Summary: The gene counts table was normalized for inherent systematic or experimental biases (e.g. sequencing depth, gene length, GC content bias etc.) using the Bioconductor package DESeq after removing genes that had zero counts over all the RNA-Seq samples (20256 genes). The output of the normalization algorithm was a table with normalized counts, which can be used for differential expression analysis with statistical algorithms developed specifically for count data. Prior to the statistical testing procedure, the gene read counts were filtered for possible artifacts that could affect the subsequent statistical testing procedures. Genes presenting any of the following were excluded from further analysis: i) genes with length less than 500 (5148 genes), ii) genes whose average reads per 100 bp was less than the 25^th quantile of the total normalized distribution of average reads per 100bp (0 genes with cutoff value 0 average reads per 100 bp), iii) genes with read counts below the median read counts of the total normalized count distribution (8503 genes with cutoff value 2 normalized read counts). The total number of genes excluded due to the application of gene filters was 5698. The total (unified) number of genes excluded due to the application of all filters was 31742. The resulting gene counts table was subjected to differential expression analysis for the contrasts MalignantWTb versus MalignantKOb, healthyWTb versus premalignantWTb, healthyKOb versus premalignantKOb, healthyWTb versus healthyKOb, premalignantWTb versus premalignantKOb, MalignantWTb versus premalignantWTb, healthyKOb versus MalignantKOb using the Bioconductor package DESeq. The final numbers of differentially expressed genes were (per contrast): for the contrast MalignantWTb versus MalignantKOb, 507 (81) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 331 (58) were up-regulated, 141 (23) were down-regulated and 35 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast healthyWTb versus premalignantWTb, 1045 (102) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 616 (85) were up-regulated, 429 (17) were down-regulated and 0 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast healthyKOb versus premalignantKOb, 1057 (151) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 693 (143) were up-regulated, 359 (8) were down-regulated and 5 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast healthyWTb versus healthyKOb, 184 (2) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 89 (0) were up-regulated, 95 (2) were down-regulated and 0 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast premalignantWTb versus premalignantKOb, 126 (3) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 104 (3) were up-regulated, 22 (0) were down-regulated and 0 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast MalignantWTb versus premalignantWTb, 1692 (563) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 1290 (474) were up-regulated, 397 (89) were down-regulated and 5 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast healthyKOb versus MalignantKOb, 3839 (2009) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 1547 (751) were up-regulated, 2269 (1256) were down-regulated and 23 (2) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale. Literature references for all the algorithms used can be found at the end of this report.

Read counts file: imported custom data frame
Conditions: MalignantWTb, MalignantKOb, healthyWTb, premalignantWTb, healthyKOb, premalignantKOb
Samples included: AE3R13_L24B, AE3R14_L33B, AE3R15_L43B, AE3R16_L59B, AE3R17_L64B, AE3R18_L9B, AE3R19_L26B, AE3R20_L29B, AE3R21_L54B, AE3R22_L58B, AE3R23_wt, AE3R24_wt, AE3R25_wt, AE3R26_wtpre, AE3R27_wtpre, AE3R28_wtpre, AE3R29_ko, AE3R30_ko, AE3R31_ko, AE3R32_kopre, AE3R33_kopre, AE3R34_kopre
Samples excluded: none
Requested contrasts: MalignantWTb_vs_MalignantKOb, healthyWTb_vs_premalignantWTb, healthyKOb_vs_premalignantKOb, healthyWTb_vs_healthyKOb, premalignantWTb_vs_premalignantKOb, MalignantWTb_vs_premalignantWTb, healthyKOb_vs_MalignantKOb
Library sizes: not available
Annotation: embedded
Organism:
Annotation source: Ensembl genomes
Count type: utr
Exon filters: none applied
Gene filters: length, avg.reads, expression, biotype

• length
  • length: 500

• avg.reads
  • average.per.bp: 100
  • quantile: 0.25

• expression
  • median: TRUE
  • mean: FALSE
  • quantile: NA
  • known: NA
  • custom: NA

• biotype
  • pseudogene: FALSE
  • snRNA: FALSE
  • protein_coding: FALSE
  • antisense: FALSE
  • miRNA: FALSE
  • snoRNA: FALSE
  • lincRNA: FALSE
  • processed_transcript: FALSE
  • misc_RNA: FALSE
  • rRNA: TRUE
  • sense_intronic: FALSE
  • sense_overlapping: FALSE
  • polymorphic_pseudogene: FALSE
  • IG_C_gene: FALSE
  • IG_J_gene: FALSE
  • IG_D_gene: FALSE
  • IG_LV_gene: FALSE
  • IG_V_gene: FALSE
  • IG_V_pseudogene: TRUE
  • TR_V_gene: FALSE
  • TR_V_pseudogene: TRUE
  • three_prime_overlapping_ncrna: FALSE

Filter application: after normalization
Normalization algorithm: DESeq
Normalization arguments: locfunc

• [[list(locfunc = function (x, na.rm = FALSE) standardGeneric("median"))locfunc

Statistical algorithm(s): DESeq
Statistical arguments for DESeq: method, sharingMode, fitType

• method: blind
• sharingMode: fit-only
• fitType: local

Meta-analysis method: no meta-analysis, reported p-values from the first supplied statistical algorithm
Multiple testing correction: Benjamini-Hochberg FDR
p-value threshold: 0.05
Logarithmic tranformation offset: 1
Analysis preset: not available
Quality control plots: multidimensional scaling, biotype detection, biotype counts, sample and biotype saturation, filtered biotypes, correlation heatmap and correlogram, pairwise scatterplots between samples, boxplots, GC-content bias, transcript length bias, mean-difference plot, mean-variance plot, DEG biotype detection, volcano plot, DEG heatmap
Figure format: png, pdf
Output directory: /data/images/proton2/run422/www/metaseqr_run422
Output data: Annotation, p-value, Adjusted p-value (FDR), Fold change, Statistics, Read counts
Output scale(s): log2 scale, Reads per Gene Model
Output values: Normalized values
Output statistics: Mean
Total run time: 31 minutes 32 seconds

Number of filtered genes: 31742 which is the union of

• Filtered because of zero reads: 20256
• Filtered because of exon filters: 0
• Filtered because of gene filters: 11486 which is the union of
  • length: 5148 genes with filter cutoff value 500
  • avg.reads: 352 genes with filter cutoff value 0
  • expression: 8503 genes further decomposed to (filter name, filtered genes, filter cutoff):
  • • median: 8503 genes with filter cutoff value 2
  • biotype: 197 genes with filter cutoff value rRNA, IG_V_pseudogene, TR_V_pseudogene

Number of differentially expressed genes per contrast:

• MalignantWTb_vs_MalignantKOb: 507 (81) statistically significant genes of which 331 (58) up regulated, 141 (23) down regulated and 35 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• healthyWTb_vs_premalignantWTb: 1045 (102) statistically significant genes of which 616 (85) up regulated, 429 (17) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• healthyKOb_vs_premalignantKOb: 1057 (151) statistically significant genes of which 693 (143) up regulated, 359 (8) down regulated and 5 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• healthyWTb_vs_healthyKOb: 184 (2) statistically significant genes of which 89 (0) up regulated, 95 (2) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• premalignantWTb_vs_premalignantKOb: 126 (3) statistically significant genes of which 104 (3) up regulated, 22 (0) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• MalignantWTb_vs_premalignantWTb: 1692 (563) statistically significant genes of which 1290 (474) up regulated, 397 (89) down regulated and 5 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
• healthyKOb_vs_MalignantKOb: 3839 (2009) statistically significant genes of which 1547 (751) up regulated, 2269 (1256) down regulated and 23 (2) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.

