Example Run
**************************************************
Launching PinAPL-Py v2.9
P. Spahn et al., UC San Diego (05/2019)
**************************************************
**************************************************
Running character sanity check ...
**************************************************
No special characters found.
Character sanity check completed.
**************************************************
Reading sample definition input ...
**************************************************
Found sample Control_1
Found sample Control_2
Found sample ToxA_1
Found sample ToxA_2
Found sample ToxB_1
Found sample ToxB_2
Sample definition completed.
**************************************************
Running sequence quality control ...
**************************************************
Started analysis of Control_R2_S15_L008_R1_001_x.fastq.gz
Approx 5% complete for Control_R2_S15_L008_R1_001_x.fastq.gz
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Analysis complete for Control_R2_S15_L008_R1_001_x.fastq.gz
Started analysis of ToxB_R1_98_S4_L008_R1_001_x.fastq.gz
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Analysis complete for ToxB_R1_98_S4_L008_R1_001_x.fastq.gz
Started analysis of ToxB_R2_S4_L005_R1_001_x.fastq.gz
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Analysis complete for ToxB_R2_S4_L005_R1_001_x.fastq.gz
Started analysis of ToxA_R1_98_S2_L008_R1_001_x.fastq.gz
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Analysis complete for ToxA_R1_98_S2_L008_R1_001_x.fastq.gz
Started analysis of Control_R1_S14_L008_R1_001_x.fastq.gz
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Analysis complete for Control_R1_S14_L008_R1_001_x.fastq.gz
Started analysis of ToxA_R2_S2_L005_R1_001_x.fastq.gz
Approx 5% complete for ToxA_R2_S2_L005_R1_001_x.fastq.gz
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Analysis complete for ToxA_R2_S2_L005_R1_001_x.fastq.gz
------------------------------------------------
Script completed.
Time elapsed (Quality control) [secs]: 43.755
Sequence quality control completed.
**************************************************
Trimming reads ...
**************************************************
Loading Control_R2_S15_L008_R1_001_x.fastq.gz
Loading ToxB_R1_98_S4_L008_R1_001_x.fastq.gz
Loading ToxB_R2_S4_L005_R1_001_x.fastq.gz
Loading ToxA_R1_98_S2_L008_R1_001_x.fastq.gz
Loading Control_R1_S14_L008_R1_001_x.fastq.gz
Loading ToxA_R2_S2_L005_R1_001_x.fastq.gz
Removing adapters ...
Extracting 20 bp sgRNA sequences ...
Adapter removal completed.
Writing logfiles...
------------------------------------------------
Script completed.
Time elapsed (Read trimming) [secs]: 25.356
Read trimming completed.
**************************************************
Mapping reads to library ...
**************************************************
Processing sample Control_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Aligning reads to library ...
499804 reads; of these:
499804 (100.00%) were unpaired; of these:
26942 (5.39%) aligned 0 times
408554 (81.74%) aligned exactly 1 time
64308 (12.87%) aligned >1 times
94.61% overall alignment rate
Alignment completed.
Time elapsed (Alignment) [secs]: 6.165
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 7.021
Processing sample Control_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Aligning reads to library ...
499792 reads; of these:
499792 (100.00%) were unpaired; of these:
28504 (5.70%) aligned 0 times
405699 (81.17%) aligned exactly 1 time
65589 (13.12%) aligned >1 times
94.30% overall alignment rate
Alignment completed.
Time elapsed (Alignment) [secs]: 6.298
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 6.699
Processing sample ToxA_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Aligning reads to library ...
499290 reads; of these:
499290 (100.00%) were unpaired; of these:
21646 (4.34%) aligned 0 times
411555 (82.43%) aligned exactly 1 time
66089 (13.24%) aligned >1 times
95.66% overall alignment rate
Alignment completed.
Time elapsed (Alignment) [secs]: 6.515
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 7.012
Processing sample ToxA_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Aligning reads to library ...
499892 reads; of these:
499892 (100.00%) were unpaired; of these:
28785 (5.76%) aligned 0 times
405753 (81.17%) aligned exactly 1 time
65354 (13.07%) aligned >1 times
94.24% overall alignment rate
Alignment completed.
Time elapsed (Alignment) [secs]: 6.608
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 7.067
Processing sample ToxB_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Aligning reads to library ...
499987 reads; of these:
499987 (100.00%) were unpaired; of these:
27292 (5.46%) aligned 0 times
414621 (82.93%) aligned exactly 1 time
58074 (11.62%) aligned >1 times
94.54% overall alignment rate
Alignment completed.
Time elapsed (Alignment) [secs]: 6.334
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 6.778
Processing sample ToxB_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Aligning reads to library ...
