001649077

[4-numGenesVsNumUmis.copd23]
regressionType = linear
p.level = 0.0001779676

[4-numGenesVsNumUmis.ctrl253]
regressionType = linear
p.level = 0.0004242681

[4-numGenesVsNumUmis.ctrl219b]
regressionType = linear
p.level = 0.0004705882

[4-numGenesVsNumUmis.ctrl396]
regressionType = linear
p.level = 0.0001670007

[4-numGenesVsNumUmis.copd56]
regressionType = linear
p.level = 0.0001762115

[4-numGenesVsNumUmis.copd184a]
regressionType = linear
p.level = 0.0002654632

[4-numGenesVsNumUmis.copd186]
regressionType = linear
p.level = 0.0001977457

[4-numGenesVsNumUmis.copd153a]
regressionType = linear
p.level = 0.0003957262

[4-numGenesVsNumUmis.copd184b]
regressionType = linear
p.level = 0.0002335903

[4-numGenesVsNumUmis.copd192b]
regressionType = linear
p.level = 0.0002585315

[4-numGenesVsNumUmis.copd192]
regressionType = linear
p.level = 0.0003118179

[4-numGenesVsNumUmis.copd192a]
regressionType = linear
p.level = 0.0002950723

[4-numGenesVsNumUmis.copd193b]
regressionType = linear
p.level = 0.0002167317

[4-numGenesVsNumUmis.ctrl160]
regressionType = linear
p.level = 0.0001831502

[4-numGenesVsNumUmis.copd194]
regressionType = linear
p.level = 0.0002721088

[4-numGenesVsNumUmis.copd237]
regressionType = linear
p.level = 0.0002070393

[4-numGenesVsNumUmis.ctrl3]
regressionType = linear
p.level = 0.0001799208

[4-numGenesVsNumUmis.ctrl439a]
regressionType = linear
p.level = 0.0001477541

[4-numGenesVsNumUmis.ctrl439b]
regressionType = linear
p.level = 0.0001490313

[4-numGenesVsNumUmis.ctrl483]
regressionType = linear
p.level = 0.0003429355

[4-numGenesVsNumUmis.copd217]
regressionType = linear
p.level = 0.000228467

[4-numGenesVsNumUmis.ctrl137a]
regressionType = linear
p.level = 0.0001717623

[4-numGenesVsNumUmis.ctrl22b]
regressionType = linear
p.level = 0.0001813565

[4-numGenesVsNumUmis.ctrl219a]
regressionType = linear
p.level = 0.000536193

[4-numGenesVsNumUmis.copd235]
regressionType = linear
p.level = 0.000182083

[4-numGenesVsNumUmis.ctrl222]
regressionType = linear
p.level = 0.0003059976

[4-numGenesVsNumUmis.copd207]
regressionType = linear
p.level = 0.0002292526

[4-numGenesVsNumUmis.ctrl296]
regressionType = linear
p.level = 0.000195122

[4-numGenesVsNumUmis.ctrl226b]
regressionType = linear
p.level = 0.0001315963

[4-numGenesVsNumUmis.copd193a]
regressionType = linear
p.level = 0.0002349624

[4-numGenesVsNumUmis.copd178]
regressionType = linear
p.level = 0.0001016157

[4-numGenesVsNumUmis.ctrl98a]
regressionType = linear
p.level = 0.0001454122

[4-numGenesVsNumUmis.ctrl465]
regressionType = linear
p.level = 0.0002201673

[4-numGenesVsNumUmis.copd152a]
regressionType = linear
p.level = 0.0001600512

[4-numGenesVsNumUmis.ctrl133]
regressionType = linear
p.level = 0.0001067236

[4-numGenesVsNumUmis.copd238]
regressionType = linear
p.level = 0.000296472

[4-numGenesVsNumUmis.ctrl192]
regressionType = linear
p.level = 0.0001654807

[4-numGenesVsNumUmis.ctrl226a]
regressionType = linear
p.level = 0.0001503533

[4-numGenesVsNumUmis.ctrl218a]
regressionType = linear
p.level = 0.0005810575

[4-numGenesVsNumUmis.ctrl22a]
regressionType = linear
p.level = 0.0001304972

[4-numGenesVsNumUmis.ctrl137b]
regressionType = linear
p.level = 0.0002944641

[4-numGenesVsNumUmis.ctrl98b]
regressionType = linear