[ 2019-07-12 20:13:02 ] INFO 2019-07-12 20:13:02: Data processing started...
[ 2019-07-12 20:13:02 ] INFO Read counts file: imported custom data frame
[ 2019-07-12 20:13:02 ] INFO Conditions: malignantWTb, malignantKOb, healthyWTb, premalignantWTb, healthyKOb, premalignantKOb
[ 2019-07-12 20:13:02 ] INFO Samples to include: AE3R13_L24B, AE3R14_L33B, AE3R15_L43B, AE3R16_L59B, AE3R17_L64B, AE3R18_L9B, AE3R19_L26B, AE3R20_L29B, AE3R21_L54B, AE3R22_L58B, AE3R23_wt, AE3R24_wt, AE3R25_wt, AE3R26_wtpre, AE3R27_wtpre, AE3R28_wtpre, AE3R29_ko, AE3R30_ko, AE3R31_ko, AE3R32_kopre, AE3R33_kopre, AE3R34_kopre
[ 2019-07-12 20:13:02 ] INFO Samples to exclude: none
[ 2019-07-12 20:13:02 ] INFO Requested contrasts: malignantWTb_vs_malignantKOb, healthyWTb_vs_premalignantWTb, healthyKOb_vs_premalignantKOb, healthyWTb_vs_healthyKOb, premalignantWTb_vs_premalignantKOb, healthyWTb_vs_premalignantWTb, malignantWTb_vs_premalignantWTb, healthyKOb_vs_premalignantKOb, healthyKOb_vs_malignantKOb
[ 2019-07-12 20:13:02 ] INFO Annotation: embedded
[ 2019-07-12 20:13:02 ] INFO Organism: custom
[ 2019-07-12 20:13:02 ] INFO Reference source: ensembl
[ 2019-07-12 20:13:02 ] INFO Count type: utr
[ 2019-07-12 20:13:02 ] INFO Exon filters: none applied
[ 2019-07-12 20:13:02 ] INFO Gene filters: length, avg.reads, expression, biotype
[ 2019-07-12 20:13:02 ] INFO length:
[ 2019-07-12 20:13:02 ] INFO length: 500
[ 2019-07-12 20:13:02 ] INFO avg.reads:
[ 2019-07-12 20:13:02 ] INFO average.per.bp: 100
[ 2019-07-12 20:13:02 ] INFO quantile: 0.25
[ 2019-07-12 20:13:02 ] INFO expression:
[ 2019-07-12 20:13:02 ] INFO median: TRUE
[ 2019-07-12 20:13:02 ] INFO mean: FALSE
[ 2019-07-12 20:13:02 ] INFO quantile: NA
[ 2019-07-12 20:13:02 ] INFO known: NA
[ 2019-07-12 20:13:02 ] INFO custom: NA
[ 2019-07-12 20:13:02 ] INFO biotype:
[ 2019-07-12 20:13:02 ] INFO pseudogene: FALSE
[ 2019-07-12 20:13:02 ] INFO snRNA: FALSE
[ 2019-07-12 20:13:02 ] INFO protein_coding: FALSE
[ 2019-07-12 20:13:02 ] INFO antisense: FALSE
[ 2019-07-12 20:13:02 ] INFO miRNA: FALSE
[ 2019-07-12 20:13:02 ] INFO snoRNA: FALSE
[ 2019-07-12 20:13:02 ] INFO lincRNA: FALSE
[ 2019-07-12 20:13:02 ] INFO processed_transcript: FALSE
[ 2019-07-12 20:13:02 ] INFO misc_RNA: FALSE
[ 2019-07-12 20:13:02 ] INFO rRNA: TRUE
[ 2019-07-12 20:13:02 ] INFO sense_intronic: FALSE
[ 2019-07-12 20:13:02 ] INFO sense_overlapping: FALSE
[ 2019-07-12 20:13:02 ] INFO polymorphic_pseudogene: FALSE
[ 2019-07-12 20:13:02 ] INFO IG_C_gene: FALSE
[ 2019-07-12 20:13:02 ] INFO IG_J_gene: FALSE
[ 2019-07-12 20:13:02 ] INFO IG_D_gene: FALSE
[ 2019-07-12 20:13:02 ] INFO IG_LV_gene: FALSE
[ 2019-07-12 20:13:02 ] INFO IG_V_gene: FALSE
[ 2019-07-12 20:13:02 ] INFO IG_V_pseudogene: TRUE
[ 2019-07-12 20:13:02 ] INFO TR_V_gene: FALSE
[ 2019-07-12 20:13:02 ] INFO TR_V_pseudogene: TRUE
[ 2019-07-12 20:13:02 ] INFO three_prime_overlapping_ncrna: FALSE
[ 2019-07-12 20:13:02 ] INFO Filter application: postnorm
[ 2019-07-12 20:13:02 ] INFO Normalization algorithm: deseq
[ 2019-07-12 20:13:02 ] INFO Normalization arguments:
[ 2019-07-12 20:13:02 ] INFO locfunc:
[ 2019-07-12 20:13:02 ] INFO [[
[ 2019-07-12 20:13:02 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median"))
[ 2019-07-12 20:13:02 ] INFO locfunc
[ 2019-07-12 20:13:02 ] INFO Statistical algorithm: deseq
[ 2019-07-12 20:13:02 ] INFO Statistical arguments:
[ 2019-07-12 20:13:02 ] INFO deseq: blind, fit-only, local
[ 2019-07-12 20:13:02 ] INFO Meta-analysis method: none
[ 2019-07-12 20:13:02 ] INFO Multiple testing correction: BH
[ 2019-07-12 20:13:02 ] INFO p-value threshold: 0.05
[ 2019-07-12 20:13:02 ] INFO Logarithmic transformation offset: 1
[ 2019-07-12 20:13:02 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap
[ 2019-07-12 20:13:02 ] INFO Figure format: png, pdf
[ 2019-07-12 20:13:02 ] INFO Output directory: /data/images/proton2/run422/www/metaseqr_run422
[ 2019-07-12 20:13:02 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, stats, counts, flags
[ 2019-07-12 20:13:02 ] INFO Output scale(s): log2, rpgm
[ 2019-07-12 20:13:02 ] INFO Output values: normalized
[ 2019-07-12 20:13:02 ] INFO Output statistics: mean
[ 2019-07-12 20:13:02 ] INFO Reading custom external gene annotation for from /data/results/tools/rnaseq/metaseqr/mm10/gene_data_mm10.txt.gz...
[ 2019-07-12 20:13:04 ] INFO Checking chromosomes in transcript counts and gene annotation...
[ 2019-07-12 20:13:04 ] INFO Processing transcripts...
[ 2019-07-12 20:13:04 ] INFO Separating transcripts (UTR regions) per gene for AE3R13_L24B...
[ 2019-07-12 20:13:21 ] INFO Separating transcripts (UTR regions) per gene for AE3R14_L33B...
[ 2019-07-12 20:13:38 ] INFO Separating transcripts (UTR regions) per gene for AE3R15_L43B...
[ 2019-07-12 20:13:56 ] INFO Separating transcripts (UTR regions) per gene for AE3R16_L59B...
[ 2019-07-12 20:14:15 ] INFO Separating transcripts (UTR regions) per gene for AE3R17_L64B...
[ 2019-07-12 20:14:34 ] INFO Separating transcripts (UTR regions) per gene for AE3R18_L9B...
[ 2019-07-12 20:14:56 ] INFO Separating transcripts (UTR regions) per gene for AE3R19_L26B...
[ 2019-07-12 20:15:17 ] INFO Separating transcripts (UTR regions) per gene for AE3R20_L29B...
[ 2019-07-12 20:15:41 ] INFO Separating transcripts (UTR regions) per gene for AE3R21_L54B...
[ 2019-07-12 20:16:01 ] INFO Separating transcripts (UTR regions) per gene for AE3R22_L58B...
[ 2019-07-12 20:16:25 ] INFO Separating transcripts (UTR regions) per gene for AE3R23_wt...
[ 2019-07-12 20:16:49 ] INFO Separating transcripts (UTR regions) per gene for AE3R24_wt...
[ 2019-07-12 20:17:11 ] INFO Separating transcripts (UTR regions) per gene for AE3R25_wt...
[ 2019-07-12 20:17:36 ] INFO Separating transcripts (UTR regions) per gene for AE3R26_wtpre...
[ 2019-07-12 20:18:00 ] INFO Separating transcripts (UTR regions) per gene for AE3R27_wtpre...
[ 2019-07-12 20:18:24 ] INFO Separating transcripts (UTR regions) per gene for AE3R28_wtpre...
[ 2019-07-12 20:18:50 ] INFO Separating transcripts (UTR regions) per gene for AE3R29_ko...
[ 2019-07-12 20:19:13 ] INFO Separating transcripts (UTR regions) per gene for AE3R30_ko...
[ 2019-07-12 20:19:34 ] INFO Separating transcripts (UTR regions) per gene for AE3R31_ko...
[ 2019-07-12 20:19:58 ] INFO Separating transcripts (UTR regions) per gene for AE3R32_kopre...
[ 2019-07-12 20:20:22 ] INFO Separating transcripts (UTR regions) per gene for AE3R33_kopre...
[ 2019-07-12 20:20:46 ] INFO Separating transcripts (UTR regions) per gene for AE3R34_kopre...
[ 2019-07-12 20:21:10 ] INFO Saving gene model to /data/images/proton2/run422/www/metaseqr_run422/data/gene_model.RData
[ 2019-07-12 20:21:16 ] INFO Summarizing count data...
[ 2019-07-12 20:21:48 ] INFO Removing genes with zero counts in all samples...
[ 2019-07-12 20:21:48 ] INFO Normalizing with: deseq
[ 2019-07-12 20:21:48 ] INFO Applying gene filter length...
[ 2019-07-12 20:21:48 ] INFO Threshold below which ignored: 500
[ 2019-07-12 20:21:48 ] INFO Applying gene filter avg.reads...
[ 2019-07-12 20:21:48 ] INFO Threshold below which ignored: 0
[ 2019-07-12 20:21:48 ] INFO Applying gene filter expression...
[ 2019-07-12 20:21:49 ] INFO Threshold below which ignored: 2
[ 2019-07-12 20:21:49 ] INFO Applying gene filter biotype...
[ 2019-07-12 20:21:49 ] INFO Biotypes ignored: rRNA, IG_V_pseudogene, TR_V_pseudogene
[ 2019-07-12 20:21:49 ] INFO 31742 genes filtered out
[ 2019-07-12 20:21:49 ] INFO 17806 genes remain after filtering
[ 2019-07-12 20:21:49 ] INFO Running statistical tests with: deseq
[ 2019-07-12 20:21:49 ] INFO Contrast: malignantWTb_vs_malignantKOb
[ 2019-07-12 20:22:12 ] INFO Contrast: healthyWTb_vs_premalignantWTb
[ 2019-07-12 20:22:27 ] INFO Contrast: healthyKOb_vs_premalignantKOb
[ 2019-07-12 20:22:42 ] INFO Contrast: healthyWTb_vs_healthyKOb
[ 2019-07-12 20:22:56 ] INFO Contrast: premalignantWTb_vs_premalignantKOb
[ 2019-07-12 20:23:11 ] INFO Contrast: healthyWTb_vs_premalignantWTb
[ 2019-07-12 20:23:26 ] INFO Contrast: malignantWTb_vs_premalignantWTb
[ 2019-07-12 20:23:47 ] INFO Contrast: healthyKOb_vs_premalignantKOb
[ 2019-07-12 20:24:02 ] INFO Contrast: healthyKOb_vs_malignantKOb
[ 2019-07-12 20:24:23 ] INFO Contrast malignantWTb_vs_malignantKOb: found 507 genes
[ 2019-07-12 20:24:23 ] INFO Contrast healthyWTb_vs_premalignantWTb: found 1045 genes
[ 2019-07-12 20:24:23 ] INFO Contrast healthyKOb_vs_premalignantKOb: found 1057 genes
[ 2019-07-12 20:24:23 ] INFO Contrast healthyWTb_vs_healthyKOb: found 184 genes
[ 2019-07-12 20:24:23 ] INFO Contrast premalignantWTb_vs_premalignantKOb: found 126 genes
[ 2019-07-12 20:24:23 ] INFO Contrast healthyWTb_vs_premalignantWTb: found 1045 genes
[ 2019-07-12 20:24:23 ] INFO Contrast malignantWTb_vs_premalignantWTb: found 1692 genes
[ 2019-07-12 20:24:23 ] INFO Contrast healthyKOb_vs_premalignantKOb: found 1057 genes
[ 2019-07-12 20:24:23 ] INFO Contrast healthyKOb_vs_malignantKOb: found 3839 genes
[ 2019-07-12 20:28:49 ] INFO 2019-07-12 20:28:49: Data processing started...
[ 2019-07-12 20:28:49 ] INFO Read counts file: imported custom data frame
[ 2019-07-12 20:28:49 ] INFO Conditions: malignantWTb, malignantKOb, healthyWTb, premalignantWTb, healthyKOb, premalignantKOb
[ 2019-07-12 20:28:49 ] INFO Samples to include: AE3R13_L24B, AE3R14_L33B, AE3R15_L43B, AE3R16_L59B, AE3R17_L64B, AE3R18_L9B, AE3R19_L26B, AE3R20_L29B, AE3R21_L54B, AE3R22_L58B, AE3R23_wt, AE3R24_wt, AE3R25_wt, AE3R26_wtpre, AE3R27_wtpre, AE3R28_wtpre, AE3R29_ko, AE3R30_ko, AE3R31_ko, AE3R32_kopre, AE3R33_kopre, AE3R34_kopre
[ 2019-07-12 20:28:49 ] INFO Samples to exclude: none
[ 2019-07-12 20:28:49 ] INFO Requested contrasts: malignantWTb_vs_malignantKOb, healthyWTb_vs_premalignantWTb, healthyKOb_vs_premalignantKOb, healthyWTb_vs_healthyKOb, premalignantWTb_vs_premalignantKOb, healthyWTb_vs_premalignantWTb, malignantWTb_vs_premalignantWTb, healthyKOb_vs_premalignantKOb
[ 2019-07-12 20:28:49 ] INFO Annotation: embedded
[ 2019-07-12 20:28:49 ] INFO Organism: custom
[ 2019-07-12 20:28:49 ] INFO Reference source: ensembl
[ 2019-07-12 20:28:49 ] INFO Count type: utr
[ 2019-07-12 20:28:49 ] INFO Exon filters: none applied
[ 2019-07-12 20:28:49 ] INFO Gene filters: length, avg.reads, expression, biotype
[ 2019-07-12 20:28:49 ] INFO length:
[ 2019-07-12 20:28:49 ] INFO length: 500
[ 2019-07-12 20:28:49 ] INFO avg.reads:
[ 2019-07-12 20:28:49 ] INFO average.per.bp: 100
[ 2019-07-12 20:28:49 ] INFO quantile: 0.25
[ 2019-07-12 20:28:49 ] INFO expression:
[ 2019-07-12 20:28:49 ] INFO median: TRUE
[ 2019-07-12 20:28:49 ] INFO mean: FALSE
[ 2019-07-12 20:28:49 ] INFO quantile: NA
[ 2019-07-12 20:28:49 ] INFO known: NA
[ 2019-07-12 20:28:49 ] INFO custom: NA
[ 2019-07-12 20:28:49 ] INFO biotype:
[ 2019-07-12 20:28:49 ] INFO pseudogene: FALSE
[ 2019-07-12 20:28:49 ] INFO snRNA: FALSE
[ 2019-07-12 20:28:49 ] INFO protein_coding: FALSE
[ 2019-07-12 20:28:49 ] INFO antisense: FALSE
[ 2019-07-12 20:28:49 ] INFO miRNA: FALSE
[ 2019-07-12 20:28:49 ] INFO snoRNA: FALSE
[ 2019-07-12 20:28:49 ] INFO lincRNA: FALSE
[ 2019-07-12 20:28:49 ] INFO processed_transcript: FALSE
[ 2019-07-12 20:28:49 ] INFO misc_RNA: FALSE
[ 2019-07-12 20:28:49 ] INFO rRNA: TRUE
[ 2019-07-12 20:28:49 ] INFO sense_intronic: FALSE
[ 2019-07-12 20:28:49 ] INFO sense_overlapping: FALSE
[ 2019-07-12 20:28:49 ] INFO polymorphic_pseudogene: FALSE
[ 2019-07-12 20:28:49 ] INFO IG_C_gene: FALSE