499999 reads; of these:
499999 (100.00%) were unpaired; of these:
28983 (5.80%) aligned 0 times
413396 (82.68%) aligned exactly 1 time
57620 (11.52%) aligned >1 times
94.20% overall alignment rate
Alignment completed.
Time elapsed (Alignment) [secs]: 5.792
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 6.199
Read alignments completed.
**************************************************
Collecting read counts ...
**************************************************
Processing sample Control_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading alignment ...
Applying matching threshold ...
Applying ambiguity threshold ...
*** Successfully mapped reads: 337067 (67.4%) ***
Writing alignment logfile ...
Plotting mapping quality ...
Plotting alignment scores ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 4.861
Processing sample Control_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading alignment ...
Applying matching threshold ...
Applying ambiguity threshold ...
*** Successfully mapped reads: 335865 (67.3%) ***
Writing alignment logfile ...
Plotting mapping quality ...
Plotting alignment scores ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 4.524
Processing sample ToxA_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading alignment ...
Applying matching threshold ...
Applying ambiguity threshold ...
*** Successfully mapped reads: 342137 (68.5%) ***
Writing alignment logfile ...
Plotting mapping quality ...
Plotting alignment scores ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 4.552
Processing sample ToxA_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading alignment ...
Applying matching threshold ...
Applying ambiguity threshold ...
*** Successfully mapped reads: 334267 (66.9%) ***
Writing alignment logfile ...
Plotting mapping quality ...
Plotting alignment scores ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 4.556
Processing sample ToxB_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading alignment ...
Applying matching threshold ...
Applying ambiguity threshold ...
*** Successfully mapped reads: 354859 (71.0%) ***
Writing alignment logfile ...
Plotting mapping quality ...
Plotting alignment scores ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 4.457
Processing sample ToxB_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading alignment ...
Applying matching threshold ...
Applying ambiguity threshold ...
*** Successfully mapped reads: 353732 (70.8%) ***
Writing alignment logfile ...
Plotting mapping quality ...
Plotting alignment scores ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 4.314
Read count acquisition completed.
**************************************************
Clearing temporary alignment files ...
**************************************************
Removing raw alignment output...
Time elapsed [secs]: 0.068
Alignment output processing completed.
**************************************************
Averaging read counts over replicates ...
**************************************************
Processing Control ...
Averaging read counts over 2 replicates ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 7.449
Processing ToxB ...
Averaging read counts over 2 replicates ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 7.904
Processing ToxA ...
Averaging read counts over 2 replicates ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 7.270
Read count averaging completed.
**************************************************
Normalizing read counts ...
**************************************************
++++++++++++++++++++++++++++++++++++++++++++++++
Normalizing to counts per million reads ...
Processing file ToxA_1_GuideCounts.txt ...
Processing file Control_2_GuideCounts.txt ...
Processing file ToxA_avg_GuideCounts.txt ...
Processing file ToxA_2_GuideCounts.txt ...
Processing file Control_1_GuideCounts.txt ...
Processing file ToxB_2_GuideCounts.txt ...
Processing file Control_avg_GuideCounts.txt ...
Processing file ToxB_avg_GuideCounts.txt ...
Processing file ToxB_1_GuideCounts.txt ...
Processing file Control_2_GeneCounts.txt ...
Processing file Control_1_GeneCounts.txt ...
Processing file ToxB_2_GeneCounts.txt ...
Processing file ToxB_avg_GeneCounts.txt ...
Processing file ToxB_1_GeneCounts.txt ...
Processing file ToxA_1_GeneCounts.txt ...
Processing file Control_avg_GeneCounts.txt ...
Processing file ToxA_avg_GeneCounts.txt ...
Processing file ToxA_2_GeneCounts.txt ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 4.439
Read count normalization completed.
**************************************************
Analyzing sgRNA read count distribution ...
**************************************************
Processing sample ToxA_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ...
Gini Index (sgRNAs): 0.95
Gini Index (genes): 0.797
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 2.466
Processing sample Control_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ...
Gini Index (sgRNAs): 0.752
Gini Index (genes): 0.445
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 2.222
Processing sample ToxA_avg ...
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ...
Gini Index (sgRNAs): 0.93
Gini Index (genes): 0.75
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 2.233
Processing sample ToxA_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ...
Gini Index (sgRNAs): 0.92
Gini Index (genes): 0.72
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 2.189
Processing sample Control_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ...
Gini Index (sgRNAs): 0.774
Gini Index (genes): 0.467
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 2.262
Processing sample ToxB_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ...
Gini Index (sgRNAs): 0.972
Gini Index (genes): 0.904
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 2.206
Processing sample Control_avg ...
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ...
