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test pipeline input
Toby Dylan Hocking edited this page Nov 15, 2018
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3 revisions
When running
R -e 'source("https://raw.githubusercontent.com/tdhock/PeakSegPipeline/master/tests/testthat/test-pipeline-input.R")'I got the following terminal output on my laptop: (last updated 15 Nov 2018)
tdhock@recycled:~$ R -e 'source("https://raw.githubusercontent.com/tdhock/PeakSegPipeline/master/tests/testthat/test-pipeline-input.R")'
R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i686-pc-linux-gnu (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> source("https://raw.githubusercontent.com/tdhock/PeakSegPipeline/master/tests/testthat/test-pipeline-input.R")
Loading required package: httr
Reading /home/tdhock/PeakSegPipeline-test/non-integer/labels/some_labels.txt
5 chunks, 19 label lines
labeled sample groups: kidney, Input
Wrote 19 labels to /home/tdhock/PeakSegPipeline-test/non-integer/samples/Input/MS010302/labels.bed
Wrote 19 labels to /home/tdhock/PeakSegPipeline-test/non-integer/samples/kidney/MS002201/labels.bed
Read 1 problems from /home/tdhock/PeakSegPipeline-test/non-integer/problems.bed
Writing 1 / 2 samples 19 labels 1 labeled problems /home/tdhock/PeakSegPipeline-test/non-integer/samples/Input/MS010302/problems
Writing 2 / 2 samples 19 labels 1 labeled problems /home/tdhock/PeakSegPipeline-test/non-integer/samples/kidney/MS002201/problems
Writing 1 jointProblems.bed.sh scripts.
Writing 5 chunks in /home/tdhock/PeakSegPipeline-test/non-integer/problems/chr10:18024675-38818835
chrom chromStart chromEnd coverage count.num.str count.int
1: chr10 33061063 33061100 0.1242 0.1242 0
2: chr10 33061100 33061116 0.2484 0.2484 0
3: chr10 33061116 33061144 0.3726 0.3726 0
4: chr10 33061144 33061163 0.4968 0.4968 0
5: chr10 33061163 33061200 0.3726 0.3726 0
---
277372: chr10 38818823 38818826 1.2420 1.242 1
277373: chr10 38818826 38818830 0.9936 0.9936 1
277374: chr10 38818830 38818833 0.8694 0.8694 1
277375: chr10 38818833 38818834 0.6210 0.621 1
277376: chr10 38818834 38818835 0.3726 0.3726 0
count.int.str
1: 0
2: 0
3: 0
4: 0
5: 0
---
277372: 1
277373: 1
277374: 1
277375: 1
277376: 0
Reading /home/tdhock/PeakSegPipeline-test/input/labels/some_labels.txt
5 chunks, 19 label lines
labeled sample groups: kidney, Input
Wrote 19 labels to /home/tdhock/PeakSegPipeline-test/input/samples/Input/MS010302/labels.bed
Wrote 19 labels to /home/tdhock/PeakSegPipeline-test/input/samples/kidney/MS002201/labels.bed
Read 1 problems from /home/tdhock/PeakSegPipeline-test/input/problems.bed
Writing 1 / 2 samples 19 labels 1 labeled problems /home/tdhock/PeakSegPipeline-test/input/samples/Input/MS010302/problems
Writing 2 / 2 samples 19 labels 1 labeled problems /home/tdhock/PeakSegPipeline-test/input/samples/kidney/MS002201/problems
Writing 1 jointProblems.bed.sh scripts.
Writing 5 chunks in /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835
bigWigToBedGraph -chrom=chr10 -start=18024675 -end=38818835 /home/tdhock/PeakSegPipeline-test/input/samples/Input/MS010302/coverage.bigWig /home/tdhock/PeakSegPipeline-test/input/samples/Input/MS010302/problems/chr10:18024675-38818835/coverage.bedGraph
19 labels in chr10:18024675-38818835
Next = 0, Inf mc.cores= 2
penalty peaks fp fn errors
1: 0 89411 19 0 19
2: Inf 0 0 2 2
0.476501 minutes elapsed / 5.000000 limit
Target interval: 5.531713 Inf change: Inf NaN
Next = 252.576236683382 mc.cores= 2
penalty peaks fp fn errors
1: 0.0000 89411 19 0 19
2: 252.5762 4938 18 0 18
3: Inf 0 0 2 2
1.008586 minutes elapsed / 5.000000 limit
Target interval: 8.337237 Inf change: 2.805524 NaN
Next = 4176.53405795013 mc.cores= 2
penalty peaks fp fn errors
1: 0.0000 89411 19 0 19
2: 252.5762 4938 18 0 18
3: 4176.5341 10 12 0 12
4: Inf 0 0 2 2
1.732639 minutes elapsed / 5.000000 limit
Target interval: 14.396637 Inf change: 6.059400 NaN
Next = 1788050.95083481 mc.cores= 2
penalty peaks fp fn errors
1: 0.0000 89411 19 0 19
2: 252.5762 4938 18 0 18
3: 4176.5341 10 12 0 12
4: 1788050.9508 1 1 2 3
5: Inf 0 0 2 2
2.324000 minutes elapsed / 5.000000 limit
Target interval: 16.685831 Inf change: 2.289194 NaN
Next = 26426.9587447508 mc.cores= 2
penalty peaks fp fn errors
1: 0.0000 89411 19 0 19
2: 252.5762 4938 18 0 18
3: 4176.5341 10 12 0 12
4: 26426.9587 3 2 0 2
5: 1788050.9508 1 1 2 3
6: Inf 0 0 2 2
3.090248 minutes elapsed / 5.000000 limit
Target interval: 16.685831 Inf change: 0.000000 NaN
Next = 91583.9843795932, 7810.66570622437 mc.cores= 2
penalty peaks fp fn errors
1: 0.0000 89411 19 0 19
2: 252.5762 4938 18 0 18
3: 4176.5341 10 12 0 12
4: 7810.6657 5 3 0 3
5: 26426.9587 3 2 0 2
6: 91583.9844 2 1 0 1
7: 1788050.9508 1 1 2 3
8: Inf 0 0 2 2
3.900735 minutes elapsed / 5.000000 limit
Target interval: 10.324785 11.936160 change: -6.361046 -Inf
19 labels in chr10:18024675-38818835
Next = 0, Inf mc.cores= 2
penalty peaks fp fn errors
1: 0 188109 19 0 19
2: Inf 0 0 11 11
0.864045 minutes elapsed / 5.000000 limit
Target interval: 5.547819 Inf change: Inf NaN
Next = 256.677224108443 mc.cores= 2
penalty peaks fp fn errors
1: 0.0000 188109 19 0 19
2: 256.6772 5303 17 0 17
3: Inf 0 0 11 11
2.118791 minutes elapsed / 5.000000 limit
Target interval: 9.079821 Inf change: 3.532002 NaN
Next = 8776.39558337603 mc.cores= 2
penalty peaks fp fn errors
1: 0.0000 188109 19 0 19
2: 256.6772 5303 17 0 17
3: 8776.3956 45 8 2 10
4: Inf 0 0 11 11
3.760995 minutes elapsed / 5.000000 limit
Target interval: 6.548532 13.767020 change: -2.531289 -Inf
Next = 698.218644190145, 952666.492166474 mc.cores= 2
penalty peaks fp fn errors
1: 0.0000 188109 19 0 19
2: 256.6772 5303 17 0 17
3: 698.2186 1611 17 0 17
4: 8776.3956 45 8 2 10
5: 952666.4922 2 4 10 14
6: Inf 0 0 11 11
6.590804 minutes elapsed / 5.000000 limit
Target interval: 7.210717 11.890233 change: 0.662185 -1.876787
Searching for /home/tdhock/PeakSegPipeline-test/input/samples/*/*/problems/*/target.tsv files for training.