[ 2019-07-12 20:28:49 ] INFO IG_J_gene: FALSE
[ 2019-07-12 20:28:49 ] INFO IG_D_gene: FALSE
[ 2019-07-12 20:28:49 ] INFO IG_LV_gene: FALSE
[ 2019-07-12 20:28:49 ] INFO IG_V_gene: FALSE
[ 2019-07-12 20:28:49 ] INFO IG_V_pseudogene: TRUE
[ 2019-07-12 20:28:49 ] INFO TR_V_gene: FALSE
[ 2019-07-12 20:28:49 ] INFO TR_V_pseudogene: TRUE
[ 2019-07-12 20:28:49 ] INFO three_prime_overlapping_ncrna: FALSE
[ 2019-07-12 20:28:49 ] INFO Filter application: postnorm
[ 2019-07-12 20:28:49 ] INFO Normalization algorithm: deseq
[ 2019-07-12 20:28:49 ] INFO Normalization arguments:
[ 2019-07-12 20:28:49 ] INFO locfunc:
[ 2019-07-12 20:28:49 ] INFO [[
[ 2019-07-12 20:28:49 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median"))
[ 2019-07-12 20:28:49 ] INFO locfunc
[ 2019-07-12 20:28:49 ] INFO Statistical algorithm: deseq
[ 2019-07-12 20:28:49 ] INFO Statistical arguments:
[ 2019-07-12 20:28:49 ] INFO deseq: blind, fit-only, local
[ 2019-07-12 20:28:49 ] INFO Meta-analysis method: none
[ 2019-07-12 20:28:49 ] INFO Multiple testing correction: BH
[ 2019-07-12 20:28:49 ] INFO p-value threshold: 0.05
[ 2019-07-12 20:28:49 ] INFO Logarithmic transformation offset: 1
[ 2019-07-12 20:28:49 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap
[ 2019-07-12 20:28:49 ] INFO Figure format: png, pdf
[ 2019-07-12 20:28:49 ] INFO Output directory: /data/images/proton2/run422/www/metaseqr_run422
[ 2019-07-12 20:28:49 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, stats, counts, flags
[ 2019-07-12 20:28:49 ] INFO Output scale(s): log2, rpgm
[ 2019-07-12 20:28:49 ] INFO Output values: normalized
[ 2019-07-12 20:28:49 ] INFO Output statistics: mean
[ 2019-07-12 20:28:49 ] INFO Reading custom external gene annotation for from /data/results/tools/rnaseq/metaseqr/mm10/gene_data_mm10.txt.gz...
[ 2019-07-12 20:28:50 ] INFO Checking chromosomes in transcript counts and gene annotation...
[ 2019-07-12 20:28:50 ] INFO Processing transcripts...
[ 2019-07-12 20:28:50 ] INFO Separating transcripts (UTR regions) per gene for AE3R13_L24B...
[ 2019-07-12 20:29:09 ] INFO Separating transcripts (UTR regions) per gene for AE3R14_L33B...
[ 2019-07-12 20:29:27 ] INFO Separating transcripts (UTR regions) per gene for AE3R15_L43B...
[ 2019-07-12 20:29:43 ] INFO Separating transcripts (UTR regions) per gene for AE3R16_L59B...
[ 2019-07-12 20:30:02 ] INFO Separating transcripts (UTR regions) per gene for AE3R17_L64B...
[ 2019-07-12 20:30:20 ] INFO Separating transcripts (UTR regions) per gene for AE3R18_L9B...
[ 2019-07-12 20:30:39 ] INFO Separating transcripts (UTR regions) per gene for AE3R19_L26B...
[ 2019-07-12 20:30:55 ] INFO Separating transcripts (UTR regions) per gene for AE3R20_L29B...
[ 2019-07-12 20:31:12 ] INFO Separating transcripts (UTR regions) per gene for AE3R21_L54B...
[ 2019-07-12 20:31:36 ] INFO Separating transcripts (UTR regions) per gene for AE3R22_L58B...
[ 2019-07-12 20:31:59 ] INFO Separating transcripts (UTR regions) per gene for AE3R23_wt...
[ 2019-07-12 20:32:20 ] INFO Separating transcripts (UTR regions) per gene for AE3R24_wt...
[ 2019-07-12 20:32:45 ] INFO Separating transcripts (UTR regions) per gene for AE3R25_wt...
[ 2019-07-12 20:33:09 ] INFO Separating transcripts (UTR regions) per gene for AE3R26_wtpre...
[ 2019-07-12 20:33:34 ] INFO Separating transcripts (UTR regions) per gene for AE3R27_wtpre...
[ 2019-07-12 20:33:57 ] INFO Separating transcripts (UTR regions) per gene for AE3R28_wtpre...
[ 2019-07-12 20:34:22 ] INFO Separating transcripts (UTR regions) per gene for AE3R29_ko...
[ 2019-07-12 20:34:48 ] INFO Separating transcripts (UTR regions) per gene for AE3R30_ko...
[ 2019-07-12 20:35:13 ] INFO Separating transcripts (UTR regions) per gene for AE3R31_ko...
[ 2019-07-12 20:35:34 ] INFO Separating transcripts (UTR regions) per gene for AE3R32_kopre...
[ 2019-07-12 20:35:58 ] INFO Separating transcripts (UTR regions) per gene for AE3R33_kopre...
[ 2019-07-12 20:36:21 ] INFO Separating transcripts (UTR regions) per gene for AE3R34_kopre...
[ 2019-07-12 20:36:45 ] INFO Saving gene model to /data/images/proton2/run422/www/metaseqr_run422/data/gene_model.RData
[ 2019-07-12 20:36:50 ] INFO Summarizing count data...
[ 2019-07-12 20:37:19 ] INFO Removing genes with zero counts in all samples...
[ 2019-07-12 20:37:19 ] INFO Normalizing with: deseq
[ 2019-07-12 20:37:19 ] INFO Applying gene filter length...
[ 2019-07-12 20:37:19 ] INFO Threshold below which ignored: 500
[ 2019-07-12 20:37:19 ] INFO Applying gene filter avg.reads...
[ 2019-07-12 20:37:20 ] INFO Threshold below which ignored: 0
[ 2019-07-12 20:37:20 ] INFO Applying gene filter expression...
[ 2019-07-12 20:37:20 ] INFO Threshold below which ignored: 2
[ 2019-07-12 20:37:20 ] INFO Applying gene filter biotype...
[ 2019-07-12 20:37:20 ] INFO Biotypes ignored: rRNA, IG_V_pseudogene, TR_V_pseudogene
[ 2019-07-12 20:37:20 ] INFO 31742 genes filtered out
[ 2019-07-12 20:37:20 ] INFO 17806 genes remain after filtering
[ 2019-07-12 20:37:20 ] INFO Running statistical tests with: deseq
[ 2019-07-12 20:37:20 ] INFO Contrast: malignantWTb_vs_malignantKOb
[ 2019-07-12 20:37:43 ] INFO Contrast: healthyWTb_vs_premalignantWTb
[ 2019-07-12 20:37:58 ] INFO Contrast: healthyKOb_vs_premalignantKOb
[ 2019-07-12 20:38:12 ] INFO Contrast: healthyWTb_vs_healthyKOb
[ 2019-07-12 20:38:26 ] INFO Contrast: premalignantWTb_vs_premalignantKOb
[ 2019-07-12 20:38:40 ] INFO Contrast: healthyWTb_vs_premalignantWTb
[ 2019-07-12 20:38:55 ] INFO Contrast: malignantWTb_vs_premalignantWTb
[ 2019-07-12 20:39:15 ] INFO Contrast: healthyKOb_vs_premalignantKOb
[ 2019-07-12 20:39:29 ] INFO Contrast malignantWTb_vs_malignantKOb: found 507 genes
[ 2019-07-12 20:39:29 ] INFO Contrast healthyWTb_vs_premalignantWTb: found 1045 genes
[ 2019-07-12 20:39:29 ] INFO Contrast healthyKOb_vs_premalignantKOb: found 1057 genes
[ 2019-07-12 20:39:29 ] INFO Contrast healthyWTb_vs_healthyKOb: found 184 genes
[ 2019-07-12 20:39:29 ] INFO Contrast premalignantWTb_vs_premalignantKOb: found 126 genes
[ 2019-07-12 20:39:29 ] INFO Contrast healthyWTb_vs_premalignantWTb: found 1045 genes
[ 2019-07-12 20:39:29 ] INFO Contrast malignantWTb_vs_premalignantWTb: found 1692 genes
[ 2019-07-12 20:39:29 ] INFO Contrast healthyKOb_vs_premalignantKOb: found 1057 genes
[ 2019-07-12 20:39:41 ] WARN "yes" and "no" for read strandedness have been deprecated. Please use "forward", "forward" or "no". Replacing "yes" with "forward"...
[ 2019-07-12 20:39:41 ] INFO Converting annotation to GenomicRanges object...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R13_L24B-1.bam for sample with name AE3R13_L24B. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R14_L33B-1.bam for sample with name AE3R14_L33B. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R15_L43B-1.bam for sample with name AE3R15_L43B. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R16_L59B-1.bam for sample with name AE3R16_L59B. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R17_L64B-1.bam for sample with name AE3R17_L64B. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R18_L9B-2.bam for sample with name AE3R18_L9B. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R19_L26B-2.bam for sample with name AE3R19_L26B. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R20_L29B-2.bam for sample with name AE3R20_L29B. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R21_L54B-2.bam for sample with name AE3R21_L54B. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R22_L58B-2.bam for sample with name AE3R22_L58B. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R23_wt-1.bam for sample with name AE3R23_wt. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R24_wt-2.bam for sample with name AE3R24_wt. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R25_wt-3.bam for sample with name AE3R25_wt. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R26_wtpre-1.bam for sample with name AE3R26_wtpre. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R27_wtpre-2.bam for sample with name AE3R27_wtpre. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R28_wtpre-3.bam for sample with name AE3R28_wtpre. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R29_ko-1.bam for sample with name AE3R29_ko. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R30_ko-2.bam for sample with name AE3R30_ko. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R31_ko-3.bam for sample with name AE3R31_ko. This might take some time...
[ 2019-07-12 20:39:41 ] INFO Reading bam file AE3R32_kopre-1.bam for sample with name AE3R32_kopre. This might take some time...
[ 2019-07-12 20:39:45 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:45 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:45 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:45 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:45 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:45 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:46 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:46 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:46 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:48 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:48 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:48 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:48 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:48 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:48 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:49 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:49 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:49 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:49 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:49 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:49 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:49 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:49 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:49 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:50 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:50 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:50 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:50 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:50 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:50 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:50 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:50 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:50 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:50 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:50 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:50 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:51 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:51 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:51 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:51 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:51 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:51 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:51 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:51 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:51 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:51 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:51 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:51 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:52 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:52 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:52 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:52 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:52 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:52 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:55 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:55 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:55 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:39:58 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:39:58 ] INFO ...for single-end reads...
