How can I properly decode error when using ASICS?
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nep63 • 0
@5d1473fa
Last seen 5 months ago
United States

Below is my output file for a pbs job script I wrote. Everything was able to run fine except for when I try to quantify the metabolites with the given error. I am not sure how to parse this error and was wondering if anyone has any suggestions. Thanks!

Activating environment...
Setting working directory
Running R Script...
Import spectra from fid files...
Begin PreprocessingChain
Begin ReadFids
dim Fid_data:  246 32768
IDs:  1_1 10_1 100_1 101_1 102_1 103_1 104_1 105_1 106_1 107_1 108_1 109_1 11_1 110_1 111_1 112_1 113_1 114_1 115_1 116_1 117_1 118_1 12_1 120_1 121_1 122_1 123_1 124_1 125_1 126_1 127_1 128_1 129_1 13_1 130_1 131_1 132_1 133_1 134_1 137_1 138_1 139_1 14_1 140_1 141_1 142_1 143_1 144_1 145_1 146_1 147_1 148_1 149_1 15_1 150_1 151_1 152_1 153_1 154_1 155_1 156_1 157_1 158_1 159_1 16_1 160_1 161_1 162_1 163_1 164_1 165_1 166_1 167_1 168_1 169_1 17_1 170_1 171_1 172_1 173_1 174_1 175_1 176_1 177_1 178_1 179_1 18_1 180_1 181_1 182_1 183_1 184_1 185_1 186_1 187_1 188_1 189_1 19_1 190_1 191_1 192_1 193_1 194_1 195_1 196_1 197_1 198_1 199_1 2_1 20_1 200_1 201_1 202_1 203_1 204_1 205_1 207_1 208_1 209_1 21_1 210_1 211_1 212_1 213_1 214_1 215_1 216_1 217_1 218_1 219_1 22_1 220_1 221_1 222_1 223_1 224_1 225_1 226_1 227_1 228_1 229_1 23_1 230_1 231_1 232_1 233_1 234_1 235_1 236_1 237_1 238_1 239_1 24_1 240_1 241_1 242_1 243_1 244_1 245_1 246_1 247_1 248_1 249_1 25_1 250_1 251_1 26_1 27_1 28_1 29_1 3_1 30_1 31_1 32_1 33_1 34_1 35_1 36_1 38_1 39_1 4_1 40_1 41_1 42_1 43_1 44_1 45_1 46_1 47_1 48_1 49_1 5_1 50_1 51_1 52_1 53_1 54_1 55_1 56_1 57_1 58_1 59_1 6_1 60_1 61_1 62_1 63_1 64_1 65_1 66_1 67_1 68_1 69_1 7_1 70_1 71_1 72_1 73_1 74_1 75_1 76_1 77_1 78_1 79_1 8_1 80_1 81_1 82_1 83_1 84_1 85_1 86_1 87_1 88_1 89_1 9_1 90_1 91_1 92_1 93_1 94_1 95_1 96_1 97_1 98_1 99_1
non-unique IDs? 0
End ReadFids
It lasted 2.81 s user time, 0.363 s system time and 21.819 s elapsed time.
Begin GroupDelayCorrection
End GroupDelayCorrection
It lasted 4.06 s user time, 0.314 s system time and 4.375 s elapsed time.
Begin SolventSuppression
End SolventSuppression
It lasted 2.226 s user time, 0.171 s system time and 2.426 s elapsed time.
Begin Apodization
End Apodization
It lasted 0.176 s user time, 0 s system time and 0.176 s elapsed time.
Begin ZeroFilling
End ZeroFilling
It lasted 0.111 s user time, 0.058 s system time and 0.171 s elapsed time.
Begin FourierTransform
End FourierTransform
t lasted 2.832 s user time, 0.413 s system time and 3.244 s elapsed time.
Begin ZeroOrderPhaseCorrection
End ZeroOrderPhaseCorrection
It lasted 11.188 s user time, 0.446 s system time and 11.635 s elapsed time.
Begin InternalReferencing
End InternalReferencing
It lasted 2.303 s user time, 0.349 s system time and 2.653 s elapsed time.
Begin WindowSelection
End WindowSelection
It lasted 0.201 s user time, 0.023 s system time and 0.224 s elapsed time.
End PreprocessingChain
It lasted 25.943 s user time, 2.137 s system time and 46.756 s elapsed time.
Begin BaselineCorrection
End BaselineCorrection
It lasted 15.695 s user time, 0.314 s system time and 16.01 s elapsed time.
Begin NegativeValuesZeroing
End NegativeValuesZeroing
It lasted 0.108 s user time, 0.022 s system time and 0.13 s elapsed time.
Alignment...

Peak detection
100%

Finding reference spectrum
Compute FFT correlations
100%

The reference spectrum is the number 191 : 49_1
Align spectra
100%

Binning
100%
Normalisation method : pqn

to_exclude= matrix(c(4.24, 6.0), ncol = 2)
resASICS <- ASICS(bin_data, exclusion.areas = to_exclude, joint.align = TRUE,  quantif.method = "both", verbose = TRUE, ncores=4)
Remove areas from spectrum and library
 0%

Error: BiocParallel errors
  4 remote errors, element index: 1, 2, 3, 4
  0 unevaluated and other errors
  first remote error: error in evaluating the argument 'i' in selecting a method for function '[': trying to get slot "ppm.grid" from an object (class "data.frame") that is not an S4 object
Execution halted
ASICSdata ASICS • 127 views
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