Found 2 target.tsv files for training.
Feature matrix:
log.quartile.100% log.data
[1,] 4.110874 12.21546
[2,] 4.189655 12.95923
Target matrix:
[,1] [,2]
[1,] 10.324790 11.93616
[2,] 7.210717 11.89023
Learned regularization parameter and weights:
0
(Intercept) 111.268536
log.quartile.100% -18.527835
log.data -1.962508
Train errors:
status targets
1: correct 2
Writing model to /home/tdhock/PeakSegPipeline-test/input/model.RData
Predicting penalty=68186.0467365162 log(penalty)=11.1299952295933 based on 2 features.
Predicting penalty=3680.1802097383 log(penalty)=8.21071700000157 based on 2 features.
Writing /home/tdhock/PeakSegPipeline-test/input/samples/Input/MS010302/problems/chr10:18024675-38818835/peaks.bed with 0 peaks.
Writing /home/tdhock/PeakSegPipeline-test/input/samples/kidney/MS002201/problems/chr10:18024675-38818835/peaks.bed with 65 peaks.
65 total peaks form 65 overlapping peak clusters.
Found 5 labeled regions with no peaks out of 19 total.
Creating 70 joint segmentation problems for chr10:18024675-38818835
1 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:32990873-33132211
2 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33132211-33156144
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33132211-33156144/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:32990873-33132211/segmentations.RData
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 5.498605 2 2
2: 5.498605 7.785429 1 1
3: 7.785429 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 5.498605 2 2
2: 5.498605 7.785429 1 1
3: 7.785429 Inf 0 0
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 4.663355 2 2
2: 4.663355 9.053152 1 1
3: 9.053152 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 4.663355 2 2
2: 4.663355 9.053152 1 1
3: 9.053152 Inf 0 0
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 7.785429 Inf 0
2: group 7.785429 Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:32990873-33132211/target.tsv
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 9.053152 Inf 0
2: group 9.053152 Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33132211-33156144/target.tsv
3 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33156144-33180464
4 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33457972-33485987
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33457972-33485987/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33156144-33180464/segmentations.RData
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 11.03558 1 0
2: 11.03558 Inf 0 1
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 11.03558 1 0
2: 11.03558 Inf 0 1
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample -Inf 11.03558 0
2: group -Inf 11.03558 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33457972-33485987/target.tsv
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.086863 1 0
2: 8.086863 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.086863 1 0
2: 8.086863 Inf 0 0
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample -Inf Inf 0
2: group -Inf Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33156144-33180464/target.tsv
5 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33618486-33642930
6 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33700559-33974944
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33618486-33642930/segmentations.RData
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.297587 1 1
2: 8.297587 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.297587 1 1
2: 8.297587 Inf 0 0
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 8.297587 Inf 0
2: group 8.297587 Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33618486-33642930/target.tsv
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33700559-33974944/segmentations.RData
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.372853 1 1
2: 8.372853 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.372853 1 1
2: 8.372853 Inf 0 0
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 8.372853 Inf 0
2: group 8.372853 Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33700559-33974944/target.tsv
7 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35182819-35261002
8 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35287904-35303135
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35287904-35303135/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35182819-35261002/segmentations.RData
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 6.281107 2 2
2: 6.281107 9.997147 1 1
3: 9.997147 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 6.281107 2 2
2: 6.281107 9.997147 1 1
3: 9.997147 Inf 0 0
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 9.997147 Inf 0
2: group 9.997147 Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35287904-35303135/target.tsv
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 4.783627 2 2
2: 4.783627 7.730658 1 1
3: 7.730658 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 4.783627 2 2
2: 4.783627 7.730658 1 1
3: 7.730658 Inf 0 0
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 7.730658 Inf 0
2: group 7.730658 Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35182819-35261002/target.tsv
9 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35307474-35336704
10 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35337315-35362580
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35337315-35362580/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35307474-35336704/segmentations.RData
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.899412 1 0
2: 8.899412 Inf 0 1
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.899412 1 0
2: 8.899412 Inf 0 1
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample -Inf 8.899412 0
2: group -Inf 8.899412 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35337315-35362580/target.tsv
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 5.491373 2 1
2: 5.491373 8.739038 1 0
3: 8.739038 Inf 0 1
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 5.491373 2 1
2: 5.491373 8.739038 1 0
3: 8.739038 Inf 0 1
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 5.491373 8.739038 0
