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annotate test-data/TOPP.log @ 7:0f60da9c484a draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
author galaxyp
date Sun, 13 Dec 2020 17:20:04 +0000
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7
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
1 2020-12-13 17:20:12 RTModel:1:: Warning: Using OLIGO kernel but out_oligo_params was not specified. Trying to write to: RTModel_2_output.tmp_additional_parameters
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
2 2020-12-13 17:20:12 RTModel:1:: Warning: Using OLIGO kernel but out_oligo_trainset was not specified. Trying to write to: RTModel_2_output.tmp_samples
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
3 2020-12-13 17:20:13 RTModel:1:: Writing to 'TOPP.log'
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
4 2020-12-13 17:20:13 RTModel:1:: Debug level (after ini file): 1
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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5 2020-12-13 17:20:13 RTModel:1:: Value of string option 'no_progress': 0
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
6 2020-12-13 17:20:13 RTModel:1:: Value of string option 'in_positive':
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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7 2020-12-13 17:20:13 RTModel:1:: Value of string option 'in': RTModel_4_input.txt
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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8 2020-12-13 17:20:13 RTModel:1:: Value of string option 'out': RTModel_4_output.tmp
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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9 2020-12-13 17:20:13 RTModel:1:: Value of string option 'additive_cv': 0
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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10 2020-12-13 17:20:13 RTModel:1:: Value of string option 'cv:skip_cv': 0
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
11 2020-12-13 17:20:13 RTModel:1:: Value of double option 'total_gradient_time': 1.0
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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12 2020-12-13 17:20:13 RTModel:1:: Value of double option 'max_std': 10.0
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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13 2020-12-13 17:20:13 RTModel:1:: Value of string option 'svm_type': NU_SVR
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
14 2020-12-13 17:20:13 RTModel:1:: Value of string option 'kernel_type': OLIGO
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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15 2020-12-13 17:20:13 RTModel:1:: Value of double option 'c': 1.953125e-03
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
16 2020-12-13 17:20:13 RTModel:1:: Value of double option 'nu': 0.5
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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17 2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:c_start': 1.953125e-03
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
18 2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:c_step_size': 2.0
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
19 2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:c_stop': 1.953125e-03
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
20 2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:nu_start': 0.4
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
21 2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:nu_step_size': 1.2
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
22 2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:nu_stop': 0.4
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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23 2020-12-13 17:20:13 RTModel:1:: Value of int option 'border_length': 22
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
24 2020-12-13 17:20:13 RTModel:1:: Value of double option 'sigma': 1.0
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
25 2020-12-13 17:20:13 RTModel:1:: Value of int option 'k_mer_length': 1
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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26 2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:sigma_start': 5.0
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
27 2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:sigma_step_size': 1.221055
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
28 2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:sigma_stop': 5.0
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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29 2020-12-13 17:20:13 RTModel:1:: CV from sigma = 5.0 to sigma = 5.0 with step size 1.221055
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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30 2020-12-13 17:20:13 RTModel:1:: Value of int option 'cv:number_of_runs': 1
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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31 2020-12-13 17:20:13 RTModel:1:: Number of CV runs: 1
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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32 2020-12-13 17:20:13 RTModel:1:: Value of int option 'cv:number_of_partitions': 5
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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33 2020-12-13 17:20:13 RTModel:1:: Number of CV partitions: 5
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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34 2020-12-13 17:20:13 RTModel:1:: Value of string option 'first_dim_rt': 0
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
35 2020-12-13 17:20:13 RTModel:1:: Value of int option 'debug': 1
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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36 2020-12-13 17:20:13 RTModel:1:: 26 sequences for training, 26 labels for training
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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37 2020-12-13 17:20:13 RTModel:1:: Best parameters found in cross validation: C: 1.953125e-03 nu: 0.4 sigma: 5.0 with performance 0.63203189556678
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
38 2020-12-13 17:20:13 RTModel:1:: Value of string option 'out': RTModel_4_output.tmp
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
39 2020-12-13 17:20:13 RTModel:1:: Value of string option 'out_oligo_params':
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
40 2020-12-13 17:20:13 RTModel:1:: Value of string option 'out_oligo_trainset':
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
parents:
diff changeset
41 2020-12-13 17:20:13 RTModel:1:: Warning: Using OLIGO kernel but out_oligo_params was not specified. Trying to write to: RTModel_4_output.tmp_additional_parameters
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
parents:
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42 2020-12-13 17:20:13 RTModel:1:: Warning: Using OLIGO kernel but out_oligo_trainset was not specified. Trying to write to: RTModel_4_output.tmp_samples
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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43 2020-12-13 17:20:23 PrecursorMassCorrector:1:: Did not find a MS1 scan to the MS/MS scan at RT=632.697998046875
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
44 2020-12-13 17:20:23 PrecursorMassCorrector:1:: Did not find a MS1 scan to the MS/MS scan at RT=632.697998046875
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
45 2020-12-13 17:20:23 PrecursorMassCorrector:1:: Did not find a MS1 scan to the MS/MS scan at RT=632.697998046875
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
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diff changeset
46 2020-12-13 17:20:23 PrecursorMassCorrector:1:: Did not find a MS1 scan to the MS/MS scan at RT=638.775024414062045
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
parents:
diff changeset
47 2020-12-13 17:20:23 PrecursorMassCorrector:1:: Did not find a MS1 scan to the MS/MS scan at RT=638.775024414062045
0f60da9c484a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
galaxyp
parents:
diff changeset
48 2020-12-13 17:20:23 PrecursorMassCorrector:1:: Did not find a MS1 scan to the MS/MS scan at RT=638.775024414062045