#9 --pl=T cause empty bigwigs

[Anonymous]

Originally created by: bucc...@gmail.com
Originally owned by: bucc...@gmail.com

What steps will reproduce the problem?
1. using Threshold pipeline end with an empty bigwig when no peaks are detectable.

gbucci@hilt:/scratch/Testa/Project_Signaroldi/Glio_Astro$ dspchip -i ../11_01_H3_NoIndex_L005_R1.bam -c ../52_input_NoIndex_L003_R1.bam --pl=NWTZ -p --ewin=20000 --fir=hanning  --name=H3_01_test --ichrom=chr10
## DSP-ChIP parameters. Version 0.8.6b6
## Analysis name: H3_01_test
## File for signal A: ../11_01_H3_NoIndex_L005_R1.bam
## File for signal B: ../52_input_NoIndex_L003_R1.bam
## Chromosome sizes file: None
## File Format for file A: sam
## File Format for file B: sam
## Map quality: 0
## Remove duplicates: False
## Downsample ratio for signal A: 1.0
## Downsample ratio for signal B: 1.0
## Profile File Format: bw
## Included chromosome: chr10
## Excluded chromosomes:
## Use all chromosomes: False
## Correlation analysis: False
## Pipeline in use: NWTZ
## Wavelet: db5
## FIR Window name: hanning
## Baseline function: min
## Expected signal size: 20000
## Windowing step size: 100
## Thresholding method: otsu
## Profile step size 100
## Search for peaks: True
## Peak Ratio: 0.4
## Peak Interspersion: 3
## Infer peak distribution model: False
## Data scale: False
## Feature to model: area
## Perform signal analysis: True
## Write profile file: True
## Save npy data: False
## Save basic statistics: False
[ Fri Oct 21 14:43:20 2011 ] Getting chromosome data from SAM file ../11_01_H3_NoIndex_L005_R1.bam
[ Fri Oct 21 14:43:20 2011 ] Processing chromosome chr10
[ Fri Oct 21 14:43:20 2011 ] Reading ../11_01_H3_NoIndex_L005_R1.bam
[ Fri Oct 21 14:43:33 2011 ] Reading ../52_input_NoIndex_L003_R1.bam
[ Fri Oct 21 14:43:48 2011 ] Normalizing...
[ Fri Oct 21 14:43:50 2011 ] Normalizing...
[ Fri Oct 21 14:43:52 2011 ] About to perform wavelet denoising
[ Fri Oct 21 14:43:52 2011 ] Getting wavelet coefficients for wavelet db5
[ Fri Oct 21 14:43:55 2011 ] Filtering coefficients. Decomposition level: 13 Wavelet peak width: 18432
[ Fri Oct 21 14:43:56 2011 ] Rebuilding signal
[ Fri Oct 21 14:43:59 2011 ] About to perform wavelet denoising
[ Fri Oct 21 14:43:59 2011 ] Getting wavelet coefficients for wavelet db5
[ Fri Oct 21 14:44:03 2011 ] Filtering coefficients. Decomposition level: 13 Wavelet peak width: 18432
[ Fri Oct 21 14:44:03 2011 ] Rebuilding signal
[ Fri Oct 21 14:44:07 2011 ] Thresholding data with otsu method
[ Fri Oct 21 14:44:16 2011 ] Thresholding data with otsu method
[ Fri Oct 21 14:44:26 2011 ] About to remove all negative values
[ Fri Oct 21 14:44:26 2011 ] About to remove all negative values
[ Fri Oct 21 14:44:27 2011 ] Writing profile data in bedgraph...
[ Fri Oct 21 14:44:28 2011 ] Finding peaks boundaries
[ Fri Oct 21 14:44:28 2011 ] Calculating Sobel filter
[ Fri Oct 21 14:45:02 2011 ] Getting maxima and minima
[ Fri Oct 21 14:45:05 2011 ] Getting peak boundaries
[ Fri Oct 21 14:45:06 2011 ] Refining and merging 1 peaks
[ Fri Oct 21 14:45:06 2011 ] No peaks for chromosome chr10
[ Fri Oct 21 14:45:06 2011 ] Converting bedgraph into bigwig
There was this error:
H3_01_test.bigwig.tmp.gz is empty of data