2: group 5.491373 8.739038 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35307474-35336704/target.tsv
11 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35362580-35391718
12 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38022122-38042838
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38022122-38042838/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35362580-35391718/segmentations.RData
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 7.305245 2 0
2: 7.305245 8.390575 1 0
3: 8.390575 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 7.305245 2 0
2: 7.305245 8.390575 1 0
3: 8.390575 Inf 0 0
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample -Inf Inf 0
2: group -Inf Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38022122-38042838/target.tsv
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 6.167176 2 2
2: 6.167176 10.772417 1 1
3: 10.772417 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 6.167176 2 2
2: 6.167176 10.772417 1 1
3: 10.772417 Inf 0 0
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 10.77242 Inf 0
2: group 10.77242 Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35362580-35391718/target.tsv
13 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38042838-38076430
14 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38081566-38099938
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38081566-38099938/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38042838-38076430/segmentations.RData
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.963439 1 1
2: 8.963439 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.963439 1 1
2: 8.963439 Inf 0 0
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 8.963439 Inf 0
2: group 8.963439 Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38081566-38099938/target.tsv
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 7.91953 1 1
2: 7.91953 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 7.91953 1 1
2: 7.91953 Inf 0 0
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 7.91953 Inf 0
2: group 7.91953 Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38042838-38076430/target.tsv
15 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38274983-38328082
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38274983-38328082/segmentations.RData
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 12.36149 1 0
2: 12.36149 Inf 0 1
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 12.36149 1 0
2: 12.36149 Inf 0 1
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample -Inf 12.36149 0
2: group -Inf 12.36149 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38274983-38328082/target.tsv
16 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38363334-38383454
17 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38383454-38395652
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38383454-38395652/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38363334-38383454/segmentations.RData
Train error for samples:
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 6.994525 2 1
2: 6.994525 9.211314 1 0
3: 9.211314 Inf 0 1
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.428366 1 1
2: 8.428366 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 6.994525 2 1
2: 6.994525 9.211314 1 0
3: 9.211314 Inf 0 1
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.428366 1 1
2: 8.428366 Inf 0 0
Target intervals of minimum error penalty values:
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 8.428366 Inf 0
2: group 8.428366 Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38363334-38383454/target.tsv
model min.log.lambda max.log.lambda errors
1: sample 6.994525 9.211314 0
2: group 6.994525 9.211314 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38383454-38395652/target.tsv
18 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38396093-38413226
19 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38414575-38442230
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38414575-38442230/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38396093-38413226/segmentations.RData
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 5.602844 2 2
2: 5.602844 9.440477 1 1
3: 9.440477 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 5.602844 2 2
2: 5.602844 9.440477 1 1
3: 9.440477 Inf 0 0
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 9.440477 Inf 0
2: group 9.440477 Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38414575-38442230/target.tsv
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 10.70833 1 0
2: 10.70833 Inf 0 1
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 10.70833 1 0
2: 10.70833 Inf 0 1
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample -Inf 10.70833 0
2: group -Inf 10.70833 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38396093-38413226/target.tsv
20 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38442230-38507228
21 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38625872-38645638
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38625872-38645638/segmentations.RDataWriting segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38442230-38507228/segmentations.RData
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 6.984532 2 0
2: 6.984532 8.730049 1 0
3: 8.730049 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 6.984532 2 0
2: 6.984532 8.730049 1 0
3: 8.730049 Inf 0 0
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.616618 1 2
2: 8.616618 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.616618 1 2
2: 8.616618 Inf 0 0
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample -Inf Inf 0
2: group -Inf Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38442230-38507228/target.tsv
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 8.616618 Inf 0
2: group 8.616618 Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38625872-38645638/target.tsv
22 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38645638-38651882
23 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38722920-38740678