[ 2019-07-12 20:39:58 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:40:16 ] INFO Reading bam file AE3R33_kopre-2.bam for sample with name AE3R33_kopre. This might take some time...
[ 2019-07-12 20:40:23 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:40:23 ] INFO ...for single-end reads...
[ 2019-07-12 20:40:23 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:40:26 ] INFO Reading bam file AE3R34_kopre-3.bam for sample with name AE3R34_kopre. This might take some time...
[ 2019-07-12 20:40:34 ] INFO Counting reads overlapping with given annotation...
[ 2019-07-12 20:40:34 ] INFO ...for single-end reads...
[ 2019-07-12 20:40:34 ] INFO ...assuming forward sequenced reads...
[ 2019-07-12 20:41:10 ] INFO 2019-07-12 20:41:10: Data processing started...
[ 2019-07-12 20:41:10 ] INFO Read counts file: imported custom data frame
[ 2019-07-12 20:41:10 ] INFO Conditions: MalignantWTb, MalignantKOb, healthyWTb, premalignantWTb, healthyKOb, premalignantKOb
[ 2019-07-12 20:41:10 ] INFO Samples to include: AE3R13_L24B, AE3R14_L33B, AE3R15_L43B, AE3R16_L59B, AE3R17_L64B, AE3R18_L9B, AE3R19_L26B, AE3R20_L29B, AE3R21_L54B, AE3R22_L58B, AE3R23_wt, AE3R24_wt, AE3R25_wt, AE3R26_wtpre, AE3R27_wtpre, AE3R28_wtpre, AE3R29_ko, AE3R30_ko, AE3R31_ko, AE3R32_kopre, AE3R33_kopre, AE3R34_kopre
[ 2019-07-12 20:41:10 ] INFO Samples to exclude: none
[ 2019-07-12 20:41:10 ] INFO Requested contrasts: MalignantWTb_vs_MalignantKOb, healthyWTb_vs_premalignantWTb, healthyKOb_vs_premalignantKOb, healthyWTb_vs_healthyKOb, premalignantWTb_vs_premalignantKOb, healthyWTb_vs_premalignantWTb, MalignantWTb_vs_premalignantWTb, healthyKOb_vs_premalignantKOb, healthyKOb_vs_MalignantKOb
[ 2019-07-12 20:41:10 ] INFO Annotation: embedded
[ 2019-07-12 20:41:10 ] INFO Organism: custom
[ 2019-07-12 20:41:10 ] INFO Reference source: ensembl
[ 2019-07-12 20:41:10 ] INFO Count type: utr
[ 2019-07-12 20:41:10 ] INFO Exon filters: none applied
[ 2019-07-12 20:41:10 ] INFO Gene filters: length, avg.reads, expression, biotype
[ 2019-07-12 20:41:10 ] INFO length:
[ 2019-07-12 20:41:10 ] INFO length: 500
[ 2019-07-12 20:41:10 ] INFO avg.reads:
[ 2019-07-12 20:41:10 ] INFO average.per.bp: 100
[ 2019-07-12 20:41:10 ] INFO quantile: 0.25
[ 2019-07-12 20:41:10 ] INFO expression:
[ 2019-07-12 20:41:10 ] INFO median: TRUE
[ 2019-07-12 20:41:10 ] INFO mean: FALSE
[ 2019-07-12 20:41:10 ] INFO quantile: NA
[ 2019-07-12 20:41:10 ] INFO known: NA
[ 2019-07-12 20:41:10 ] INFO custom: NA
[ 2019-07-12 20:41:10 ] INFO biotype:
[ 2019-07-12 20:41:10 ] INFO pseudogene: FALSE
[ 2019-07-12 20:41:10 ] INFO snRNA: FALSE
[ 2019-07-12 20:41:10 ] INFO protein_coding: FALSE
[ 2019-07-12 20:41:10 ] INFO antisense: FALSE
[ 2019-07-12 20:41:10 ] INFO miRNA: FALSE
[ 2019-07-12 20:41:10 ] INFO snoRNA: FALSE
[ 2019-07-12 20:41:10 ] INFO lincRNA: FALSE
[ 2019-07-12 20:41:10 ] INFO processed_transcript: FALSE
[ 2019-07-12 20:41:10 ] INFO misc_RNA: FALSE
[ 2019-07-12 20:41:10 ] INFO rRNA: TRUE
[ 2019-07-12 20:41:10 ] INFO sense_intronic: FALSE
[ 2019-07-12 20:41:10 ] INFO sense_overlapping: FALSE
[ 2019-07-12 20:41:10 ] INFO polymorphic_pseudogene: FALSE
[ 2019-07-12 20:41:10 ] INFO IG_C_gene: FALSE
[ 2019-07-12 20:41:10 ] INFO IG_J_gene: FALSE
[ 2019-07-12 20:41:10 ] INFO IG_D_gene: FALSE
[ 2019-07-12 20:41:10 ] INFO IG_LV_gene: FALSE
[ 2019-07-12 20:41:10 ] INFO IG_V_gene: FALSE
[ 2019-07-12 20:41:10 ] INFO IG_V_pseudogene: TRUE
[ 2019-07-12 20:41:10 ] INFO TR_V_gene: FALSE
[ 2019-07-12 20:41:10 ] INFO TR_V_pseudogene: TRUE
[ 2019-07-12 20:41:10 ] INFO three_prime_overlapping_ncrna: FALSE
[ 2019-07-12 20:41:10 ] INFO Filter application: postnorm
[ 2019-07-12 20:41:10 ] INFO Normalization algorithm: deseq
[ 2019-07-12 20:41:10 ] INFO Normalization arguments:
[ 2019-07-12 20:41:10 ] INFO locfunc:
[ 2019-07-12 20:41:10 ] INFO [[
[ 2019-07-12 20:41:10 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median"))
[ 2019-07-12 20:41:10 ] INFO locfunc
[ 2019-07-12 20:41:10 ] INFO Statistical algorithm: deseq
[ 2019-07-12 20:41:10 ] INFO Statistical arguments:
[ 2019-07-12 20:41:10 ] INFO deseq: blind, fit-only, local
[ 2019-07-12 20:41:10 ] INFO Meta-analysis method: none
[ 2019-07-12 20:41:10 ] INFO Multiple testing correction: BH
[ 2019-07-12 20:41:10 ] INFO p-value threshold: 0.05
[ 2019-07-12 20:41:10 ] INFO Logarithmic transformation offset: 1
[ 2019-07-12 20:41:10 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap
[ 2019-07-12 20:41:10 ] INFO Figure format: png, pdf
[ 2019-07-12 20:41:10 ] INFO Output directory: /data/images/proton2/run422/www/metaseqr_run422
[ 2019-07-12 20:41:10 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, stats, counts, flags
[ 2019-07-12 20:41:10 ] INFO Output scale(s): log2, rpgm
[ 2019-07-12 20:41:10 ] INFO Output values: normalized
[ 2019-07-12 20:41:10 ] INFO Output statistics: mean
[ 2019-07-12 20:41:10 ] INFO Reading custom external gene annotation for from /data/results/tools/rnaseq/metaseqr/mm10/gene_data_mm10.txt.gz...
[ 2019-07-12 20:41:12 ] INFO Checking chromosomes in transcript counts and gene annotation...
[ 2019-07-12 20:41:12 ] INFO Processing transcripts...
[ 2019-07-12 20:41:12 ] INFO Separating transcripts (UTR regions) per gene for AE3R13_L24B...
[ 2019-07-12 20:41:31 ] INFO Separating transcripts (UTR regions) per gene for AE3R14_L33B...
[ 2019-07-12 20:41:49 ] INFO Separating transcripts (UTR regions) per gene for AE3R15_L43B...
[ 2019-07-12 20:42:07 ] INFO Separating transcripts (UTR regions) per gene for AE3R16_L59B...
[ 2019-07-12 20:42:25 ] INFO Separating transcripts (UTR regions) per gene for AE3R17_L64B...
[ 2019-07-12 20:42:43 ] INFO Separating transcripts (UTR regions) per gene for AE3R18_L9B...
[ 2019-07-12 20:43:01 ] INFO Separating transcripts (UTR regions) per gene for AE3R19_L26B...
[ 2019-07-12 20:43:19 ] INFO Separating transcripts (UTR regions) per gene for AE3R20_L29B...
[ 2019-07-12 20:43:39 ] INFO Separating transcripts (UTR regions) per gene for AE3R21_L54B...
[ 2019-07-12 20:43:55 ] INFO Separating transcripts (UTR regions) per gene for AE3R22_L58B...
[ 2019-07-12 20:44:14 ] INFO Separating transcripts (UTR regions) per gene for AE3R23_wt...
[ 2019-07-12 20:44:31 ] INFO Separating transcripts (UTR regions) per gene for AE3R24_wt...
[ 2019-07-12 20:44:50 ] INFO Separating transcripts (UTR regions) per gene for AE3R25_wt...
[ 2019-07-12 20:45:08 ] INFO Separating transcripts (UTR regions) per gene for AE3R26_wtpre...
[ 2019-07-12 20:45:26 ] INFO Separating transcripts (UTR regions) per gene for AE3R27_wtpre...
[ 2019-07-12 20:45:43 ] INFO Separating transcripts (UTR regions) per gene for AE3R28_wtpre...
[ 2019-07-12 20:46:00 ] INFO Separating transcripts (UTR regions) per gene for AE3R29_ko...
[ 2019-07-12 20:46:18 ] INFO Separating transcripts (UTR regions) per gene for AE3R30_ko...
[ 2019-07-12 20:46:35 ] INFO Separating transcripts (UTR regions) per gene for AE3R31_ko...
[ 2019-07-12 20:46:54 ] INFO Separating transcripts (UTR regions) per gene for AE3R32_kopre...
[ 2019-07-12 20:47:14 ] INFO Separating transcripts (UTR regions) per gene for AE3R33_kopre...
[ 2019-07-12 20:47:33 ] INFO Separating transcripts (UTR regions) per gene for AE3R34_kopre...
[ 2019-07-12 20:47:51 ] INFO Saving gene model to /data/images/proton2/run422/www/metaseqr_run422/data/gene_model.RData
[ 2019-07-12 20:47:56 ] INFO Summarizing count data...
[ 2019-07-12 20:48:24 ] INFO Removing genes with zero counts in all samples...
[ 2019-07-12 20:48:25 ] INFO Normalizing with: deseq
[ 2019-07-12 20:48:26 ] INFO Applying gene filter length...
[ 2019-07-12 20:48:26 ] INFO Threshold below which ignored: 500
[ 2019-07-12 20:48:26 ] INFO Applying gene filter avg.reads...
[ 2019-07-12 20:48:26 ] INFO Threshold below which ignored: 0
[ 2019-07-12 20:48:26 ] INFO Applying gene filter expression...
[ 2019-07-12 20:48:26 ] INFO Threshold below which ignored: 2
[ 2019-07-12 20:48:26 ] INFO Applying gene filter biotype...
[ 2019-07-12 20:48:26 ] INFO Biotypes ignored: rRNA, IG_V_pseudogene, TR_V_pseudogene
[ 2019-07-12 20:48:26 ] INFO 31742 genes filtered out
[ 2019-07-12 20:48:26 ] INFO 17806 genes remain after filtering
[ 2019-07-12 20:48:26 ] INFO Running statistical tests with: deseq
[ 2019-07-12 20:48:27 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 20:48:52 ] INFO Contrast: healthyWTb_vs_premalignantWTb
[ 2019-07-12 20:49:06 ] INFO Contrast: healthyKOb_vs_premalignantKOb
[ 2019-07-12 20:49:21 ] INFO Contrast: healthyWTb_vs_healthyKOb
[ 2019-07-12 20:49:36 ] INFO Contrast: premalignantWTb_vs_premalignantKOb
[ 2019-07-12 20:49:52 ] INFO Contrast: healthyWTb_vs_premalignantWTb
[ 2019-07-12 20:50:07 ] INFO Contrast: MalignantWTb_vs_premalignantWTb
[ 2019-07-12 20:50:27 ] INFO Contrast: healthyKOb_vs_premalignantKOb
[ 2019-07-12 20:50:42 ] INFO Contrast: healthyKOb_vs_MalignantKOb
[ 2019-07-12 20:51:02 ] INFO Contrast MalignantWTb_vs_MalignantKOb: found 507 genes
[ 2019-07-12 20:51:02 ] INFO Contrast healthyWTb_vs_premalignantWTb: found 1045 genes
[ 2019-07-12 20:51:02 ] INFO Contrast healthyKOb_vs_premalignantKOb: found 1057 genes
[ 2019-07-12 20:51:02 ] INFO Contrast healthyWTb_vs_healthyKOb: found 184 genes
[ 2019-07-12 20:51:02 ] INFO Contrast premalignantWTb_vs_premalignantKOb: found 126 genes
[ 2019-07-12 20:51:02 ] INFO Contrast healthyWTb_vs_premalignantWTb: found 1045 genes
[ 2019-07-12 20:51:02 ] INFO Contrast MalignantWTb_vs_premalignantWTb: found 1692 genes
[ 2019-07-12 20:51:02 ] INFO Contrast healthyKOb_vs_premalignantKOb: found 1057 genes
[ 2019-07-12 20:51:02 ] INFO Contrast healthyKOb_vs_MalignantKOb: found 3839 genes
[ 2019-07-12 20:53:50 ] INFO 2019-07-12 20:53:50: Data processing started...
[ 2019-07-12 20:53:50 ] INFO Read counts file: imported custom data frame
[ 2019-07-12 20:53:50 ] INFO Conditions: MalignantWTb, MalignantKOb, healthyWTb, premalignantWTb, healthyKOb, premalignantKOb
[ 2019-07-12 20:53:50 ] INFO Samples to include: AE3R13_L24B, AE3R14_L33B, AE3R15_L43B, AE3R16_L59B, AE3R17_L64B, AE3R18_L9B, AE3R19_L26B, AE3R20_L29B, AE3R21_L54B, AE3R22_L58B, AE3R23_wt, AE3R24_wt, AE3R25_wt, AE3R26_wtpre, AE3R27_wtpre, AE3R28_wtpre, AE3R29_ko, AE3R30_ko, AE3R31_ko, AE3R32_kopre, AE3R33_kopre, AE3R34_kopre
[ 2019-07-12 20:53:50 ] INFO Samples to exclude: none
[ 2019-07-12 20:53:50 ] INFO Requested contrasts: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 20:53:50 ] INFO Annotation: embedded
[ 2019-07-12 20:53:50 ] INFO Organism: custom
[ 2019-07-12 20:53:50 ] INFO Reference source: ensembl
[ 2019-07-12 20:53:50 ] INFO Count type: utr
[ 2019-07-12 20:53:50 ] INFO Exon filters: none applied
[ 2019-07-12 20:53:50 ] INFO Gene filters: length, avg.reads, expression, biotype
[ 2019-07-12 20:53:50 ] INFO length:
[ 2019-07-12 20:53:50 ] INFO length: 500
[ 2019-07-12 20:53:50 ] INFO avg.reads:
[ 2019-07-12 20:53:50 ] INFO average.per.bp: 100
[ 2019-07-12 20:53:50 ] INFO quantile: 0.25
[ 2019-07-12 20:53:50 ] INFO expression:
[ 2019-07-12 20:53:50 ] INFO median: TRUE
[ 2019-07-12 20:53:50 ] INFO mean: FALSE
[ 2019-07-12 20:53:50 ] INFO quantile: NA
[ 2019-07-12 20:53:50 ] INFO known: NA
[ 2019-07-12 20:53:50 ] INFO custom: NA
[ 2019-07-12 20:53:50 ] INFO biotype:
[ 2019-07-12 20:53:50 ] INFO pseudogene: FALSE
[ 2019-07-12 20:53:50 ] INFO snRNA: FALSE
[ 2019-07-12 20:53:50 ] INFO protein_coding: FALSE
[ 2019-07-12 20:53:50 ] INFO antisense: FALSE
[ 2019-07-12 20:53:50 ] INFO miRNA: FALSE
[ 2019-07-12 20:53:50 ] INFO snoRNA: FALSE
[ 2019-07-12 20:53:50 ] INFO lincRNA: FALSE
[ 2019-07-12 20:53:50 ] INFO processed_transcript: FALSE
[ 2019-07-12 20:53:50 ] INFO misc_RNA: FALSE
[ 2019-07-12 20:53:50 ] INFO rRNA: TRUE
[ 2019-07-12 20:53:50 ] INFO sense_intronic: FALSE
[ 2019-07-12 20:53:50 ] INFO sense_overlapping: FALSE
[ 2019-07-12 20:53:50 ] INFO polymorphic_pseudogene: FALSE
[ 2019-07-12 20:53:50 ] INFO IG_C_gene: FALSE
[ 2019-07-12 20:53:50 ] INFO IG_J_gene: FALSE
[ 2019-07-12 20:53:50 ] INFO IG_D_gene: FALSE
[ 2019-07-12 20:53:50 ] INFO IG_LV_gene: FALSE
[ 2019-07-12 20:53:50 ] INFO IG_V_gene: FALSE
[ 2019-07-12 20:53:50 ] INFO IG_V_pseudogene: TRUE
[ 2019-07-12 20:53:50 ] INFO TR_V_gene: FALSE
[ 2019-07-12 20:53:50 ] INFO TR_V_pseudogene: TRUE
[ 2019-07-12 20:53:50 ] INFO three_prime_overlapping_ncrna: FALSE
[ 2019-07-12 20:53:50 ] INFO Filter application: postnorm
[ 2019-07-12 20:53:50 ] INFO Normalization algorithm: deseq
[ 2019-07-12 20:53:50 ] INFO Normalization arguments:
[ 2019-07-12 20:53:50 ] INFO locfunc:
[ 2019-07-12 20:53:50 ] INFO [[
[ 2019-07-12 20:53:50 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median"))
[ 2019-07-12 20:53:50 ] INFO locfunc
[ 2019-07-12 20:53:50 ] INFO Statistical algorithm: deseq
[ 2019-07-12 20:53:50 ] INFO Statistical arguments:
[ 2019-07-12 20:53:50 ] INFO deseq: blind, fit-only, local
[ 2019-07-12 20:53:50 ] INFO Meta-analysis method: none
[ 2019-07-12 20:53:50 ] INFO Multiple testing correction: BH
[ 2019-07-12 20:53:50 ] INFO p-value threshold: 0.05
[ 2019-07-12 20:53:50 ] INFO Logarithmic transformation offset: 1
[ 2019-07-12 20:53:50 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap
[ 2019-07-12 20:53:50 ] INFO Figure format: png, pdf
[ 2019-07-12 20:53:50 ] INFO Output directory: /data/images/proton2/run422/www/metaseqr_run422
[ 2019-07-12 20:53:50 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, stats, counts, flags
[ 2019-07-12 20:53:50 ] INFO Output scale(s): log2, rpgm
[ 2019-07-12 20:53:50 ] INFO Output values: normalized
[ 2019-07-12 20:53:50 ] INFO Output statistics: mean
[ 2019-07-12 20:53:50 ] INFO Reading custom external gene annotation for from /data/results/tools/rnaseq/metaseqr/mm10/gene_data_mm10.txt.gz...
[ 2019-07-12 20:53:51 ] INFO Checking chromosomes in transcript counts and gene annotation...
[ 2019-07-12 20:53:51 ] INFO Processing transcripts...
[ 2019-07-12 20:53:51 ] INFO Separating transcripts (UTR regions) per gene for AE3R13_L24B...
[ 2019-07-12 20:54:10 ] INFO Separating transcripts (UTR regions) per gene for AE3R14_L33B...
[ 2019-07-12 20:54:31 ] INFO Separating transcripts (UTR regions) per gene for AE3R15_L43B...
[ 2019-07-12 20:54:52 ] INFO Separating transcripts (UTR regions) per gene for AE3R16_L59B...
[ 2019-07-12 20:55:15 ] INFO Separating transcripts (UTR regions) per gene for AE3R17_L64B...
[ 2019-07-12 20:55:36 ] INFO Separating transcripts (UTR regions) per gene for AE3R18_L9B...
[ 2019-07-12 20:55:56 ] INFO Separating transcripts (UTR regions) per gene for AE3R19_L26B...
[ 2019-07-12 20:56:16 ] INFO Separating transcripts (UTR regions) per gene for AE3R20_L29B...
[ 2019-07-12 20:56:39 ] INFO Separating transcripts (UTR regions) per gene for AE3R21_L54B...
[ 2019-07-12 20:57:01 ] INFO Separating transcripts (UTR regions) per gene for AE3R22_L58B...
[ 2019-07-12 20:57:23 ] INFO Separating transcripts (UTR regions) per gene for AE3R23_wt...
[ 2019-07-12 20:57:47 ] INFO Separating transcripts (UTR regions) per gene for AE3R24_wt...
[ 2019-07-12 20:58:10 ] INFO Separating transcripts (UTR regions) per gene for AE3R25_wt...
[ 2019-07-12 20:58:32 ] INFO Separating transcripts (UTR regions) per gene for AE3R26_wtpre...
[ 2019-07-12 20:58:55 ] INFO Separating transcripts (UTR regions) per gene for AE3R27_wtpre...
[ 2019-07-12 20:59:18 ] INFO Separating transcripts (UTR regions) per gene for AE3R28_wtpre...
[ 2019-07-12 20:59:42 ] INFO Separating transcripts (UTR regions) per gene for AE3R29_ko...
[ 2019-07-12 21:00:05 ] INFO Separating transcripts (UTR regions) per gene for AE3R30_ko...
[ 2019-07-12 21:00:31 ] INFO Separating transcripts (UTR regions) per gene for AE3R31_ko...
[ 2019-07-12 21:00:54 ] INFO Separating transcripts (UTR regions) per gene for AE3R32_kopre...
[ 2019-07-12 21:01:18 ] INFO Separating transcripts (UTR regions) per gene for AE3R33_kopre...
[ 2019-07-12 21:01:43 ] INFO Separating transcripts (UTR regions) per gene for AE3R34_kopre...
[ 2019-07-12 21:02:05 ] INFO Saving gene model to /data/images/proton2/run422/www/metaseqr_run422/data/gene_model.RData
[ 2019-07-12 21:02:11 ] INFO Summarizing count data...
[ 2019-07-12 21:02:39 ] INFO Removing genes with zero counts in all samples...
[ 2019-07-12 21:02:39 ] INFO Normalizing with: deseq
[ 2019-07-12 21:02:39 ] INFO Applying gene filter length...
[ 2019-07-12 21:02:39 ] INFO Threshold below which ignored: 500
[ 2019-07-12 21:02:39 ] INFO Applying gene filter avg.reads...
[ 2019-07-12 21:02:40 ] INFO Threshold below which ignored: 0
[ 2019-07-12 21:02:40 ] INFO Applying gene filter expression...
[ 2019-07-12 21:02:40 ] INFO Threshold below which ignored: 2
[ 2019-07-12 21:02:40 ] INFO Applying gene filter biotype...
[ 2019-07-12 21:02:40 ] INFO Biotypes ignored: rRNA, IG_V_pseudogene, TR_V_pseudogene
[ 2019-07-12 21:02:40 ] INFO 31742 genes filtered out
[ 2019-07-12 21:02:40 ] INFO 17806 genes remain after filtering
[ 2019-07-12 21:02:40 ] INFO Running statistical tests with: deseq
[ 2019-07-12 21:02:40 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 21:03:03 ] INFO Contrast MalignantWTb_vs_MalignantKOb: found 507 genes
[ 2019-07-12 21:03:03 ] INFO Building output files...
[ 2019-07-12 21:03:05 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 21:03:05 ] INFO Adding non-filtered data...
[ 2019-07-12 21:03:05 ] INFO binding annotation...
[ 2019-07-12 21:03:06 ] INFO binding p-values...
[ 2019-07-12 21:03:06 ] INFO binding FDRs...
[ 2019-07-12 21:03:06 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 21:03:06 ] INFO binding normalized mean counts...
[ 2019-07-12 21:03:07 ] INFO binding normalized mean counts...
[ 2019-07-12 21:03:07 ] INFO binding all normalized counts for MalignantWTb...
[ 2019-07-12 21:03:08 ] INFO binding all normalized counts for MalignantKOb...
[ 2019-07-12 21:03:09 ] INFO binding filtering flags...
[ 2019-07-12 21:03:11 ] INFO Writing output...
[ 2019-07-12 21:03:11 ] INFO Adding filtered data...
[ 2019-07-12 21:03:11 ] INFO binding annotation...
[ 2019-07-12 21:03:11 ] INFO binding p-values...
[ 2019-07-12 21:03:11 ] INFO binding FDRs...
[ 2019-07-12 21:03:11 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 21:03:11 ] INFO binding normalized mean counts...
[ 2019-07-12 21:03:12 ] INFO binding normalized mean counts...
[ 2019-07-12 21:03:12 ] INFO binding all normalized counts for MalignantWTb...
[ 2019-07-12 21:03:12 ] INFO binding all normalized counts for MalignantKOb...
[ 2019-07-12 21:03:12 ] INFO binding filtering flags...
[ 2019-07-12 21:03:13 ] INFO Writing output...
[ 2019-07-12 21:03:16 ] INFO Creating quality control graphs...
[ 2019-07-12 21:03:16 ] INFO Plotting in png format...
[ 2019-07-12 21:03:16 ] INFO Plotting mds...
[ 2019-07-12 21:03:16 ] INFO Plotting biodetection...
[ 2019-07-12 21:03:19 ] INFO Plotting countsbio...
[ 2019-07-12 21:03:23 ] INFO Plotting saturation...
[ 2019-07-12 21:03:45 ] INFO Plotting readnoise...
[ 2019-07-12 21:03:57 ] INFO Plotting correl...
[ 2019-07-12 21:03:57 ] INFO Plotting pairwise...
[ 2019-07-12 21:07:13 ] INFO Plotting boxplot...
[ 2019-07-12 21:07:13 ] INFO Plotting gcbias...
[ 2019-07-12 21:07:16 ] INFO Plotting lengthbias...
[ 2019-07-12 21:07:17 ] INFO Plotting meandiff...
[ 2019-07-12 21:07:23 ] INFO Plotting meanvar...
[ 2019-07-12 21:08:08 ] INFO Plotting boxplot...
[ 2019-07-12 21:08:09 ] INFO Plotting gcbias...
[ 2019-07-12 21:08:11 ] INFO Plotting lengthbias...
[ 2019-07-12 21:08:13 ] INFO Plotting meandiff...
[ 2019-07-12 21:08:19 ] INFO Plotting meanvar...
[ 2019-07-12 21:09:07 ] INFO Plotting biodist...
[ 2019-07-12 21:09:07 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 21:09:07 ] INFO Plotting volcano...
[ 2019-07-12 21:09:07 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 21:09:08 ] INFO Plotting deheatmap...
[ 2019-07-12 21:09:08 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 21:10:02 ] INFO Plotting filtered...
[ 2019-07-12 21:10:02 ] INFO Plotting in pdf format...
[ 2019-07-12 21:10:02 ] INFO Plotting mds...
[ 2019-07-12 21:10:02 ] INFO Plotting biodetection...
[ 2019-07-12 21:10:03 ] INFO Plotting countsbio...
[ 2019-07-12 21:10:06 ] INFO Plotting saturation...
[ 2019-07-12 21:10:21 ] INFO Plotting readnoise...
[ 2019-07-12 21:10:31 ] INFO Plotting correl...
[ 2019-07-12 21:10:32 ] INFO Plotting pairwise...
[ 2019-07-12 21:12:10 ] INFO Plotting boxplot...
[ 2019-07-12 21:12:10 ] INFO Plotting gcbias...
[ 2019-07-12 21:12:13 ] INFO Plotting lengthbias...
[ 2019-07-12 21:12:16 ] INFO Plotting meandiff...
[ 2019-07-12 21:12:23 ] INFO Plotting meanvar...
[ 2019-07-12 21:13:07 ] INFO Plotting boxplot...
[ 2019-07-12 21:13:07 ] INFO Plotting gcbias...
[ 2019-07-12 21:13:10 ] INFO Plotting lengthbias...
[ 2019-07-12 21:13:13 ] INFO Plotting meandiff...
[ 2019-07-12 21:13:20 ] INFO Plotting meanvar...
[ 2019-07-12 21:14:09 ] INFO Plotting biodist...
[ 2019-07-12 21:14:09 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 21:14:09 ] INFO Plotting volcano...
[ 2019-07-12 21:14:09 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 21:14:09 ] INFO Plotting deheatmap...
[ 2019-07-12 21:14:09 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 21:15:02 ] INFO Plotting filtered...
[ 2019-07-12 21:15:02 ] INFO Creating HTML report...
[ 2019-07-12 21:15:02 ] INFO Compressing figures...
[ 2019-07-12 21:15:05 ] INFO 2019-07-12 21:15:05: Data processing finished!
[ 2019-07-12 21:15:05 ] INFO Total processing time: 21 minutes 15 seconds
[ 2019-07-12 22:49:22 ] INFO 2019-07-12 22:49:22: Data processing started...
[ 2019-07-12 22:49:22 ] INFO Read counts file: imported custom data frame
[ 2019-07-12 22:49:22 ] INFO Conditions: MalignantWTb, MalignantKOb, healthyWTb, premalignantWTb, healthyKOb, premalignantKOb
[ 2019-07-12 22:49:22 ] INFO Samples to include: AE3R13_L24B, AE3R14_L33B, AE3R15_L43B, AE3R16_L59B, AE3R17_L64B, AE3R18_L9B, AE3R19_L26B, AE3R20_L29B, AE3R21_L54B, AE3R22_L58B, AE3R23_wt, AE3R24_wt, AE3R25_wt, AE3R26_wtpre, AE3R27_wtpre, AE3R28_wtpre, AE3R29_ko, AE3R30_ko, AE3R31_ko, AE3R32_kopre, AE3R33_kopre, AE3R34_kopre
[ 2019-07-12 22:49:22 ] INFO Samples to exclude: none