gbucci@hilt:/scratch/Testa/Project_Signaroldi/Glio_Astro$ dspchip -i ../11_01_H3_NoIndex_L005_R1.bam -c ../52_input_NoIndex_L003_R1.bam --pl=NWTZ -p --scale --fir=hanning  --name=H3_01_test --ichrom=chr10
## DSP-ChIP parameters. Version 0.8.6b6
## Analysis name: H3_01_test
## File for signal A: ../11_01_H3_NoIndex_L005_R1.bam
## File for signal B: ../52_input_NoIndex_L003_R1.bam
## Chromosome sizes file: None
## File Format for file A: sam
## File Format for file B: sam
## Map quality: 0
## Remove duplicates: False
## Downsample ratio for signal A: 1.0
## Downsample ratio for signal B: 1.0
## Profile File Format: bw
## Included chromosome: chr10
## Excluded chromosomes:
## Use all chromosomes: False
## Correlation analysis: False
## Pipeline in use: NWTZ
## Wavelet: db5
## FIR Window name: hanning
## Baseline function: min
## Expected signal size: 10000
## Windowing step size: 100
## Thresholding method: otsu
## Profile step size 100
## Search for peaks: True
## Peak Ratio: 0.4
## Peak Interspersion: 3
## Infer peak distribution model: False
## Data scale: True
## Feature to model: area
## Perform signal analysis: True
## Write profile file: True
## Save npy data: False
## Save basic statistics: False
[ Fri Oct 21 15:10:36 2011 ] Getting chromosome data from SAM file ../11_01_H3_NoIndex_L005_R1.bam
[ Fri Oct 21 15:10:36 2011 ] Processing chromosome chr10
[ Fri Oct 21 15:10:36 2011 ] Reading ../11_01_H3_NoIndex_L005_R1.bam
[ Fri Oct 21 15:10:49 2011 ] Reading ../52_input_NoIndex_L003_R1.bam
[ Fri Oct 21 15:11:03 2011 ] Normalizing...
[ Fri Oct 21 15:11:04 2011 ] Normalizing...
[ Fri Oct 21 15:11:06 2011 ] About to perform wavelet denoising
[ Fri Oct 21 15:11:06 2011 ] Getting wavelet coefficients for wavelet db5
[ Fri Oct 21 15:11:10 2011 ] Filtering coefficients. Decomposition level: 12 Wavelet peak width: 9216
[ Fri Oct 21 15:11:10 2011 ] Rebuilding signal
[ Fri Oct 21 15:11:13 2011 ] About to perform wavelet denoising
[ Fri Oct 21 15:11:13 2011 ] Getting wavelet coefficients for wavelet db5
[ Fri Oct 21 15:11:17 2011 ] Filtering coefficients. Decomposition level: 12 Wavelet peak width: 9216
[ Fri Oct 21 15:11:17 2011 ] Rebuilding signal
[ Fri Oct 21 15:11:20 2011 ] Thresholding data with otsu method
[ Fri Oct 21 15:11:30 2011 ] Thresholding data with otsu method
[ Fri Oct 21 15:11:39 2011 ] About to remove all negative values
[ Fri Oct 21 15:11:40 2011 ] About to remove all negative values
[ Fri Oct 21 15:11:41 2011 ] Scaling data ( 76609.0675512 x )
[ Fri Oct 21 15:11:41 2011 ] Writing profile data in bedgraph...
[ Fri Oct 21 15:11:42 2011 ] Finding peaks boundaries
[ Fri Oct 21 15:11:42 2011 ] Calculating Sobel filter
[ Fri Oct 21 15:12:14 2011 ] Getting maxima and minima
[ Fri Oct 21 15:12:17 2011 ] Getting peak boundaries
[ Fri Oct 21 15:12:18 2011 ] Refining and merging 1 peaks
[ Fri Oct 21 15:12:18 2011 ] No peaks for chromosome chr10
[ Fri Oct 21 15:12:18 2011 ] Converting bedgraph into bigwig
There was this error:
H3_01_test.bigwig.tmp.gz is empty of data

dspchip -i ../11_01_H3_NoIndex_L005_R1.bam -c ../52_input_NoIndex_L003_R1.bam --pl=NWZ -p --ewin=20000 --scale --fir=hanning  --name=H3_01_test --ichrom=chr10