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38645638-38651882/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38722920-38740678/segmentations.RData
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 9.189528 1 0
2: 9.189528 Inf 0 1
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 9.189528 1 0
2: 9.189528 Inf 0 1
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample -Inf 9.189528 0
2: group -Inf 9.189528 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38645638-38651882/target.tsv
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 7.844070 2 1
2: 7.844070 9.501095 1 0
3: 9.501095 Inf 0 1
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 7.844070 2 1
2: 7.844070 9.501095 1 0
3: 9.501095 Inf 0 1
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 7.84407 9.501095 0
2: group 7.84407 9.501095 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38722920-38740678/target.tsv
24 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38740678-38790607
25 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38807475-38814105
FoundFound 22 samples to jointly segment.
samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38807475-38814105/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38740678-38790607/segmentations.RData
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 6.220042 2 2
2: 6.220042 6.385140 1 1
3: 6.385140 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 6.220042 2 2
2: 6.220042 6.385140 1 1
3: 6.385140 Inf 0 0
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 6.38514 Inf 0
2: group 6.38514 Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38807475-38814105/target.tsv
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.196585 2 2
2: 8.196585 8.681261 1 1
3: 8.681261 Inf 0 0
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 8.196585 2 2
2: 8.196585 8.681261 1 1
3: 8.681261 Inf 0 0
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda errors
1: sample 8.681261 Inf 0
2: group 8.681261 Inf 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38740678-38790607/target.tsv
26 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38815199-38816357
27 / 27 labeled joint problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38818375-38818835
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38815199-38816357/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38818375-38818835/segmentations.RData
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 6.454707 2 0
2: 6.454707 7.583618 1 1
3: 7.583618 Inf 0 2
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 6.454707 2 0
2: 6.454707 7.583618 1 1
3: 7.583618 Inf 0 2
Train error for samples:
min.log.lambda max.log.lambda complexity errors
1: -Inf 5.314800 2 0
2: 5.314800 6.157343 1 1
3: 6.157343 Inf 0 2
Train error for groups:
min.log.lambda max.log.lambda complexity errors
1: -Inf 5.314800 2 0
2: 5.314800 6.157343 1 1
3: 6.157343 Inf 0 2
Target intervals of minimum error penalty values:
Target intervals of minimum error penalty values:
model min.log.lambda max.log.lambda model errors
1: sample -Inf min.log.lambda 6.454707 0
2: group -Inf max.log.lambda 6.454707 0
errors
1: sample -Inf 5.3148Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38815199-38816357/target.tsv
0
2: group -Inf 5.3148 0
Writing target intervals to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38818375-38818835/target.tsv
$sample.target
[,1] [,2]
[1,] 7.785429 Inf
[2,] 9.053152 Inf
[3,] -Inf Inf
[4,] -Inf 11.035581
[5,] 8.297587 Inf
[6,] 8.372853 Inf
[7,] 7.730658 Inf
[8,] 9.997147 Inf
[9,] 5.491373 8.739038
[10,] -Inf 8.899412
[11,] 10.772417 Inf
[12,] -Inf Inf
[13,] 7.919530 Inf
[14,] 8.963439 Inf
[15,] -Inf 12.361491
[16,] 8.428366 Inf
[17,] 6.994525 9.211314
[18,] -Inf 10.708334
[19,] 9.440477 Inf
[20,] -Inf Inf
[21,] 8.616618 Inf
[22,] -Inf 9.189528
[23,] 7.844070 9.501095
[24,] 8.681261 Inf
[25,] 6.385140 Inf
[26,] -Inf 6.454707
[27,] -Inf 5.314800
$group.target
[,1] [,2]
[1,] 7.785429 Inf
[2,] 9.053152 Inf
[3,] -Inf Inf
[4,] -Inf 11.035581
[5,] 8.297587 Inf
[6,] 8.372853 Inf
[7,] 7.730658 Inf
[8,] 9.997147 Inf
[9,] 5.491373 8.739038
[10,] -Inf 8.899412
[11,] 10.772417 Inf
[12,] -Inf Inf
[13,] 7.919530 Inf
[14,] 8.963439 Inf
[15,] -Inf 12.361491
[16,] 8.428366 Inf
[17,] 6.994525 9.211314
[18,] -Inf 10.708334
[19,] 9.440477 Inf
[20,] -Inf Inf
[21,] 8.616618 Inf
[22,] -Inf 9.189528
[23,] 7.844070 9.501095
[24,] 8.681261 Inf
[25,] 6.385140 Inf
[26,] -Inf 6.454707
[27,] -Inf 5.314800
$features
quartile.0% quartile.25% quartile.50% quartile.75% quartile.100%
[1,] 0 3 6 10 39
[2,] 0 5 7 13 32
[3,] 0 3 6 11 31
[4,] 0 6 16 25 57
[5,] 0 2 5 10 50
[6,] 0 3 5 9 31
[7,] 0 1 3 5 24
[8,] 0 8 13 24 52
[9,] 1 15 20 28 57
[10,] 0 13 18 25 52
[11,] 0 3 7 15 39
[12,] 0 1 3 4 18
[13,] 0 2 5 9 28
[14,] 0 4 7 11 33
[15,] 0 3 10 24 82
[16,] 0 1 4 7 22
[17,] 0 11 17 24 53
[18,] 0 4 7 17 61
[19,] 0 2 4 8 29
[20,] 0 1 3 6 28
[21,] 0 1 3 7 29
[22,] 0 12 18 24 44
[23,] 0 7 13 18 46
[24,] 0 1 2 5 27
[25,] 0 2 2 5 16
[26,] 1 1 9 13 20
[27,] 1 12 16 24 32
mean sd mad bases sum loss.0peaks loss.1peak
[1,] 7.063038 5.119672 4.4478 142422 502966 -1.7996707 -1.83092240
[2,] 8.384490 5.623962 5.9304 47866 200666 -3.8791389 -4.23774800
[3,] 7.511965 5.020206 4.4478 48640 182691 -2.6312227 -2.80327005
[4,] 16.639229 11.637466 13.3434 56030 466148 -22.7638654 -24.95640793
[5,] 6.672230 7.283853 4.4478 48888 163096 -1.7196298 -1.88296688
[6,] 5.657583 4.304249 4.4478 548770 1552356 -0.3076492 -0.30764917
[7,] 3.830679 3.506995 2.9652 156366 299494 1.2593598 1.25935982
[8,] 15.921148 10.263988 8.8956 30462 242495 -19.7156100 -21.13625260
[9,] 21.471365 9.519627 10.3782 58460 627608 -31.6730548 -31.95067225
[10,] 19.362755 8.225931 7.4130 50530 489200 -26.8373353 -27.12907865
[11,] 8.904352 7.513552 7.4130 58276 259455 -4.8988602 -6.38660235
[12,] 3.107943 3.200762 2.9652 41318 64207 1.5171004 1.47012974
[13,] 5.901675 4.632154 4.4478 67002 197712 -0.4733933 -0.54052100
[14,] 8.073645 6.101952 4.4478 36744 148329 -3.4206894 -3.80214336
[15,] 14.276936 13.398569 11.8608 106198 758091 -15.7404069 -19.85550206
[16,] 4.608350 4.009066 2.9652 40240 92720 0.7482056 0.53847628