p.level = 0.0001405086

[4-numGenesVsNumUmis.copd52]
regressionType = linear
p.level = 0.000222321

[5-doubletScores.copd152b]
binStep = 0.02
probabilityThreshold = 0.9437163

[5-doubletScores.copd8]
binStep = 0.02
probabilityThreshold = 0.9793362

[5-doubletScores.copd137]
binStep = 0.02
probabilityThreshold = 0.9319908

[5-doubletScores.copd153b]
binStep = 0.02
probabilityThreshold = 0.8280486

[5-doubletScores.ctrl1]
binStep = 0.02
probabilityThreshold = 0.7620693

[5-doubletScores.ctrl84]
binStep = 0.02
probabilityThreshold = 0.9773266

[5-doubletScores.ctrl92b]
binStep = 0.02
probabilityThreshold = 0.5007703

[5-doubletScores.ctrl81]
binStep = 0.02
probabilityThreshold = 0.7260983

[5-doubletScores.ctrl2]
binStep = 0.02
probabilityThreshold = 0.752387

[5-doubletScores.ctrl388]
binStep = 0.02
probabilityThreshold = 0.8113949

[5-doubletScores.ctrl137]
binStep = 0.02
probabilityThreshold = 0.8522731

[5-doubletScores.ctrl65]
binStep = 0.02
probabilityThreshold = 0.7746893

[5-doubletScores.ctrl208]
binStep = 0.02
probabilityThreshold = 0.7636167

[5-doubletScores.ctrl454]
binStep = 0.02
probabilityThreshold = 0.888818

[5-doubletScores.ctrl218b]
binStep = 0.02
probabilityThreshold = 0.8787954

[5-doubletScores.ctrl244]
binStep = 0.02
probabilityThreshold = 0.9408553

[5-doubletScores.ctrl484]
binStep = 0.02
probabilityThreshold = 0.6254817

[5-doubletScores.ctrl34]
binStep = 0.02
probabilityThreshold = 0.5645942

[5-doubletScores.ctrl92]
binStep = 0.02
probabilityThreshold = 0.4634013

[5-doubletScores.copd23]
binStep = 0.02
probabilityThreshold = 0.7145349

[5-doubletScores.ctrl253]
binStep = 0.02
probabilityThreshold = 0.8663648

[5-doubletScores.ctrl219b]
binStep = 0.02
probabilityThreshold = 0.852098

[5-doubletScores.ctrl396]
binStep = 0.02
probabilityThreshold = 0.6161397

[5-doubletScores.copd56]
binStep = 0.02
probabilityThreshold = 0.7079945

[5-doubletScores.copd184a]
binStep = 0.02
probabilityThreshold = 0.613679

[5-doubletScores.copd186]
binStep = 0.02
probabilityThreshold = 0.5620615

[5-doubletScores.copd153a]
binStep = 0.02
probabilityThreshold = 0.8657725

[5-doubletScores.copd184b]
binStep = 0.02
probabilityThreshold = 0.6871076

[5-doubletScores.copd192b]
binStep = 0.02
probabilityThreshold = 0.6941504

[5-doubletScores.copd192]
binStep = 0.02
probabilityThreshold = 0.7922575

[5-doubletScores.copd192a]
binStep = 0.02
probabilityThreshold = 0.6408296

[5-doubletScores.copd193b]
binStep = 0.02
probabilityThreshold = 0.6090826

[5-doubletScores.ctrl160]
binStep = 0.02
probabilityThreshold = 0.4356238

[5-doubletScores.copd194]
binStep = 0.02
probabilityThreshold = 0.7390267

[5-doubletScores.copd237]
binStep = 0.02
probabilityThreshold = 0.6893234

[5-doubletScores.ctrl3]
binStep = 0.02
probabilityThreshold = 0.6647377

[5-doubletScores.ctrl439a]
binStep = 0.02
probabilityThreshold = 0.7639157

[5-doubletScores.ctrl439b]
binStep = 0.02
probabilityThreshold = 0.5124775

[5-doubletScores.ctrl483]
binStep = 0.02
probabilityThreshold = 0.7987304

[5-doubletScores.copd217]
binStep = 0.02
probabilityThreshold = 0.683211

[5-doubletScores.ctrl137a]
binStep = 0.02
probabilityThreshold = 0.808622

[5-doubletScores.ctrl22b]
binStep = 0.02
probabilityThreshold = 0.7239491

[5-doubletScores.ctrl219a]