[ 2019-07-12 22:49:22 ] INFO Requested contrasts: MalignantWTb_vs_MalignantKOb, healthyWTb_vs_premalignantWTb, healthyKOb_vs_premalignantKOb, healthyWTb_vs_healthyKOb
[ 2019-07-12 22:49:22 ] INFO Annotation: embedded
[ 2019-07-12 22:49:22 ] INFO Organism: custom
[ 2019-07-12 22:49:22 ] INFO Reference source: ensembl
[ 2019-07-12 22:49:22 ] INFO Count type: utr
[ 2019-07-12 22:49:22 ] INFO Exon filters: none applied
[ 2019-07-12 22:49:22 ] INFO Gene filters: length, avg.reads, expression, biotype
[ 2019-07-12 22:49:22 ] INFO length:
[ 2019-07-12 22:49:22 ] INFO length: 500
[ 2019-07-12 22:49:22 ] INFO avg.reads:
[ 2019-07-12 22:49:22 ] INFO average.per.bp: 100
[ 2019-07-12 22:49:22 ] INFO quantile: 0.25
[ 2019-07-12 22:49:22 ] INFO expression:
[ 2019-07-12 22:49:22 ] INFO median: TRUE
[ 2019-07-12 22:49:22 ] INFO mean: FALSE
[ 2019-07-12 22:49:22 ] INFO quantile: NA
[ 2019-07-12 22:49:22 ] INFO known: NA
[ 2019-07-12 22:49:22 ] INFO custom: NA
[ 2019-07-12 22:49:22 ] INFO biotype:
[ 2019-07-12 22:49:22 ] INFO pseudogene: FALSE
[ 2019-07-12 22:49:22 ] INFO snRNA: FALSE
[ 2019-07-12 22:49:22 ] INFO protein_coding: FALSE
[ 2019-07-12 22:49:22 ] INFO antisense: FALSE
[ 2019-07-12 22:49:22 ] INFO miRNA: FALSE
[ 2019-07-12 22:49:22 ] INFO snoRNA: FALSE
[ 2019-07-12 22:49:23 ] INFO lincRNA: FALSE
[ 2019-07-12 22:49:23 ] INFO processed_transcript: FALSE
[ 2019-07-12 22:49:23 ] INFO misc_RNA: FALSE
[ 2019-07-12 22:49:23 ] INFO rRNA: TRUE
[ 2019-07-12 22:49:23 ] INFO sense_intronic: FALSE
[ 2019-07-12 22:49:23 ] INFO sense_overlapping: FALSE
[ 2019-07-12 22:49:23 ] INFO polymorphic_pseudogene: FALSE
[ 2019-07-12 22:49:23 ] INFO IG_C_gene: FALSE
[ 2019-07-12 22:49:23 ] INFO IG_J_gene: FALSE
[ 2019-07-12 22:49:23 ] INFO IG_D_gene: FALSE
[ 2019-07-12 22:49:23 ] INFO IG_LV_gene: FALSE
[ 2019-07-12 22:49:23 ] INFO IG_V_gene: FALSE
[ 2019-07-12 22:49:23 ] INFO IG_V_pseudogene: TRUE
[ 2019-07-12 22:49:23 ] INFO TR_V_gene: FALSE
[ 2019-07-12 22:49:23 ] INFO TR_V_pseudogene: TRUE
[ 2019-07-12 22:49:23 ] INFO three_prime_overlapping_ncrna: FALSE
[ 2019-07-12 22:49:23 ] INFO Filter application: postnorm
[ 2019-07-12 22:49:23 ] INFO Normalization algorithm: deseq
[ 2019-07-12 22:49:23 ] INFO Normalization arguments:
[ 2019-07-12 22:49:23 ] INFO locfunc:
[ 2019-07-12 22:49:23 ] INFO [[
[ 2019-07-12 22:49:23 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median"))
[ 2019-07-12 22:49:23 ] INFO locfunc
[ 2019-07-12 22:49:23 ] INFO Statistical algorithm: deseq
[ 2019-07-12 22:49:23 ] INFO Statistical arguments:
[ 2019-07-12 22:49:23 ] INFO deseq: blind, fit-only, local
[ 2019-07-12 22:49:23 ] INFO Meta-analysis method: none
[ 2019-07-12 22:49:23 ] INFO Multiple testing correction: BH
[ 2019-07-12 22:49:23 ] INFO p-value threshold: 0.05
[ 2019-07-12 22:49:23 ] INFO Logarithmic transformation offset: 1
[ 2019-07-12 22:49:23 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap
[ 2019-07-12 22:49:23 ] INFO Figure format: png, pdf
[ 2019-07-12 22:49:23 ] INFO Output directory: /data/images/proton2/run422/www/metaseqr_run422
[ 2019-07-12 22:49:23 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, stats, counts, flags
[ 2019-07-12 22:49:23 ] INFO Output scale(s): log2, rpgm
[ 2019-07-12 22:49:23 ] INFO Output values: normalized
[ 2019-07-12 22:49:23 ] INFO Output statistics: mean
[ 2019-07-12 22:49:23 ] INFO Reading custom external gene annotation for from /data/results/tools/rnaseq/metaseqr/mm10/gene_data_mm10.txt.gz...
[ 2019-07-12 22:49:24 ] INFO Checking chromosomes in transcript counts and gene annotation...
[ 2019-07-12 22:49:24 ] INFO Processing transcripts...
[ 2019-07-12 22:49:24 ] INFO Separating transcripts (UTR regions) per gene for AE3R13_L24B...
[ 2019-07-12 22:49:41 ] INFO Separating transcripts (UTR regions) per gene for AE3R14_L33B...
[ 2019-07-12 22:49:57 ] INFO Separating transcripts (UTR regions) per gene for AE3R15_L43B...
[ 2019-07-12 22:50:14 ] INFO Separating transcripts (UTR regions) per gene for AE3R16_L59B...
[ 2019-07-12 22:50:30 ] INFO Separating transcripts (UTR regions) per gene for AE3R17_L64B...
[ 2019-07-12 22:50:45 ] INFO Separating transcripts (UTR regions) per gene for AE3R18_L9B...
[ 2019-07-12 22:51:00 ] INFO Separating transcripts (UTR regions) per gene for AE3R19_L26B...
[ 2019-07-12 22:51:17 ] INFO Separating transcripts (UTR regions) per gene for AE3R20_L29B...
[ 2019-07-12 22:51:38 ] INFO Separating transcripts (UTR regions) per gene for AE3R21_L54B...
[ 2019-07-12 22:51:58 ] INFO Separating transcripts (UTR regions) per gene for AE3R22_L58B...
[ 2019-07-12 22:52:17 ] INFO Separating transcripts (UTR regions) per gene for AE3R23_wt...
[ 2019-07-12 22:52:38 ] INFO Separating transcripts (UTR regions) per gene for AE3R24_wt...
[ 2019-07-12 22:52:59 ] INFO Separating transcripts (UTR regions) per gene for AE3R25_wt...
[ 2019-07-12 22:53:22 ] INFO 2019-07-12 22:53:22: Data processing started...
[ 2019-07-12 22:53:22 ] INFO Read counts file: imported custom data frame
[ 2019-07-12 22:53:22 ] INFO Conditions: MalignantWTb, MalignantKOb, healthyWTb, premalignantWTb, healthyKOb, premalignantKOb
[ 2019-07-12 22:53:22 ] INFO Samples to include: AE3R13_L24B, AE3R14_L33B, AE3R15_L43B, AE3R16_L59B, AE3R17_L64B, AE3R18_L9B, AE3R19_L26B, AE3R20_L29B, AE3R21_L54B, AE3R22_L58B, AE3R23_wt, AE3R24_wt, AE3R25_wt, AE3R26_wtpre, AE3R27_wtpre, AE3R28_wtpre, AE3R29_ko, AE3R30_ko, AE3R31_ko, AE3R32_kopre, AE3R33_kopre, AE3R34_kopre
[ 2019-07-12 22:53:22 ] INFO Samples to exclude: none
[ 2019-07-12 22:53:22 ] INFO Requested contrasts: MalignantWTb_vs_MalignantKOb, healthyWTb_vs_premalignantWTb, healthyKOb_vs_premalignantKOb, healthyWTb_vs_healthyKOb, premalignantWTb_vs_premalignantKOb, MalignantWTb_vs_premalignantWTb, healthyKOb_vs_premalignantKOb, healthyKOb_vs_MalignantKOb
[ 2019-07-12 22:53:22 ] INFO Annotation: embedded
[ 2019-07-12 22:53:22 ] INFO Organism: custom
[ 2019-07-12 22:53:22 ] INFO Reference source: ensembl
[ 2019-07-12 22:53:22 ] INFO Count type: utr
[ 2019-07-12 22:53:22 ] INFO Exon filters: none applied
[ 2019-07-12 22:53:22 ] INFO Gene filters: length, avg.reads, expression, biotype
[ 2019-07-12 22:53:22 ] INFO length:
[ 2019-07-12 22:53:22 ] INFO length: 500
[ 2019-07-12 22:53:22 ] INFO avg.reads:
[ 2019-07-12 22:53:22 ] INFO average.per.bp: 100
[ 2019-07-12 22:53:22 ] INFO quantile: 0.25
[ 2019-07-12 22:53:22 ] INFO expression:
[ 2019-07-12 22:53:22 ] INFO median: TRUE
[ 2019-07-12 22:53:22 ] INFO mean: FALSE
[ 2019-07-12 22:53:22 ] INFO quantile: NA
[ 2019-07-12 22:53:22 ] INFO known: NA
[ 2019-07-12 22:53:22 ] INFO custom: NA
[ 2019-07-12 22:53:22 ] INFO biotype:
[ 2019-07-12 22:53:22 ] INFO pseudogene: FALSE
[ 2019-07-12 22:53:22 ] INFO snRNA: FALSE
[ 2019-07-12 22:53:22 ] INFO protein_coding: FALSE
[ 2019-07-12 22:53:22 ] INFO antisense: FALSE
[ 2019-07-12 22:53:22 ] INFO miRNA: FALSE
[ 2019-07-12 22:53:22 ] INFO snoRNA: FALSE
[ 2019-07-12 22:53:22 ] INFO lincRNA: FALSE
[ 2019-07-12 22:53:22 ] INFO processed_transcript: FALSE
[ 2019-07-12 22:53:22 ] INFO misc_RNA: FALSE
[ 2019-07-12 22:53:22 ] INFO rRNA: TRUE
[ 2019-07-12 22:53:22 ] INFO sense_intronic: FALSE
[ 2019-07-12 22:53:22 ] INFO sense_overlapping: FALSE
[ 2019-07-12 22:53:22 ] INFO polymorphic_pseudogene: FALSE
[ 2019-07-12 22:53:22 ] INFO IG_C_gene: FALSE
[ 2019-07-12 22:53:22 ] INFO IG_J_gene: FALSE
[ 2019-07-12 22:53:22 ] INFO IG_D_gene: FALSE
[ 2019-07-12 22:53:22 ] INFO IG_LV_gene: FALSE
[ 2019-07-12 22:53:22 ] INFO IG_V_gene: FALSE
[ 2019-07-12 22:53:22 ] INFO IG_V_pseudogene: TRUE
[ 2019-07-12 22:53:22 ] INFO TR_V_gene: FALSE
[ 2019-07-12 22:53:22 ] INFO TR_V_pseudogene: TRUE
[ 2019-07-12 22:53:22 ] INFO three_prime_overlapping_ncrna: FALSE
[ 2019-07-12 22:53:22 ] INFO Filter application: postnorm
[ 2019-07-12 22:53:22 ] INFO Normalization algorithm: deseq
[ 2019-07-12 22:53:22 ] INFO Normalization arguments:
[ 2019-07-12 22:53:22 ] INFO locfunc:
[ 2019-07-12 22:53:22 ] INFO [[
[ 2019-07-12 22:53:22 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median"))
[ 2019-07-12 22:53:22 ] INFO locfunc
[ 2019-07-12 22:53:22 ] INFO Statistical algorithm: deseq
[ 2019-07-12 22:53:22 ] INFO Statistical arguments:
[ 2019-07-12 22:53:22 ] INFO deseq: blind, fit-only, local
[ 2019-07-12 22:53:22 ] INFO Meta-analysis method: none
[ 2019-07-12 22:53:22 ] INFO Multiple testing correction: BH
[ 2019-07-12 22:53:22 ] INFO p-value threshold: 0.05
[ 2019-07-12 22:53:22 ] INFO Logarithmic transformation offset: 1
[ 2019-07-12 22:53:22 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap
[ 2019-07-12 22:53:22 ] INFO Figure format: png, pdf
[ 2019-07-12 22:53:22 ] INFO Output directory: /data/images/proton2/run422/www/metaseqr_run422
[ 2019-07-12 22:53:22 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, stats, counts, flags
[ 2019-07-12 22:53:22 ] INFO Output scale(s): log2, rpgm
[ 2019-07-12 22:53:22 ] INFO Output values: normalized
[ 2019-07-12 22:53:22 ] INFO Output statistics: mean
[ 2019-07-12 22:53:22 ] INFO Reading custom external gene annotation for from /data/results/tools/rnaseq/metaseqr/mm10/gene_data_mm10.txt.gz...
[ 2019-07-12 22:53:24 ] INFO Checking chromosomes in transcript counts and gene annotation...
[ 2019-07-12 22:53:24 ] INFO Processing transcripts...
[ 2019-07-12 22:53:24 ] INFO Separating transcripts (UTR regions) per gene for AE3R13_L24B...
[ 2019-07-12 22:53:40 ] INFO Separating transcripts (UTR regions) per gene for AE3R14_L33B...
[ 2019-07-12 22:53:58 ] INFO Separating transcripts (UTR regions) per gene for AE3R15_L43B...
[ 2019-07-12 22:54:14 ] INFO Separating transcripts (UTR regions) per gene for AE3R16_L59B...
[ 2019-07-12 22:54:31 ] INFO Separating transcripts (UTR regions) per gene for AE3R17_L64B...
[ 2019-07-12 22:54:47 ] INFO Separating transcripts (UTR regions) per gene for AE3R18_L9B...
[ 2019-07-12 22:55:05 ] INFO Separating transcripts (UTR regions) per gene for AE3R19_L26B...
[ 2019-07-12 22:55:20 ] INFO Separating transcripts (UTR regions) per gene for AE3R20_L29B...
[ 2019-07-12 22:55:41 ] INFO Separating transcripts (UTR regions) per gene for AE3R21_L54B...
[ 2019-07-12 22:56:01 ] INFO Separating transcripts (UTR regions) per gene for AE3R22_L58B...
[ 2019-07-12 22:56:23 ] INFO Separating transcripts (UTR regions) per gene for AE3R23_wt...
[ 2019-07-12 22:56:44 ] INFO Separating transcripts (UTR regions) per gene for AE3R24_wt...
[ 2019-07-12 22:57:02 ] INFO Separating transcripts (UTR regions) per gene for AE3R25_wt...
[ 2019-07-12 22:57:21 ] INFO Separating transcripts (UTR regions) per gene for AE3R26_wtpre...
[ 2019-07-12 22:57:43 ] INFO Separating transcripts (UTR regions) per gene for AE3R27_wtpre...
[ 2019-07-12 22:58:03 ] INFO Separating transcripts (UTR regions) per gene for AE3R28_wtpre...
[ 2019-07-12 22:58:58 ] INFO 2019-07-12 22:58:58: Data processing started...
[ 2019-07-12 22:58:58 ] INFO Read counts file: imported custom data frame
[ 2019-07-12 22:58:58 ] INFO Conditions: MalignantWTb, MalignantKOb, healthyWTb, premalignantWTb, healthyKOb, premalignantKOb
[ 2019-07-12 22:58:58 ] INFO Samples to include: AE3R13_L24B, AE3R14_L33B, AE3R15_L43B, AE3R16_L59B, AE3R17_L64B, AE3R18_L9B, AE3R19_L26B, AE3R20_L29B, AE3R21_L54B, AE3R22_L58B, AE3R23_wt, AE3R24_wt, AE3R25_wt, AE3R26_wtpre, AE3R27_wtpre, AE3R28_wtpre, AE3R29_ko, AE3R30_ko, AE3R31_ko, AE3R32_kopre, AE3R33_kopre, AE3R34_kopre
[ 2019-07-12 22:58:58 ] INFO Samples to exclude: none