[17,] 18.211920 9.819705 8.8956 24396 222149 -26.6479755 -27.58559235
[18,] 10.964571 10.575633 7.4130 34266 187856 -7.2342454 -9.46668034
[19,] 5.446791 4.712834 4.4478 55310 150631 -0.1152239 -0.53320254
[20,] 3.884781 3.631771 2.9652 129996 252503 1.2131319 1.10964088
[21,] 4.478094 4.093936 2.9652 39532 88514 0.8250239 0.80762032
[22,] 17.300321 9.167490 8.8956 12460 107781 -21.0240943 -22.46584538
[23,] 13.201261 8.132117 8.8956 35516 234428 -13.9777559 -14.79883563
[24,] 3.675059 3.838097 1.4826 99858 183492 0.9636002 0.92999313
[25,] 3.560633 3.131928 1.4826 13260 23607 0.2171849 0.06752974
[26,] 7.806563 5.975353 7.4130 2316 9040 -4.2220892 -6.35415795
[27,] 17.891304 7.461776 5.9304 920 8230 -22.4249177 -23.73404631
loss.diff log+1.quartile.0% log+1.quartile.25% log+1.quartile.50%
[1,] 0.03125171 0.0000000 1.7917595 2.708050
[2,] 0.35860915 0.0000000 2.4849066 2.890372
[3,] 0.17204738 0.0000000 1.7917595 2.708050
[4,] 2.19254257 0.0000000 2.4849066 3.806662
[5,] 0.16333713 0.0000000 1.3862944 2.484907
[6,] 0.00000000 0.0000000 1.7917595 2.484907
[7,] 0.00000000 0.0000000 0.6931472 1.791759
[8,] 1.42064261 0.0000000 2.7725887 3.583519
[9,] 0.27761748 0.6931472 3.7376696 4.043051
[10,] 0.29174331 0.0000000 3.2580965 3.931826
[11,] 1.48774216 0.0000000 1.7917595 2.890372
[12,] 0.04697062 0.0000000 0.6931472 1.791759
[13,] 0.06712772 0.0000000 1.3862944 2.484907
[14,] 0.38145394 0.0000000 2.0794415 2.890372
[15,] 4.11509520 0.0000000 1.7917595 3.295837
[16,] 0.20972931 0.0000000 0.6931472 2.197225
[17,] 0.93761685 0.0000000 3.0910425 3.871201
[18,] 2.23243498 0.0000000 2.1972246 2.890372
[19,] 0.41797867 0.0000000 1.3862944 2.197225
[20,] 0.10349098 0.0000000 0.6931472 1.791759
[21,] 0.01740356 0.0000000 0.6931472 1.791759
[22,] 1.44175107 0.0000000 3.4965076 3.931826
[23,] 0.82107976 0.0000000 2.0794415 3.258097
[24,] 0.03360710 0.0000000 0.6931472 1.098612
[25,] 0.14965519 0.0000000 1.0986123 1.098612
[26,] 2.13206876 0.6931472 0.6931472 2.890372
[27,] 1.30912864 0.6931472 3.1780538 3.806662
log+1.quartile.75% log+1.quartile.100% log+1.mean log+1.sd log+1.mad
[1,] 3.555348 6.025866 2.984066 2.524633 2.2868627
[2,] 3.988984 5.634790 3.239032 2.634643 2.7551126
[3,] 3.737670 5.583496 3.080286 2.492189 2.2868627
[4,] 4.700480 6.445720 3.945540 3.473849 3.4634903
[5,] 3.555348 6.173786 2.869776 2.931150 2.2868627
[6,] 3.401197 5.583496 2.657561 2.287397 2.2868627
[7,] 2.484907 5.123964 2.135106 2.025163 1.8186128
[8,] 4.653960 6.222576 3.923253 3.316814 3.0390845
[9,] 4.969813 6.445720 4.375598 3.309343 3.5073344
[10,] 4.700480 6.222576 4.148754 3.062938 2.8452239
[11,] 4.094345 5.852202 3.217662 2.939958 2.8452239
[12,] 2.197225 4.595120 1.848293 1.908768 1.8186128
[13,] 3.401197 5.411646 2.730589 2.390231 2.2868627
[14,] 3.688879 5.620401 3.132446 2.736317 2.2868627
[15,] 4.653960 7.037906 3.808235 3.652500 3.3410056
[16,] 2.995732 4.962845 2.390360 2.194826 1.8186128
[17,] 4.653960 6.352629 4.130660 3.297069 3.0390845
[18,] 4.356709 6.530878 3.609166 3.440267 3.0727682
[19,] 3.218876 5.429346 2.621505 2.403352 2.2868627
[20,] 2.708050 5.411646 2.140461 2.069034 1.8186128
[21,] 2.995732 5.429346 2.347633 2.226347 1.8186128
[22,] 4.653960 5.953243 4.097665 3.188124 3.0390845
[23,] 3.931826 6.068426 3.468628 2.986410 3.0390845
[24,] 2.302585 5.347108 2.009486 2.139376 0.9093064
[25,] 1.791759 4.276666 1.746096 1.781790 0.9093064
[26,] 3.583519 4.564348 2.858625 2.604943 2.8452239
[27,] 4.890349 5.480639 4.232032 3.079146 2.6045183
log+1.bases log+1.sum log+1.loss.0peaks log+1.loss.1peak log+1.loss.diff
[1,] 22.34683 24.80683 NaN NaN 0.03094547
[2,] 20.16611 22.94639 NaN NaN 0.31362840
[3,] 20.19819 22.78233 NaN NaN 0.16322853
[4,] 20.48106 24.00928 NaN NaN 1.18005623
[5,] 20.20836 22.50697 NaN NaN 0.15129271
[6,] 25.04458 27.07324 -0.8698988 -0.8698988 0.00000000
[7,] 22.53364 23.82211 0.9708067 0.9708067 0.00000000
[8,] 19.26231 22.77803 NaN NaN 0.92742848
[9,] 20.56597 24.60925 NaN NaN 0.25766788
[10,] 20.27443 24.03539 NaN NaN 0.26312431
[11,] 20.55967 23.27201 NaN NaN 0.93017844
[12,] 19.87191 20.67882 1.1123463 1.0812211 0.04590087
[13,] 20.83872 22.97169 -0.9832407 -1.1453887 0.06598746
[14,] 19.63727 22.26594 NaN NaN 0.32313652
[15,] 21.75986 25.15414 NaN NaN 1.66666278
[16,] 19.81904 21.48840 0.6355505 0.4720343 0.19445434
[17,] 18.81822 22.57945 NaN NaN 0.71065625
[18,] 19.49764 22.71525 NaN NaN 1.20547664
[19,] 20.45520 22.44434 -0.2665201 -1.3762923 0.35592026
[20,] 22.16425 23.45032 0.9227297 0.8620177 0.09996432
[21,] 19.78354 21.38945 0.6814249 0.6676974 0.01725385
[22,] 17.47458 21.20960 NaN NaN 0.93403993
[23,] 19.56930 22.45355 NaN NaN 0.65675684
[24,] 21.63675 22.66078 0.7158985 0.6847228 0.03305472
[25,] 17.59902 17.75750 -0.1199815 -0.4564865 0.13946207
[26,] 14.11063 16.26504 NaN NaN 1.39594979
[27,] 12.26680 16.17457 NaN NaN 0.98415324
log.quartile.0% log.quartile.25% log.quartile.50% log.quartile.75%
[1,] -Inf 0.6931472 2.0794415 3.178054
[2,] -Inf 1.7917595 2.3025851 3.688879
[3,] -Inf 0.6931472 2.0794415 3.401197
[4,] -Inf 1.6094379 3.3322045 4.430817
[5,] -Inf 0.0000000 1.7917595 3.178054
[6,] -Inf 0.6931472 1.7917595 2.995732
[7,] -Inf -Inf 0.6931472 1.791759
[8,] -Inf 1.9459101 3.0910425 4.382027
[9,] -Inf 3.2580965 3.5835189 4.744932
[10,] -Inf 2.4849066 3.4657359 4.430817
[11,] -Inf 0.6931472 2.3025851 3.784190
[12,] -Inf -Inf 0.6931472 1.386294
[13,] -Inf 0.0000000 1.7917595 2.995732
[14,] -Inf 1.0986123 2.3025851 3.332205
[15,] -Inf 0.6931472 2.7725887 4.382027
[16,] -Inf -Inf 1.3862944 2.484907
[17,] -Inf 2.3025851 3.4011974 4.382027
[18,] -Inf 1.3862944 2.3025851 4.094345
[19,] -Inf 0.0000000 1.3862944 2.772589
[20,] -Inf -Inf 0.6931472 2.079442
[21,] -Inf -Inf 0.6931472 2.484907
[22,] -Inf 2.9957323 3.4657359 4.382027
[23,] -Inf -Inf 2.4849066 3.465736
[24,] -Inf -Inf -Inf 1.386294
[25,] -Inf -Inf -Inf -Inf
[26,] -Inf -Inf 2.0794415 3.091042
[27,] -Inf 2.3978953 3.3322045 4.682131
log.quartile.100% log.mean log.sd log.mad log.bases log.sum
[1,] 5.924256 2.4600148 1.8510717 1.4807418 22.34681 24.80682