binStep = 0.02
probabilityThreshold = 0.8756719

[5-doubletScores.copd235]
binStep = 0.02
probabilityThreshold = 0.5575005

[5-doubletScores.ctrl222]
binStep = 0.02
probabilityThreshold = 0.7402604

[5-doubletScores.copd207]
binStep = 0.02
probabilityThreshold = 0.6985903

[5-doubletScores.ctrl296]
binStep = 0.02
probabilityThreshold = 0.7709072

[5-doubletScores.ctrl226b]
binStep = 0.02
probabilityThreshold = 0.5755085

[5-doubletScores.copd193a]
binStep = 0.02
probabilityThreshold = 0.5701009

[5-doubletScores.copd178]
binStep = 0.02
probabilityThreshold = 0.5124815

[5-doubletScores.ctrl98a]
binStep = 0.02
probabilityThreshold = 0.5036845

[5-doubletScores.ctrl465]
binStep = 0.02
probabilityThreshold = 0.7061974

[5-doubletScores.copd152a]
binStep = 0.02
probabilityThreshold = 0.5023012

[5-doubletScores.ctrl133]
binStep = 0.02
probabilityThreshold = 0.4636738

[5-doubletScores.copd238]
binStep = 0.02
probabilityThreshold = 0.8045704

[5-doubletScores.ctrl192]
binStep = 0.02
probabilityThreshold = 0.663654

[5-doubletScores.ctrl226a]
binStep = 0.02
probabilityThreshold = 0.4634903

[5-doubletScores.ctrl218a]
binStep = 0.02
probabilityThreshold = 0.867962

[5-doubletScores.ctrl22a]
binStep = 0.02
probabilityThreshold = 0.4991584

[5-doubletScores.ctrl137b]
binStep = 0.02
probabilityThreshold = 0.7630812

[5-doubletScores.ctrl98b]
binStep = 0.02
probabilityThreshold = 0.5183172

[5-doubletScores.copd52]
binStep = 0.02
probabilityThreshold = 0.6751922

[6-dataIntegration.dataIntegration]
method = harmony
numGenes = 2000
normalisation = logNormalize

[6-dataIntegration.dimensionalityReduction]
method = rpca
numPCs = null

[7-configureEmbedding.embeddingSettings]
method = umap
distanceMetric = cosine
minimumDistance = 0.3

[7-configureEmbedding.clusteringSettings]
method = louvain
resolution = 0.8

3

Hello Arnaud, a timeout during data integration is frequently caused by running out of memory for big datasets. How big is your analysis ? If that is the case, we are currently beta testing a new infrastructure to add more memory. If you share your analysis ID I can check it out.

4

Hello,
Thank you very much for your answer.
Indeed the analysis has 62 samples so that’s quite big.
The project ID is: Project ID: 7127520a-7b22-4e4d-af6a-3d5c95ebd992.

5

I’ve checked the analysis and it did run out of memory. We are currently testing a new infrastructure with more memory to allow users to run bigger experiments. I will move your analysis to the new infrastructure and test it o ut. I will let you know when it’s done. You will notice no changes on your side. Be advised that the feature is still in beta testing so you might experience issues as we continue to improve it. Any feedback is greatly appreciated.

6

I’ve moved your experiment to the new infrastructure where it runs successfully. I’ve sent you an email too. Let us know if you have any more issues. We are still improving the performance for big datasets so some sections like “Configure Embedding” might still be slow.

7

I have the same problem (never used this system before) with processing step5/7. My data is not so big but it has twice stopped working at this step. I have 12 samples amounting to ~2gigs of data (mainly in the matrix files)
thanks
Robby