[ 2019-07-12 22:58:58 ] INFO Requested contrasts: MalignantWTb_vs_MalignantKOb, healthyWTb_vs_premalignantWTb, healthyKOb_vs_premalignantKOb, healthyWTb_vs_healthyKOb, premalignantWTb_vs_premalignantKOb, MalignantWTb_vs_premalignantWTb, healthyKOb_vs_MalignantKOb
[ 2019-07-12 22:58:58 ] INFO Annotation: embedded
[ 2019-07-12 22:58:58 ] INFO Organism: custom
[ 2019-07-12 22:58:58 ] INFO Reference source: ensembl
[ 2019-07-12 22:58:58 ] INFO Count type: utr
[ 2019-07-12 22:58:58 ] INFO Exon filters: none applied
[ 2019-07-12 22:58:58 ] INFO Gene filters: length, avg.reads, expression, biotype
[ 2019-07-12 22:58:58 ] INFO length:
[ 2019-07-12 22:58:58 ] INFO length: 500
[ 2019-07-12 22:58:58 ] INFO avg.reads:
[ 2019-07-12 22:58:58 ] INFO average.per.bp: 100
[ 2019-07-12 22:58:58 ] INFO quantile: 0.25
[ 2019-07-12 22:58:58 ] INFO expression:
[ 2019-07-12 22:58:58 ] INFO median: TRUE
[ 2019-07-12 22:58:58 ] INFO mean: FALSE
[ 2019-07-12 22:58:58 ] INFO quantile: NA
[ 2019-07-12 22:58:58 ] INFO known: NA
[ 2019-07-12 22:58:58 ] INFO custom: NA
[ 2019-07-12 22:58:58 ] INFO biotype:
[ 2019-07-12 22:58:58 ] INFO pseudogene: FALSE
[ 2019-07-12 22:58:58 ] INFO snRNA: FALSE
[ 2019-07-12 22:58:58 ] INFO protein_coding: FALSE
[ 2019-07-12 22:58:58 ] INFO antisense: FALSE
[ 2019-07-12 22:58:58 ] INFO miRNA: FALSE
[ 2019-07-12 22:58:58 ] INFO snoRNA: FALSE
[ 2019-07-12 22:58:58 ] INFO lincRNA: FALSE
[ 2019-07-12 22:58:58 ] INFO processed_transcript: FALSE
[ 2019-07-12 22:58:58 ] INFO misc_RNA: FALSE
[ 2019-07-12 22:58:58 ] INFO rRNA: TRUE
[ 2019-07-12 22:58:58 ] INFO sense_intronic: FALSE
[ 2019-07-12 22:58:58 ] INFO sense_overlapping: FALSE
[ 2019-07-12 22:58:58 ] INFO polymorphic_pseudogene: FALSE
[ 2019-07-12 22:58:58 ] INFO IG_C_gene: FALSE
[ 2019-07-12 22:58:58 ] INFO IG_J_gene: FALSE
[ 2019-07-12 22:58:58 ] INFO IG_D_gene: FALSE
[ 2019-07-12 22:58:58 ] INFO IG_LV_gene: FALSE
[ 2019-07-12 22:58:58 ] INFO IG_V_gene: FALSE
[ 2019-07-12 22:58:58 ] INFO IG_V_pseudogene: TRUE
[ 2019-07-12 22:58:58 ] INFO TR_V_gene: FALSE
[ 2019-07-12 22:58:58 ] INFO TR_V_pseudogene: TRUE
[ 2019-07-12 22:58:58 ] INFO three_prime_overlapping_ncrna: FALSE
[ 2019-07-12 22:58:58 ] INFO Filter application: postnorm
[ 2019-07-12 22:58:58 ] INFO Normalization algorithm: deseq
[ 2019-07-12 22:58:58 ] INFO Normalization arguments:
[ 2019-07-12 22:58:58 ] INFO locfunc:
[ 2019-07-12 22:58:58 ] INFO [[
[ 2019-07-12 22:58:58 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median"))
[ 2019-07-12 22:58:58 ] INFO locfunc
[ 2019-07-12 22:58:58 ] INFO Statistical algorithm: deseq
[ 2019-07-12 22:58:58 ] INFO Statistical arguments:
[ 2019-07-12 22:58:58 ] INFO deseq: blind, fit-only, local
[ 2019-07-12 22:58:58 ] INFO Meta-analysis method: none
[ 2019-07-12 22:58:58 ] INFO Multiple testing correction: BH
[ 2019-07-12 22:58:58 ] INFO p-value threshold: 0.05
[ 2019-07-12 22:58:58 ] INFO Logarithmic transformation offset: 1
[ 2019-07-12 22:58:58 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap
[ 2019-07-12 22:58:58 ] INFO Figure format: png, pdf
[ 2019-07-12 22:58:58 ] INFO Output directory: /data/images/proton2/run422/www/metaseqr_run422
[ 2019-07-12 22:58:58 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, stats, counts, flags
[ 2019-07-12 22:58:58 ] INFO Output scale(s): log2, rpgm
[ 2019-07-12 22:58:58 ] INFO Output values: normalized
[ 2019-07-12 22:58:58 ] INFO Output statistics: mean
[ 2019-07-12 22:58:58 ] INFO Reading custom external gene annotation for from /data/results/tools/rnaseq/metaseqr/mm10/gene_data_mm10.txt.gz...
[ 2019-07-12 22:58:59 ] INFO Checking chromosomes in transcript counts and gene annotation...
[ 2019-07-12 22:58:59 ] INFO Processing transcripts...
[ 2019-07-12 22:58:59 ] INFO Separating transcripts (UTR regions) per gene for AE3R13_L24B...
[ 2019-07-12 22:59:23 ] INFO Separating transcripts (UTR regions) per gene for AE3R14_L33B...
[ 2019-07-12 22:59:43 ] INFO Separating transcripts (UTR regions) per gene for AE3R15_L43B...
[ 2019-07-12 23:00:09 ] INFO Separating transcripts (UTR regions) per gene for AE3R16_L59B...
[ 2019-07-12 23:00:32 ] INFO Separating transcripts (UTR regions) per gene for AE3R17_L64B...
[ 2019-07-12 23:00:57 ] INFO Separating transcripts (UTR regions) per gene for AE3R18_L9B...
[ 2019-07-12 23:01:12 ] INFO Separating transcripts (UTR regions) per gene for AE3R19_L26B...
[ 2019-07-12 23:01:30 ] INFO Separating transcripts (UTR regions) per gene for AE3R20_L29B...
[ 2019-07-12 23:01:46 ] INFO Separating transcripts (UTR regions) per gene for AE3R21_L54B...
[ 2019-07-12 23:02:01 ] INFO Separating transcripts (UTR regions) per gene for AE3R22_L58B...
[ 2019-07-12 23:02:18 ] INFO Separating transcripts (UTR regions) per gene for AE3R23_wt...
[ 2019-07-12 23:02:34 ] INFO Separating transcripts (UTR regions) per gene for AE3R24_wt...
[ 2019-07-12 23:02:49 ] INFO Separating transcripts (UTR regions) per gene for AE3R25_wt...
[ 2019-07-12 23:03:06 ] INFO Separating transcripts (UTR regions) per gene for AE3R26_wtpre...
[ 2019-07-12 23:03:21 ] INFO Separating transcripts (UTR regions) per gene for AE3R27_wtpre...
[ 2019-07-12 23:03:38 ] INFO Separating transcripts (UTR regions) per gene for AE3R28_wtpre...
[ 2019-07-12 23:03:54 ] INFO Separating transcripts (UTR regions) per gene for AE3R29_ko...
[ 2019-07-12 23:04:10 ] INFO Separating transcripts (UTR regions) per gene for AE3R30_ko...
[ 2019-07-12 23:04:28 ] INFO Separating transcripts (UTR regions) per gene for AE3R31_ko...
[ 2019-07-12 23:04:44 ] INFO Separating transcripts (UTR regions) per gene for AE3R32_kopre...
[ 2019-07-12 23:05:01 ] INFO Separating transcripts (UTR regions) per gene for AE3R33_kopre...
[ 2019-07-12 23:05:19 ] INFO Separating transcripts (UTR regions) per gene for AE3R34_kopre...
[ 2019-07-12 23:05:35 ] INFO Saving gene model to /data/images/proton2/run422/www/metaseqr_run422/data/gene_model.RData
[ 2019-07-12 23:05:40 ] INFO Summarizing count data...
[ 2019-07-12 23:06:21 ] INFO Removing genes with zero counts in all samples...
[ 2019-07-12 23:06:22 ] INFO Normalizing with: deseq
[ 2019-07-12 23:06:22 ] INFO Applying gene filter length...
[ 2019-07-12 23:06:22 ] INFO Threshold below which ignored: 500
[ 2019-07-12 23:06:22 ] INFO Applying gene filter avg.reads...
[ 2019-07-12 23:06:22 ] INFO Threshold below which ignored: 0
[ 2019-07-12 23:06:22 ] INFO Applying gene filter expression...
[ 2019-07-12 23:06:22 ] INFO Threshold below which ignored: 2
[ 2019-07-12 23:06:22 ] INFO Applying gene filter biotype...
[ 2019-07-12 23:06:22 ] INFO Biotypes ignored: rRNA, IG_V_pseudogene, TR_V_pseudogene
[ 2019-07-12 23:06:22 ] INFO 31742 genes filtered out
[ 2019-07-12 23:06:22 ] INFO 17806 genes remain after filtering
[ 2019-07-12 23:06:22 ] INFO Running statistical tests with: deseq
[ 2019-07-12 23:06:23 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 23:06:46 ] INFO Contrast: healthyWTb_vs_premalignantWTb
[ 2019-07-12 23:07:00 ] INFO Contrast: healthyKOb_vs_premalignantKOb
[ 2019-07-12 23:07:14 ] INFO Contrast: healthyWTb_vs_healthyKOb
[ 2019-07-12 23:07:28 ] INFO Contrast: premalignantWTb_vs_premalignantKOb
[ 2019-07-12 23:07:43 ] INFO Contrast: MalignantWTb_vs_premalignantWTb
[ 2019-07-12 23:08:02 ] INFO Contrast: healthyKOb_vs_MalignantKOb
[ 2019-07-12 23:08:22 ] INFO Contrast MalignantWTb_vs_MalignantKOb: found 507 genes
[ 2019-07-12 23:08:22 ] INFO Contrast healthyWTb_vs_premalignantWTb: found 1045 genes
[ 2019-07-12 23:08:22 ] INFO Contrast healthyKOb_vs_premalignantKOb: found 1057 genes
[ 2019-07-12 23:08:22 ] INFO Contrast healthyWTb_vs_healthyKOb: found 184 genes
[ 2019-07-12 23:08:22 ] INFO Contrast premalignantWTb_vs_premalignantKOb: found 126 genes
[ 2019-07-12 23:08:22 ] INFO Contrast MalignantWTb_vs_premalignantWTb: found 1692 genes
[ 2019-07-12 23:08:22 ] INFO Contrast healthyKOb_vs_MalignantKOb: found 3839 genes
[ 2019-07-12 23:08:23 ] INFO Building output files...
[ 2019-07-12 23:08:25 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 23:08:25 ] INFO Adding non-filtered data...
[ 2019-07-12 23:08:25 ] INFO binding annotation...
[ 2019-07-12 23:08:25 ] INFO binding p-values...
[ 2019-07-12 23:08:25 ] INFO binding FDRs...
[ 2019-07-12 23:08:26 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 23:08:26 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:26 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:27 ] INFO binding all normalized counts for MalignantWTb...
[ 2019-07-12 23:08:28 ] INFO binding all normalized counts for MalignantKOb...
[ 2019-07-12 23:08:29 ] INFO binding filtering flags...
[ 2019-07-12 23:08:30 ] INFO Writing output...
[ 2019-07-12 23:08:30 ] INFO Adding filtered data...
[ 2019-07-12 23:08:30 ] INFO binding annotation...
[ 2019-07-12 23:08:30 ] INFO binding p-values...
[ 2019-07-12 23:08:30 ] INFO binding FDRs...
[ 2019-07-12 23:08:30 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 23:08:30 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:31 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:32 ] INFO binding all normalized counts for MalignantWTb...
[ 2019-07-12 23:08:32 ] INFO binding all normalized counts for MalignantKOb...
[ 2019-07-12 23:08:32 ] INFO binding filtering flags...
[ 2019-07-12 23:08:33 ] INFO Writing output...
[ 2019-07-12 23:08:35 ] INFO Contrast: healthyWTb_vs_premalignantWTb
[ 2019-07-12 23:08:35 ] INFO Adding non-filtered data...
[ 2019-07-12 23:08:35 ] INFO binding annotation...
[ 2019-07-12 23:08:36 ] INFO binding p-values...
[ 2019-07-12 23:08:36 ] INFO binding FDRs...
[ 2019-07-12 23:08:37 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 23:08:37 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:37 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:38 ] INFO binding all normalized counts for healthyWTb...
[ 2019-07-12 23:08:38 ] INFO binding all normalized counts for premalignantWTb...
[ 2019-07-12 23:08:39 ] INFO binding filtering flags...
[ 2019-07-12 23:08:40 ] INFO Writing output...
[ 2019-07-12 23:08:40 ] INFO Adding filtered data...
[ 2019-07-12 23:08:40 ] INFO binding annotation...
[ 2019-07-12 23:08:40 ] INFO binding p-values...
[ 2019-07-12 23:08:40 ] INFO binding FDRs...
[ 2019-07-12 23:08:40 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 23:08:40 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:41 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:42 ] INFO binding all normalized counts for healthyWTb...
[ 2019-07-12 23:08:42 ] INFO binding all normalized counts for premalignantWTb...
[ 2019-07-12 23:08:42 ] INFO binding filtering flags...
[ 2019-07-12 23:08:42 ] INFO Writing output...
[ 2019-07-12 23:08:44 ] INFO Contrast: healthyKOb_vs_premalignantKOb
[ 2019-07-12 23:08:44 ] INFO Adding non-filtered data...
[ 2019-07-12 23:08:44 ] INFO binding annotation...
[ 2019-07-12 23:08:45 ] INFO binding p-values...
[ 2019-07-12 23:08:45 ] INFO binding FDRs...
[ 2019-07-12 23:08:46 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 23:08:46 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:46 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:47 ] INFO binding all normalized counts for healthyKOb...
[ 2019-07-12 23:08:47 ] INFO binding all normalized counts for premalignantKOb...
[ 2019-07-12 23:08:48 ] INFO binding filtering flags...
[ 2019-07-12 23:08:49 ] INFO Writing output...
[ 2019-07-12 23:08:49 ] INFO Adding filtered data...