[2,] 5.509388 2.7803418 1.9898421 2.1738890 20.16603 22.94637
[3,] 5.455321 2.5841980 1.8029472 1.4807418 20.19811 22.78231
[4,] 6.349139 3.5282714 2.9767127 2.8670361 20.48099 24.00926
[5,] 6.061457 2.2986609 2.3480679 1.4807418 20.20828 22.50694
[6,] 5.455321 2.0286584 1.5140309 1.4807418 25.04458 27.07323
[7,] 4.962845 1.2884777 1.1217928 0.7875946 22.53362 23.82209
[8,] 6.111467 3.5158200 2.7916793 2.3970325 19.26218 22.77800
[9,] 6.349139 4.0433319 2.8242028 3.0901797 20.56590 24.60923
[10,] 6.111467 3.7610204 2.4985126 2.1738890 20.27435 24.03537
[11,] 5.730100 2.7123961 2.3419500 2.1738890 20.55960 23.27199
[12,] 4.382027 0.8069364 0.9337428 0.7875946 19.87181 20.67875
[13,] 5.273000 2.1330113 1.6646578 1.4807418 20.83866 22.97167
[14,] 5.488938 2.6287441 2.1196357 1.4807418 19.63717 22.26591
[15,] 6.962243 3.3943034 3.1852114 2.7335048 21.75983 25.15413
[16,] 4.787492 1.6694181 1.3786087 0.7875946 19.81894 21.48836
[17,] 6.253829 3.7613639 2.7858495 2.3970325 18.81805 22.57942
[18,] 6.436150 3.2177020 2.9765310 2.5793541 19.49752 22.71523
[19,] 5.288267 1.9891906 1.6766011 1.4807418 20.45512 22.44431
[20,] 5.273000 1.2860799 1.1894895 0.7875946 22.16422 23.45030
[21,] 5.288267 1.6059697 1.4283997 0.7875946 19.78344 21.38941
[22,] 5.828946 3.7352675 2.6444294 2.3970325 17.47426 21.20953
[23,] 5.953243 2.8843219 2.3685885 2.3970325 19.56918 22.45350
[24,] 5.204007 1.0240417 1.2963804 -Inf 21.63671 22.66076
[25,] 4.007333 0.1583256 0.5925280 -Inf 17.59872 17.75705
[26,] 4.317488 2.1553572 1.8802431 2.1738890 14.10890 16.26426
[27,] 5.332719 3.9113367 2.5861121 1.8862069 12.26245 16.17379
log.loss.0peaks log.loss.1peak log.loss.diff log.log.quartile.0%
[1,] NaN NaN -8.63625957 NaN
[2,] NaN NaN -4.62823402 NaN
[3,] NaN NaN -5.24794213 NaN
[4,] NaN NaN -2.78038499 NaN
[5,] NaN NaN -Inf NaN
[6,] NaN NaN -Inf NaN
[7,] -0.9657083 -0.9657083 -Inf NaN
[8,] NaN NaN -2.23159193 NaN
[9,] NaN NaN -4.11711024 NaN
[10,] NaN NaN -4.68365881 NaN
[11,] NaN NaN -3.05295206 NaN
[12,] -0.6455273 -0.7378357 -Inf NaN
[13,] NaN NaN -6.82562338 NaN
[14,] NaN NaN -Inf NaN
[15,] NaN NaN -1.71828076 NaN
[16,] -1.9671447 -2.7368186 -5.31470855 NaN
[17,] NaN NaN -2.32575486 NaN
[18,] NaN NaN -2.24511934 NaN
[19,] NaN NaN -4.65488124 NaN
[20,] -1.1939646 -1.3536616 -6.41275441 NaN
[21,] -1.8860583 -1.9510673 -Inf NaN
[22,] NaN NaN -2.27285100 NaN
[23,] NaN NaN -2.23074928 NaN
[24,] -2.4958792 -2.9331560 -Inf NaN
[25,] NaN NaN -Inf NaN
[26,] NaN NaN -0.09789951 NaN
[27,] NaN NaN -1.00398399 NaN
log.log.quartile.25% log.log.quartile.50% log.log.quartile.75%
[1,] -Inf -0.03987866 0.90983234
[2,] -0.2724651 0.10937207 1.20798436
[3,] -Inf -0.03987866 1.05908308
[4,] -Inf 0.60390886 1.43997831
[5,] -Inf -0.27246509 0.90983234
[6,] -Inf -0.27246509 0.80251926
[7,] NaN -Inf -0.27246509
[8,] -Inf 0.50807846 1.42382296
[9,] 0.5754258 0.69487221 1.61867180
[10,] -Inf 0.65326852 1.43997831
[11,] -Inf 0.10937207 1.20122564
[12,] NaN -Inf -0.73302584
[13,] -Inf -0.27246509 0.80251926
[14,] -Inf 0.10937207 0.99236407
[15,] -Inf 0.36558645 1.42382296
[16,] NaN -0.73302584 0.42068209
[17,] -Inf 0.62971597 1.42382296
[18,] -0.7330258 0.10937207 1.38612009
[19,] -Inf -0.73302584 0.65326852
[20,] NaN -Inf -0.03987866
[21,] NaN -Inf 0.42068209
[22,] 0.4675195 0.65326852 1.42382296
[23,] NaN -Inf 0.65326852
[24,] NaN NaN -Inf
[25,] NaN NaN NaN
[26,] NaN -Inf 0.50807846
[27,] -Inf 0.60390886 1.64458321
log.log.quartile.100% log.log.mean log.log.sd log.log.mad log.log.bases
[1,] 2.169920 0.37073778 -0.189148817 -0.84854843 4.827072
[2,] 2.021857 0.61258796 -0.093307017 0.16674107 4.621704
[3,] 2.003324 0.47397327 -0.255257971 -0.84854843 4.624884
[4,] 2.272770 0.83966792 0.481438913 -0.02639040 4.652700
[5,] 2.173027 0.18891684 0.123891823 -0.84854843 4.625890
[6,] 2.003324 -0.02287248 -0.590350756 -0.84854843 5.055020
[7,] 1.816530 -0.90705816 -1.161001441 -1.86383792 4.843722
[8,] 2.186586 0.87024526 0.357372934 -0.23715548 4.529992
[9,] 2.272770 1.19301192 0.520522531 0.77813402 4.660975
[10,] 2.186586 0.97478497 0.192557842 -0.35525410 4.632419
[11,] 2.078225 0.43961393 0.048958130 -0.35525410 4.660361
[12,] 1.566132 -2.44000350 -1.554852180 -1.86383792 4.592310
[13,] 1.938168 0.10084528 -0.389136372 -0.84854843 4.687326
[14,] 2.003100 0.44530864 0.009798839 -0.84854843 4.568554
[15,] 2.452400 0.83027225 0.615843992 -0.08189306 4.773837
[16,] 1.744268 -0.36138323 -0.770239443 -1.86383792 4.586982
[17,] 2.247261 1.03160975 0.416535652 -0.23715548 4.483339
[18,] 2.295504 0.87432801 0.609356681 0.48376252 4.554281
[19,] 1.935977 -0.02571161 -0.408227854 -0.84854843 4.650172
[20,] 1.938168 -0.99034110 -1.049645107 -1.86383792 4.810665
[21,] 1.935977 -0.44840250 -0.681695405 -1.86383792 4.583396
[22,] 2.094299 1.04732101 0.277781683 -0.23715548 4.335164
[23,] 2.143044 0.04903514 -0.069253884 -0.23715548 4.561618
[24,] 1.912361 -2.76321381 -0.884639081 NaN 4.762489
[25,] 1.350476 NaN NaN NaN 4.349358
[26,] 1.472114 -0.62120489 -0.581840309 -0.35525410 3.907317
[27,] 1.929982 1.19861662 0.485163847 -0.53152697 3.626790
log.log.sum log.log.loss.0peaks log.log.loss.1peak log.log.loss.diff
[1,] 5.035526 NaN NaN NaN
[2,] 4.879361 NaN NaN NaN
[3,] 4.865187 NaN NaN NaN
[4,] 4.965042 NaN NaN NaN
[5,] 4.840460 NaN NaN NaN
[6,] 5.210516 NaN NaN NaN
[7,] 4.954853 NaN NaN NaN
[8,] 4.859863 NaN NaN NaN
[9,] 5.014717 NaN NaN NaN
[10,] 4.966607 NaN NaN NaN
[11,] 4.906084 NaN NaN NaN
[12,] 4.671211 NaN NaN NaN
[13,] 4.881992 NaN NaN NaN
[14,] 4.818474 NaN NaN NaN
[15,] 5.060036 NaN NaN NaN
[16,] 4.748728 NaN NaN NaN
[17,] 4.842028 NaN NaN NaN
[18,] 4.858294 NaN NaN NaN
[19,] 4.835664 NaN NaN NaN
[20,] 4.923167 NaN NaN NaN
[21,] 4.739444 NaN NaN NaN
[22,] 4.716917 NaN NaN NaN
[23,] 4.828397 NaN NaN NaN
[24,] 4.853423 NaN NaN NaN
[25,] 4.352306 NaN NaN NaN
[26,] 4.182163 NaN NaN NaN
[27,] 4.172674 NaN NaN NaN
1 / 1 problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835
Skipping since jointTargets.rds exists.
Training sample model using 24 finite targets.
Train errors:
status targets
1: correct 21
2: low 2
3: high 1
Training group model using 24 finite targets.
