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JetBrains-Research / span

SPAN Semi-supervised Peak Analyzer
https://doi.org/10.1093/bioinformatics/btab376
MIT License
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Inconsistent LOG format in output #29

Closed olegs closed 4 years ago

olegs commented 4 years ago

First two lines are different from the rest output.

11:42:03.245 [main] INFO org.jetbrains.bio.span.SpanCLA - SPAN 0.12.0.5096 built on April 14, 2020
11:42:03.255 [main] INFO org.jetbrains.bio.span.SpanCLA - COMMAND:
analyze -m fit/wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1_wgEncodeBroadHistoneGm12878ControlStdAlnRep1_200#32f4e.span -cs /mnt/stripe/bio/genomes/hg19/hg19.chrom.sizes --fdr 0.01 --gap 10 --peaks wgEnco
[Jun 3, 2020 11:42:03] LOG: /mnt/stripe/shpynov/BenchmarkChIPseqPeakCallers_Code/H3K4me3Data/logs/wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1_0.01_10.log
[Jun 3, 2020 11:42:03] MODEL: /mnt/stripe/shpynov/BenchmarkChIPseqPeakCallers_Code/H3K4me3Data/fit/wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1_wgEncodeBroadHistoneGm12878ControlStdAlnRep1_200#32f4e.span
[Jun 3, 2020 11:42:03] Loading model: /mnt/stripe/shpynov/BenchmarkChIPseqPeakCallers_Code/H3K4me3Data/fit/wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1_wgEncodeBroadHistoneGm12878ControlStdAlnRep1_200#32f
[Jun 3, 2020 11:42:04] Completed loading model: /mnt/stripe/shpynov/BenchmarkChIPseqPeakCallers_Code/H3K4me3Data/fit/wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1_wgEncodeBroadHistoneGm12878ControlStdAlnRe
[Jun 3, 2020 11:42:04] WORKING DIR: /mnt/stripe/shpynov/BenchmarkChIPseqPeakCallers_Code/H3K4me3Data
[Jun 3, 2020 11:42:04] TREATMENT: /mnt/stripe/shpynov/BenchmarkChIPseqPeakCallers_Code/H3K4me3Data/wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1.bam
[Jun 3, 2020 11:42:04] CONTROL: /mnt/stripe/shpynov/BenchmarkChIPseqPeakCallers_Code/H3K4me3Data/wgEncodeBroadHistoneGm12878ControlStdAlnRep1.bam
[Jun 3, 2020 11:42:04] CHROM.SIZES: /mnt/stripe/bio/genomes/hg19/hg19.chrom.sizes
[Jun 3, 2020 11:42:04] BIN: 200
[Jun 3, 2020 11:42:04] FRAGMENT: auto
[Jun 3, 2020 11:42:04] KEEP DUPLICATES: false
[Jun 3, 2020 11:42:04] FDR: 0.01
[Jun 3, 2020 11:42:04] GAP: 10
[Jun 3, 2020 11:42:04] PEAKS: /mnt/stripe/shpynov/BenchmarkChIPseqPeakCallers_Code/H3K4me3Data/wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1_0.01_10.peak
[Jun 3, 2020 11:42:04] THREADS: 32
[Jun 3, 2020 11:42:04] Library: wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1.bam, Depth: 21,459,725, Reads: single-ended, Fragment size: 36 bp (cross-correlation estimate)
[Jun 3, 2020 11:42:04] Library: wgEncodeBroadHistoneGm12878ControlStdAlnRep1.bam, Depth: 6,477,015, Reads: single-ended, Fragment size: 36 bp (cross-correlation estimate)
[Jun 3, 2020 11:42:10] Saved result to /mnt/stripe/shpynov/BenchmarkChIPseqPeakCallers_Code/H3K4me3Data/wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1_0.01_10.peak
[Jun 3, 2020 11:42:10] Library: wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1.bam, Depth: 21,459,725, Reads: single-ended, Fragment size: 36 bp (cross-correlation estimate)
[Jun 3, 2020 11:42:11]
Source: /mnt/stripe/shpynov/BenchmarkChIPseqPeakCallers_Code/H3K4me3Data/wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1_0.01_10.peak
File size: 3,2 mb
Count: 35 010
Total length: 108 337 600
Genome coverage: 0.04%
Min length: 200
Max length: 88 000
Mean length: 3 094
Median length: 1 800
FRIP: 0.30823885208221447
Signal mean: 10.361862323636037
Noise mean: 0.9123737659992885
Signal to noise: 11.357036675919082