[ 2019-07-12 23:08:49 ] INFO binding annotation...
[ 2019-07-12 23:08:49 ] INFO binding p-values...
[ 2019-07-12 23:08:49 ] INFO binding FDRs...
[ 2019-07-12 23:08:49 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 23:08:49 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:50 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:51 ] INFO binding all normalized counts for healthyKOb...
[ 2019-07-12 23:08:51 ] INFO binding all normalized counts for premalignantKOb...
[ 2019-07-12 23:08:51 ] INFO binding filtering flags...
[ 2019-07-12 23:08:51 ] INFO Writing output...
[ 2019-07-12 23:08:53 ] INFO Contrast: healthyWTb_vs_healthyKOb
[ 2019-07-12 23:08:53 ] INFO Adding non-filtered data...
[ 2019-07-12 23:08:53 ] INFO binding annotation...
[ 2019-07-12 23:08:54 ] INFO binding p-values...
[ 2019-07-12 23:08:54 ] INFO binding FDRs...
[ 2019-07-12 23:08:55 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 23:08:55 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:55 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:56 ] INFO binding all normalized counts for healthyWTb...
[ 2019-07-12 23:08:57 ] INFO binding all normalized counts for healthyKOb...
[ 2019-07-12 23:08:57 ] INFO binding filtering flags...
[ 2019-07-12 23:08:58 ] INFO Writing output...
[ 2019-07-12 23:08:58 ] INFO Adding filtered data...
[ 2019-07-12 23:08:58 ] INFO binding annotation...
[ 2019-07-12 23:08:58 ] INFO binding p-values...
[ 2019-07-12 23:08:58 ] INFO binding FDRs...
[ 2019-07-12 23:08:58 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 23:08:58 ] INFO binding normalized mean counts...
[ 2019-07-12 23:08:59 ] INFO binding normalized mean counts...
[ 2019-07-12 23:09:00 ] INFO binding all normalized counts for healthyWTb...
[ 2019-07-12 23:09:00 ] INFO binding all normalized counts for healthyKOb...
[ 2019-07-12 23:09:00 ] INFO binding filtering flags...
[ 2019-07-12 23:09:00 ] INFO Writing output...
[ 2019-07-12 23:09:02 ] INFO Contrast: premalignantWTb_vs_premalignantKOb
[ 2019-07-12 23:09:02 ] INFO Adding non-filtered data...
[ 2019-07-12 23:09:02 ] INFO binding annotation...
[ 2019-07-12 23:09:03 ] INFO binding p-values...
[ 2019-07-12 23:09:03 ] INFO binding FDRs...
[ 2019-07-12 23:09:04 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 23:09:04 ] INFO binding normalized mean counts...
[ 2019-07-12 23:09:04 ] INFO binding normalized mean counts...
[ 2019-07-12 23:09:05 ] INFO binding all normalized counts for premalignantWTb...
[ 2019-07-12 23:09:06 ] INFO binding all normalized counts for premalignantKOb...
[ 2019-07-12 23:09:06 ] INFO binding filtering flags...
[ 2019-07-12 23:09:07 ] INFO Writing output...
[ 2019-07-12 23:09:07 ] INFO Adding filtered data...
[ 2019-07-12 23:09:07 ] INFO binding annotation...
[ 2019-07-12 23:09:07 ] INFO binding p-values...
[ 2019-07-12 23:09:07 ] INFO binding FDRs...
[ 2019-07-12 23:09:08 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 23:09:08 ] INFO binding normalized mean counts...
[ 2019-07-12 23:09:08 ] INFO binding normalized mean counts...
[ 2019-07-12 23:09:09 ] INFO binding all normalized counts for premalignantWTb...
[ 2019-07-12 23:09:09 ] INFO binding all normalized counts for premalignantKOb...
[ 2019-07-12 23:09:09 ] INFO binding filtering flags...
[ 2019-07-12 23:09:10 ] INFO Writing output...
[ 2019-07-12 23:09:12 ] INFO Contrast: MalignantWTb_vs_premalignantWTb
[ 2019-07-12 23:09:12 ] INFO Adding non-filtered data...
[ 2019-07-12 23:09:12 ] INFO binding annotation...
[ 2019-07-12 23:09:13 ] INFO binding p-values...
[ 2019-07-12 23:09:13 ] INFO binding FDRs...
[ 2019-07-12 23:09:13 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 23:09:13 ] INFO binding normalized mean counts...
[ 2019-07-12 23:09:14 ] INFO binding normalized mean counts...
[ 2019-07-12 23:09:15 ] INFO binding all normalized counts for MalignantWTb...
[ 2019-07-12 23:09:16 ] INFO binding all normalized counts for premalignantWTb...
[ 2019-07-12 23:09:17 ] INFO binding filtering flags...
[ 2019-07-12 23:09:18 ] INFO Writing output...
[ 2019-07-12 23:09:18 ] INFO Adding filtered data...
[ 2019-07-12 23:09:18 ] INFO binding annotation...
[ 2019-07-12 23:09:18 ] INFO binding p-values...
[ 2019-07-12 23:09:18 ] INFO binding FDRs...
[ 2019-07-12 23:09:19 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 23:09:19 ] INFO binding normalized mean counts...
[ 2019-07-12 23:09:19 ] INFO binding normalized mean counts...
[ 2019-07-12 23:09:20 ] INFO binding all normalized counts for MalignantWTb...
[ 2019-07-12 23:09:20 ] INFO binding all normalized counts for premalignantWTb...
[ 2019-07-12 23:09:20 ] INFO binding filtering flags...
[ 2019-07-12 23:09:21 ] INFO Writing output...
[ 2019-07-12 23:09:23 ] INFO Contrast: healthyKOb_vs_MalignantKOb
[ 2019-07-12 23:09:23 ] INFO Adding non-filtered data...
[ 2019-07-12 23:09:23 ] INFO binding annotation...
[ 2019-07-12 23:09:24 ] INFO binding p-values...
[ 2019-07-12 23:09:24 ] INFO binding FDRs...
[ 2019-07-12 23:09:25 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 23:09:25 ] INFO binding normalized mean counts...
[ 2019-07-12 23:09:25 ] INFO binding normalized mean counts...
[ 2019-07-12 23:09:26 ] INFO binding all normalized counts for healthyKOb...
[ 2019-07-12 23:09:27 ] INFO binding all normalized counts for MalignantKOb...
[ 2019-07-12 23:09:28 ] INFO binding filtering flags...
[ 2019-07-12 23:09:29 ] INFO Writing output...
[ 2019-07-12 23:09:29 ] INFO Adding filtered data...
[ 2019-07-12 23:09:29 ] INFO binding annotation...
[ 2019-07-12 23:09:29 ] INFO binding p-values...
[ 2019-07-12 23:09:29 ] INFO binding FDRs...
[ 2019-07-12 23:09:30 ] INFO binding log2 normalized fold changes...
[ 2019-07-12 23:09:30 ] INFO binding normalized mean counts...
[ 2019-07-12 23:09:31 ] INFO binding normalized mean counts...
[ 2019-07-12 23:09:31 ] INFO binding all normalized counts for healthyKOb...
[ 2019-07-12 23:09:31 ] INFO binding all normalized counts for MalignantKOb...
[ 2019-07-12 23:09:31 ] INFO binding filtering flags...
[ 2019-07-12 23:09:32 ] INFO Writing output...
[ 2019-07-12 23:09:34 ] INFO Creating quality control graphs...
[ 2019-07-12 23:09:34 ] INFO Plotting in png format...
[ 2019-07-12 23:09:34 ] INFO Plotting mds...
[ 2019-07-12 23:09:35 ] INFO Plotting biodetection...
[ 2019-07-12 23:09:38 ] INFO Plotting countsbio...
[ 2019-07-12 23:09:42 ] INFO Plotting saturation...
[ 2019-07-12 23:09:58 ] INFO Plotting readnoise...
[ 2019-07-12 23:10:07 ] INFO Plotting correl...
[ 2019-07-12 23:10:08 ] INFO Plotting pairwise...
[ 2019-07-12 23:13:18 ] INFO Plotting boxplot...
[ 2019-07-12 23:13:19 ] INFO Plotting gcbias...
[ 2019-07-12 23:13:21 ] INFO Plotting lengthbias...
[ 2019-07-12 23:13:23 ] INFO Plotting meandiff...
[ 2019-07-12 23:13:29 ] INFO Plotting meanvar...
[ 2019-07-12 23:14:17 ] INFO Plotting boxplot...
[ 2019-07-12 23:14:18 ] INFO Plotting gcbias...
[ 2019-07-12 23:14:20 ] INFO Plotting lengthbias...
[ 2019-07-12 23:14:22 ] INFO Plotting meandiff...
[ 2019-07-12 23:14:27 ] INFO Plotting meanvar...
[ 2019-07-12 23:15:13 ] INFO Plotting biodist...
[ 2019-07-12 23:15:13 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 23:15:14 ] INFO Contrast: healthyWTb_vs_premalignantWTb
[ 2019-07-12 23:15:14 ] INFO Contrast: healthyKOb_vs_premalignantKOb
[ 2019-07-12 23:15:14 ] INFO Contrast: healthyWTb_vs_healthyKOb
[ 2019-07-12 23:15:15 ] INFO Contrast: premalignantWTb_vs_premalignantKOb
[ 2019-07-12 23:15:15 ] INFO Contrast: MalignantWTb_vs_premalignantWTb
[ 2019-07-12 23:15:15 ] INFO Contrast: healthyKOb_vs_MalignantKOb
[ 2019-07-12 23:15:16 ] INFO Plotting volcano...
[ 2019-07-12 23:15:16 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 23:15:16 ] INFO Contrast: healthyWTb_vs_premalignantWTb
[ 2019-07-12 23:15:17 ] INFO Contrast: healthyKOb_vs_premalignantKOb
[ 2019-07-12 23:15:17 ] INFO Contrast: healthyWTb_vs_healthyKOb
[ 2019-07-12 23:15:18 ] INFO Contrast: premalignantWTb_vs_premalignantKOb
[ 2019-07-12 23:15:19 ] INFO Contrast: MalignantWTb_vs_premalignantWTb
[ 2019-07-12 23:15:19 ] INFO Contrast: healthyKOb_vs_MalignantKOb
[ 2019-07-12 23:15:20 ] INFO Plotting deheatmap...
[ 2019-07-12 23:15:20 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 23:16:10 ] INFO Contrast: healthyWTb_vs_premalignantWTb
[ 2019-07-12 23:16:54 ] INFO Contrast: healthyKOb_vs_premalignantKOb
[ 2019-07-12 23:17:38 ] INFO Contrast: healthyWTb_vs_healthyKOb
[ 2019-07-12 23:18:22 ] INFO Contrast: premalignantWTb_vs_premalignantKOb
[ 2019-07-12 23:19:06 ] INFO Contrast: MalignantWTb_vs_premalignantWTb
[ 2019-07-12 23:19:54 ] INFO Contrast: healthyKOb_vs_MalignantKOb
[ 2019-07-12 23:20:41 ] INFO Plotting filtered...
[ 2019-07-12 23:20:41 ] INFO Plotting in pdf format...
[ 2019-07-12 23:20:41 ] INFO Plotting mds...
[ 2019-07-12 23:20:41 ] INFO Plotting biodetection...
[ 2019-07-12 23:20:43 ] INFO Plotting countsbio...
[ 2019-07-12 23:20:45 ] INFO Plotting saturation...
[ 2019-07-12 23:21:01 ] INFO Plotting readnoise...
[ 2019-07-12 23:21:11 ] INFO Plotting correl...
[ 2019-07-12 23:21:11 ] INFO Plotting pairwise...
[ 2019-07-12 23:22:48 ] INFO Plotting boxplot...
[ 2019-07-12 23:22:48 ] INFO Plotting gcbias...
[ 2019-07-12 23:22:51 ] INFO Plotting lengthbias...
[ 2019-07-12 23:22:54 ] INFO Plotting meandiff...
[ 2019-07-12 23:23:02 ] INFO Plotting meanvar...
[ 2019-07-12 23:23:53 ] INFO Plotting boxplot...
[ 2019-07-12 23:23:53 ] INFO Plotting gcbias...
[ 2019-07-12 23:23:57 ] INFO Plotting lengthbias...
[ 2019-07-12 23:23:59 ] INFO Plotting meandiff...
[ 2019-07-12 23:24:08 ] INFO Plotting meanvar...
[ 2019-07-12 23:24:59 ] INFO Plotting biodist...
[ 2019-07-12 23:24:59 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 23:24:59 ] INFO Contrast: healthyWTb_vs_premalignantWTb
[ 2019-07-12 23:25:00 ] INFO Contrast: healthyKOb_vs_premalignantKOb
[ 2019-07-12 23:25:00 ] INFO Contrast: healthyWTb_vs_healthyKOb
[ 2019-07-12 23:25:00 ] INFO Contrast: premalignantWTb_vs_premalignantKOb
[ 2019-07-12 23:25:00 ] INFO Contrast: MalignantWTb_vs_premalignantWTb
[ 2019-07-12 23:25:01 ] INFO Contrast: healthyKOb_vs_MalignantKOb
[ 2019-07-12 23:25:01 ] INFO Plotting volcano...
[ 2019-07-12 23:25:01 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 23:25:01 ] INFO Contrast: healthyWTb_vs_premalignantWTb
[ 2019-07-12 23:25:02 ] INFO Contrast: healthyKOb_vs_premalignantKOb
[ 2019-07-12 23:25:02 ] INFO Contrast: healthyWTb_vs_healthyKOb
[ 2019-07-12 23:25:02 ] INFO Contrast: premalignantWTb_vs_premalignantKOb
[ 2019-07-12 23:25:03 ] INFO Contrast: MalignantWTb_vs_premalignantWTb
[ 2019-07-12 23:25:03 ] INFO Contrast: healthyKOb_vs_MalignantKOb
[ 2019-07-12 23:25:03 ] INFO Plotting deheatmap...
[ 2019-07-12 23:25:03 ] INFO Contrast: MalignantWTb_vs_MalignantKOb
[ 2019-07-12 23:25:57 ] INFO Contrast: healthyWTb_vs_premalignantWTb
[ 2019-07-12 23:26:40 ] INFO Contrast: healthyKOb_vs_premalignantKOb
[ 2019-07-12 23:27:24 ] INFO Contrast: healthyWTb_vs_healthyKOb
[ 2019-07-12 23:28:08 ] INFO Contrast: premalignantWTb_vs_premalignantKOb
[ 2019-07-12 23:28:51 ] INFO Contrast: MalignantWTb_vs_premalignantWTb
[ 2019-07-12 23:29:37 ] INFO Contrast: healthyKOb_vs_MalignantKOb
[ 2019-07-12 23:30:27 ] INFO Plotting filtered...
[ 2019-07-12 23:30:27 ] INFO Creating HTML report...
[ 2019-07-12 23:30:27 ] INFO Compressing figures...

Get all the figures in png, pdf format.