Train errors:
status targets
1: correct 21
2: low 2
3: high 1
Saved /home/tdhock/PeakSegPipeline-test/input/joint.model.RData
Saved 1 jobProblems.bed files to /home/tdhock/PeakSegPipeline-test/input/jobs
1 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:32990873-33132211
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:32990873-33132211/segmentations.RData
2 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33132211-33156144
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33132211-33156144/segmentations.RData
Writing Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:32990873-33132211/peakInfo.rds
/home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33132211-33156144/peakInfo.rds
3 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33156144-33180464
4 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33180464-33190124
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33156144-33180464/segmentations.RData
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33180464-33190124/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33156144-33180464/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33180464-33190124/peakInfo.rds
5 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33190124-33206237
6 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33206237-33224554
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33190124-33206237/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33206237-33224554/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33190124-33206237/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33206237-33224554/peakInfo.rds
7 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33224554-33260703
8 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33457972-33485987
Found 2 samples to jointly segment.
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33457972-33485987/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33224554-33260703/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33457972-33485987/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33224554-33260703/peakInfo.rds
10 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33525512-33586032
9 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33485987-33525512
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33485987-33525512/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33525512-33586032/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33485987-33525512/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33525512-33586032/peakInfo.rds
11 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33618486-33642930
12 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33700559-33974944
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33700559-33974944/segmentations.RData
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33618486-33642930/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33700559-33974944/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:33618486-33642930/peakInfo.rds
13 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34390457-34411424
14 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34481840-34515686
Found Found 2 samples to jointly segment.
2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34390457-34411424/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34481840-34515686/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34481840-34515686/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34390457-34411424/peakInfo.rds
15 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34522098-34578838
16 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34594088-34613201
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34594088-34613201/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34522098-34578838/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34594088-34613201/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34522098-34578838/peakInfo.rds
17 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34636789-34677679
18 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34677679-34702389
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34677679-34702389/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34636789-34677679/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34677679-34702389/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34636789-34677679/peakInfo.rds
19 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34834234-35028541
20 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35045705-35101578
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35045705-35101578/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34834234-35028541/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35045705-35101578/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:34834234-35028541/peakInfo.rds
21 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35101578-35123386
22 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35182819-35261002
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35182819-35261002/segmentations.RData
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35101578-35123386/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35182819-35261002/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35101578-35123386/peakInfo.rds
23 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35287904-35303135
24 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35307474-35336704
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35307474-35336704/segmentations.RData
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35287904-35303135/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35307474-35336704/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35287904-35303135/peakInfo.rds
25 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35337315-35362580
26 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35362580-35391718
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35337315-35362580/segmentations.RData
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35362580-35391718/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35337315-35362580/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35362580-35391718/peakInfo.rds
27 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35404710-35416229
28 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35416229-35426665
FoundFound 2 2 samples to jointly segment.
samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35404710-35416229/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35416229-35426665/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35416229-35426665/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35404710-35416229/peakInfo.rds
29 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35426665-35456441
30 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35456441-35475841
FoundFound 22 samples to jointly segment.
samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35456441-35475841/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35426665-35456441/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35456441-35475841/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35426665-35456441/peakInfo.rds
31 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35475841-35484716
32 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35484716-35493813
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35475841-35484716/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35484716-35493813/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35475841-35484716/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35484716-35493813/peakInfo.rds
33 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35493813-35512116
34 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35583854-35625467
Found Found 2 samples to jointly segment.
2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35493813-35512116/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35583854-35625467/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35583854-35625467/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35493813-35512116/peakInfo.rds
36 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35764095-35789019
Found 2 samples to jointly segment.
35 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35625467-35642768
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35625467-35642768/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35764095-35789019/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35625467-35642768/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35764095-35789019/peakInfo.rds
37 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35812614-35831715
38 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35831823-35853321
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35812614-35831715/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35831823-35853321/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35812614-35831715/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35831823-35853321/peakInfo.rds
39 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35853321-35876498
40 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35978205-36117051
FoundFound 2 2 samples to jointly segment.
samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35853321-35876498/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35978205-36117051/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35853321-35876498/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:35978205-36117051/peakInfo.rds
41 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:36904544-36924902
42 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:37228810-37275007
FoundFound 2 samples to jointly segment.
2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:36904544-36924902/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:37228810-37275007/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:36904544-36924902/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:37228810-37275007/peakInfo.rds
43 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:37714855-37915957
44 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:37984749-38022122
FoundFound 2 samples to jointly segment.
2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:37984749-38022122/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:37984749-38022122/peakInfo.rds
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:37714855-37915957/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:37714855-37915957/peakInfo.rds
45 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38022122-38042838
46 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38042838-38076430
Loading model from Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38042838-38076430/segmentations.RData
/home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38022122-38042838/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38042838-38076430/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38022122-38042838/peakInfo.rds
47 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38081566-38099938
48 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38112252-38126890
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38081566-38099938/segmentations.RDataFound
2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38112252-38126890/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38081566-38099938/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38112252-38126890/peakInfo.rds
49 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38126890-38146639
50 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38146639-38192848
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38126890-38146639/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38146639-38192848/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38146639-38192848/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38126890-38146639/peakInfo.rds
51 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38192848-38232240
52 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38232240-38259689
Found 2 samples to jointly segment.
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38232240-38259689/segmentations.RDataWriting segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38192848-38232240/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38192848-38232240/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38232240-38259689/peakInfo.rds
53 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38274983-38328082
54 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38328082-38341997
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38274983-38328082/segmentations.RData
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38328082-38341997/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38274983-38328082/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38328082-38341997/peakInfo.rds
55 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38344154-38359217
56 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38363334-38383454
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38363334-38383454/segmentations.RData
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38344154-38359217/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38363334-38383454/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38344154-38359217/peakInfo.rds
57 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38383454-38395652
58 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38396093-38413226
Loading model from Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38396093-38413226/segmentations.RData
/home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38383454-38395652/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38396093-38413226/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38383454-38395652/peakInfo.rds
59 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38414575-38442230
60 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38442230-38507228
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38442230-38507228/segmentations.RData
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38414575-38442230/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38442230-38507228/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38414575-38442230/peakInfo.rds
61 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38625872-38645638
62 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38645638-38651882
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38645638-38651882/segmentations.RData
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38625872-38645638/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38645638-38651882/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38625872-38645638/peakInfo.rds
64 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38685426-38708891
Found 2 samples to jointly segment.
63 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38651882-38672368
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38651882-38672368/segmentations.RData
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38685426-38708891/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38651882-38672368/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38685426-38708891/peakInfo.rds
66 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38722920-38740678
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38722920-38740678/segmentations.RData
65 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38708891-38722920
Found 2 samples to jointly segment.
