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loosolab / jlu-bda-2020

Code repository for the JLU practical in Biodatenanalyse in winter 2020/2021
MIT License
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Redo Analysis: Segmentation Fault #33

Closed rwiegan closed 3 years ago

rwiegan commented 3 years ago

I ran python bin/tf_analyzer.py -g hg19 -b kidney -t ar -c chr1 After successfully finishing the run i tried to redo the analysis with: python bin/tf_analyzer.py -g hg19 -b kidney -t ar -c chr1 -r This led to the following error:

Now starting normalisation process. 15 files will be normalised.
------ Log scaling files ------
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433194.chr1.bw (RAM usage: 0.61GB (1.4%))
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433194.chr1.bed (RAM usage: 0.61GB (1.4%))
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433193.chr1.bw (RAM usage: 0.61GB (1.4%))
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433193.chr1.bed (RAM usage: 0.61GB (1.4%))
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433192.chr1.bw (RAM usage: 0.61GB (1.4%))
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433192.chr1.bed (RAM usage: 0.61GB (1.4%))
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433191.chr1.bw (RAM usage: 0.61GB (1.4%))
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433191.chr1.bed (RAM usage: 0.61GB (1.4%))
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433189.chr1.bw (RAM usage: 0.61GB (1.4%))
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433189.chr1.bed (RAM usage: 0.61GB (1.4%))
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433190.chr1.bw (RAM usage: 0.61GB (1.4%))
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433190.chr1.bed (RAM usage: 0.61GB (1.4%))
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/atac-seq/E086-DNase.pval.signal.chr1.bw (RAM usage: 0.61GB (1.4%))
/mnt/workspace/rwiegan/git/jlu-bda-2020/bin/scripts/normalize_signal_values.py:182: RuntimeWarning: invalid value encountered in log
  log_values = numpy.log(signal_values)
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/atac-seq/E086-DNase.fc.signal.chr1.bw (RAM usage: 0.61GB (1.4%))
- Log-scaling /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/atac-seq/ENCFF107HEL.chr1.bw (RAM usage: 0.65GB (1.5%))
------ Finding global min/max values ------
- /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433194.chr1.bw.ln (RAM usage: 0.64GB (1.5%))
- /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433194.chr1.bed.ln (RAM usage: 0.64GB (1.5%))
- /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433193.chr1.bw.ln (RAM usage: 0.64GB (1.5%))
- /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433193.chr1.bed.ln (RAM usage: 0.64GB (1.5%))
- /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433192.chr1.bw.ln (RAM usage: 0.64GB (1.5%))
- /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433192.chr1.bed.ln (RAM usage: 0.64GB (1.5%))
- /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433191.chr1.bw.ln (RAM usage: 0.64GB (1.5%))
- /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433191.chr1.bed.ln (RAM usage: 0.64GB (1.5%))
- /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433189.chr1.bw.ln (RAM usage: 0.64GB (1.5%))
- /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433189.chr1.bed.ln (RAM usage: 0.64GB (1.5%))
- /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433190.chr1.bw.ln (RAM usage: 0.64GB (1.5%))
- /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/chip-seq/ar/SRX433190.chr1.bed.ln (RAM usage: 0.64GB (1.5%))
- /mnt/workspace/rwiegan/git/jlu-bda-2020/data/hg19/kidney/atac-seq/E086-DNase.pval.signal.chr1.bw.ln (RAM usage: 0.64GB (1.5%))
Segmentation fault

I reproduced the error by deleting the results and data folder and redoing the steps above.

Jasmin-Walter commented 3 years ago

The error was caused by an error in normalization which led to empty .ln files. The error was fixed within the fix of the memory issue in commit 5050f3b.