## DSP-ChIP parameters. Version 0.8.6b6
## Analysis name: H3_01_test
## File for signal A: ../11_01_H3_NoIndex_L005_R1.bam
## File for signal B: ../52_input_NoIndex_L003_R1.bam
## Chromosome sizes file: None
## File Format for file A: sam
## File Format for file B: sam
## Map quality: 0
## Remove duplicates: False
## Downsample ratio for signal A: 1.0
## Downsample ratio for signal B: 1.0
## Profile File Format: bw
## Included chromosome: chr10
## Excluded chromosomes:
## Use all chromosomes: False
## Correlation analysis: False
## Pipeline in use: NWZ
## Wavelet: db5
## FIR Window name: hanning
## Baseline function: min
## Expected signal size: 20000
## Windowing step size: 100
## Thresholding method: otsu
## Profile step size 100
## Search for peaks: True
## Peak Ratio: 0.4
## Peak Interspersion: 3
## Infer peak distribution model: False
## Data scale: True
## Feature to model: area
## Perform signal analysis: True
## Write profile file: True
## Save npy data: False
## Save basic statistics: False
[ Fri Oct 21 15:20:31 2011 ] Getting chromosome data from SAM file ../11_01_H3_NoIndex_L005_R1.bam
[ Fri Oct 21 15:20:31 2011 ] Processing chromosome chr10
[ Fri Oct 21 15:20:31 2011 ] Reading ../11_01_H3_NoIndex_L005_R1.bam
[ Fri Oct 21 15:20:46 2011 ] Reading ../52_input_NoIndex_L003_R1.bam
[ Fri Oct 21 15:21:03 2011 ] Normalizing...
[ Fri Oct 21 15:21:05 2011 ] Normalizing...
[ Fri Oct 21 15:21:06 2011 ] About to perform wavelet denoising
[ Fri Oct 21 15:21:06 2011 ] Getting wavelet coefficients for wavelet db5
[ Fri Oct 21 15:21:10 2011 ] Filtering coefficients. Decomposition level: 13 Wavelet peak width: 18432
[ Fri Oct 21 15:21:10 2011 ] Rebuilding signal
[ Fri Oct 21 15:21:14 2011 ] About to perform wavelet denoising
[ Fri Oct 21 15:21:14 2011 ] Getting wavelet coefficients for wavelet db5
[ Fri Oct 21 15:21:17 2011 ] Filtering coefficients. Decomposition level: 13 Wavelet peak width: 18432
[ Fri Oct 21 15:21:18 2011 ] Rebuilding signal
[ Fri Oct 21 15:21:21 2011 ] About to remove all negative values
[ Fri Oct 21 15:21:21 2011 ] About to remove all negative values
[ Fri Oct 21 15:21:22 2011 ] Scaling data ( 78111.2429431 x )
[ Fri Oct 21 15:21:23 2011 ] Writing profile data in bedgraph...
[ Fri Oct 21 15:21:45 2011 ] Finding peaks boundaries
[ Fri Oct 21 15:21:45 2011 ] Applying otsu thresholding
[ Fri Oct 21 15:21:54 2011 ] Getting peak boundaries
[ Fri Oct 21 15:21:59 2011 ] Refining and merging 1 peaks
[ Fri Oct 21 15:21:59 2011 ] No peaks for chromosome chr10
[ Fri Oct 21 15:21:59 2011 ] Converting bedgraph into bigwig
[ Fri Oct 21 15:22:02 2011 ] Removed bedgraph file and created bigWig