Writing segmentation and features to /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38708891-38722920/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38722920-38740678/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38708891-38722920/peakInfo.rds
67 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38740678-38790607
68 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38807475-38814105
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38807475-38814105/segmentations.RData
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38740678-38790607/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38807475-38814105/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38740678-38790607/peakInfo.rds
69 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38815199-38816357
70 / 70 joint prediction problems /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38818375-38818835
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38818375-38818835/segmentations.RData
Loading model from /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38815199-38816357/segmentations.RData
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38818375-38818835/peakInfo.rds
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/jointProblems/chr10:38815199-38816357/peakInfo.rds
problem.name jprob.name chrom peakStart peakEnd
1: chr10:18024675-38818835 chr10:33180464-33190124 chr10 33183570 33189976
2: chr10:18024675-38818835 chr10:33457972-33485987 chr10 33465654 33481514
3: chr10:18024675-38818835 chr10:33485987-33525512 chr10 33494262 33516821
4: chr10:18024675-38818835 chr10:33525512-33586032 chr10 33534251 33560124
5: chr10:18024675-38818835 chr10:35287904-35303135 chr10 35296445 35302727
6: chr10:18024675-38818835 chr10:35307474-35336704 chr10 35312789 35326798
7: chr10:18024675-38818835 chr10:35362580-35391718 chr10 35364686 35378202
8: chr10:18024675-38818835 chr10:35493813-35512116 chr10 35494006 35503061
9: chr10:18024675-38818835 chr10:35583854-35625467 chr10 35603838 35623822
10: chr10:18024675-38818835 chr10:35812614-35831715 chr10 35818984 35825348
11: chr10:18024675-38818835 chr10:35853321-35876498 chr10 35854798 35865645
12: chr10:18024675-38818835 chr10:38112252-38126890 chr10 38116253 38122523
13: chr10:18024675-38818835 chr10:38232240-38259689 chr10 38238327 38247236
14: chr10:18024675-38818835 chr10:38274983-38328082 chr10 38300958 38327017
15: chr10:18024675-38818835 chr10:38344154-38359217 chr10 38349546 38351347
16: chr10:18024675-38818835 chr10:38383454-38395652 chr10 38384461 38387347
17: chr10:18024675-38818835 chr10:38396093-38413226 chr10 38401804 38407515
18: chr10:18024675-38818835 chr10:38645638-38651882 chr10 38646902 38651723
19: chr10:18024675-38818835 chr10:38651882-38672368 chr10 38652010 38662178
20: chr10:18024675-38818835 chr10:38685426-38708891 chr10 38696463 38707514
21: chr10:18024675-38818835 chr10:38722920-38740678 chr10 38733532 38737797
22: chr10:18024675-38818835 chr10:38815199-38816357 chr10 38815694 38816169
23: chr10:18024675-38818835 chr10:38818375-38818835 chr10 38818438 38818533
problem.name jprob.name chrom peakStart peakEnd
peak.mean.vec sample.loss.diff.vec background.mean.vec sample.peaks.vec
1: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
2: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
3: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
4: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
5: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
6: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
7: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
8: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
9: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
10: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
11: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
12: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
13: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
14: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
15: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
16: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
17: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
18: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
19: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
20: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
21: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
22: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
23: <dgeMatrix> <dgeMatrix> <dgeMatrix> <lgCMatrix>
peak.mean.vec sample.loss.diff.vec background.mean.vec sample.peaks.vec
group.peaks.vec sample.loss.diff group.loss.diff
1: <lgCMatrix> 13999.8299 13999.8299
2: <lgCMatrix> 62042.8711 62042.8711
3: <lgCMatrix> 22318.3721 22318.3721
4: <lgCMatrix> 30798.7158 30798.7158
5: <lgCMatrix> 21963.7111 21963.7111
6: <lgCMatrix> 6241.8881 6241.8881
7: <lgCMatrix> 47687.1265 47687.1265
8: <lgCMatrix> 32472.2433 32472.2433
9: <lgCMatrix> 57036.7569 57036.7569
10: <lgCMatrix> 10442.6066 10442.6066
11: <lgCMatrix> 71493.6243 71493.6243
12: <lgCMatrix> 18544.4296 18544.4296
13: <lgCMatrix> 16343.6442 16343.6442
14: <lgCMatrix> 233629.2985 233629.2985
15: <lgCMatrix> 26075.7247 26075.7247
16: <lgCMatrix> 10009.7382 10009.7382
17: <lgCMatrix> 44727.0454 44727.0454
18: <lgCMatrix> 9794.0312 9794.0312
19: <lgCMatrix> 16701.4813 16701.4813
20: <lgCMatrix> 30321.0719 30321.0719
21: <lgCMatrix> 13374.3657 13374.3657
22: <lgCMatrix> 2601.4151 2601.4151
23: <lgCMatrix> 675.4956 675.4956
group.peaks.vec sample.loss.diff group.loss.diff
Reading predicted peaks in 1 jobPeaks.RData files.
Read Read 8 labels.
6 labels.
Read 70 joint problems, plotting 12 in chunk.
Read 70 joint problems, plotting 5 in chunk.
Read 2 samples of coverage.
Read 1 samples of separate peak predictions.
Read joint peak predictions: 3 peaks in 3 peakInfo.RData files, 5 problems.
Read 2 samples of coverage.
Read 1 samples of separate peak predictions.
Read joint peak predictions: 4 peaks in 4 peakInfo.RData files, 12 problems.
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/chunks/chr10:35182820-35398459/figure-predictions.png
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/chunks/chr10:33061897-33974942/figure-predictions.png
Read 10 labels.
Read 70 joint problems, plotting 16 in chunk.
Read 2 samples of coverage.
Read 1 samples of separate peak predictions.
Read joint peak predictions: 6 peaks in 6 peakInfo.RData files, 16 problems.
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/chunks/chr10:38041023-38444133/figure-predictions.png
Read 6 labels.
Read 70 joint problems, plotting 3 in chunk.
Read 8 labels.
Read 70 joint problems, plotting 7 in chunk.
Read 2 samples of coverage.
Read 0 samples of separate peak predictions.
Read joint peak predictions: 4 peaks in 2 peakInfo.RData files, 3 problems.
Read 2 samples of coverage.
Read 1 samples of separate peak predictions.
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/chunks/chr10:38807475-38819342/figure-predictions.png
Read joint peak predictions: 4 peaks in 4 peakInfo.RData files, 7 problems.
Writing /home/tdhock/PeakSegPipeline-test/input/problems/chr10:18024675-38818835/chunks/chr10:38585584-38790663/figure-predictions.png
pass1 - making usageList (1 chroms): 0 millis
pass2 - checking and writing primary data (19 records, 9 fields): 9 millis
pass1 - making usageList (1 chroms): 1 millis
pass2 - checking and writing primary data (1 records, 3 fields): 0 millis
pass1 - making usageList (1 chroms): 0 millis
pass2 - checking and writing primary data (70 records, 3 fields): 1 millis
pass1 - making usageList (1 chroms): 0 millis
pass2 - checking and writing primary data (21 records, 5 fields): 1 millis
Created http://hubs.hpc.mcgill.ca/~thocking/PeakSegFPOP-/hub.txt
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tdhock@recycled:~$