Gini Index (sgRNAs): 0.664
Gini Index (genes): 0.374
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 2.198
Processing sample ToxB_avg ...
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ...
Gini Index (sgRNAs): 0.968
Gini Index (genes): 0.895
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 2.208
Processing sample ToxB_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Computing Gini coefficients ...
Gini Index (sgRNAs): 0.971
Gini Index (genes): 0.895
Plotting Lorenz curves ...
Generating boxplots...
Generating histograms...
Writing distribution file ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 2.209
Read count distribution analysis completed.
**************************************************
Analyzing control samples ...
**************************************************
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA counts ...
Estimating mean and variance ...
Overdispersion detected at p=0.0. Choosing negative binomial model ...
Computing distribution parameters ...
Writing dataframe ...
Generating dispersion plot ...
Generating log regression plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 6.341
Control sample analysis completed.
**************************************************
sgRNA enrichment analysis ...
**************************************************
Processing sample ToxA_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA read counts ...
Computing fold-changes ...
Computing p-values (Neg. Binomial model) ...
Multiple tests correction ...
Plotting p-value histogram ...
Writing results dataframe ...
Converting to xlsx ...
------------------------------------------------
Script completed.
Time elapsed [mins]: 2.711
Processing sample ToxA_avg ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA read counts ...
Computing fold-changes ...
Computing p-values (Neg. Binomial model) ...
Multiple tests correction ...
Plotting p-value histogram ...
Writing results dataframe ...
Converting to xlsx ...
------------------------------------------------
Script completed.
Time elapsed [mins]: 2.730
Processing sample ToxA_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA read counts ...
Computing fold-changes ...
Computing p-values (Neg. Binomial model) ...
Multiple tests correction ...
Plotting p-value histogram ...
Writing results dataframe ...
Converting to xlsx ...
------------------------------------------------
Script completed.
Time elapsed [mins]: 2.719
Processing sample ToxB_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA read counts ...
Computing fold-changes ...
Computing p-values (Neg. Binomial model) ...
Multiple tests correction ...
Plotting p-value histogram ...
Writing results dataframe ...
Converting to xlsx ...
------------------------------------------------
Script completed.
Time elapsed [mins]: 2.715
Processing sample ToxB_avg ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA read counts ...
Computing fold-changes ...
Computing p-values (Neg. Binomial model) ...
Multiple tests correction ...
Plotting p-value histogram ...
Writing results dataframe ...
Converting to xlsx ...
------------------------------------------------
Script completed.
Time elapsed [mins]: 2.735
Processing sample ToxB_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA read counts ...
Computing fold-changes ...
Computing p-values (Neg. Binomial model) ...
Multiple tests correction ...
Plotting p-value histogram ...
Writing results dataframe ...
Converting to xlsx ...
------------------------------------------------
Script completed.
Time elapsed [mins]: 2.695
sgRNA enrichment analysis completed.
**************************************************
Plotting sgRNA read counts ...
**************************************************
Processing sample ToxA_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.853
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.846
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.721
Processing sample ToxA_avg ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.928
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.878
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.742
Processing sample ToxA_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.879
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.800
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.723
Processing sample ToxB_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.912
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.855
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.750
Processing sample ToxB_avg ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.939
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.877
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.702
Processing sample ToxB_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.930
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.995
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.040
Read count scatterplots completed.
**************************************************
Plotting sgRNA read counts densities ...
**************************************************
Processing sample ToxA_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating density plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 59.401
Processing sample ToxA_avg ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating density plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 59.106
Processing sample ToxA_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating density plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 59.857
Processing sample ToxB_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating density plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 59.922
Processing sample ToxB_avg ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating density plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [mins]: 1.015
Processing sample ToxB_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating density plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 59.790
Density plots completed.
**************************************************
Analyzing replicate correlation ...
**************************************************
Processing sample Control ...
++++++++++++++++++++++++++++++++++++++++++++++++
Sample 1: Control_1 | Sample 2: Control_2
Reading sgRNA counts ...
Log10 transformation ...
Computing correlation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.034
Processing sample ToxB ...
++++++++++++++++++++++++++++++++++++++++++++++++
Sample 1: ToxB_1 | Sample 2: ToxB_2
Reading sgRNA counts ...
Log10 transformation ...
Computing correlation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.072
Processing sample ToxA ...
++++++++++++++++++++++++++++++++++++++++++++++++
Sample 1: ToxA_1 | Sample 2: ToxA_2
Reading sgRNA counts ...
Log10 transformation ...
Computing correlation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.075
Replicate correlation analysis completed.
**************************************************
Analyzing sample clusters ...
**************************************************
++++++++++++++++++++++++++++++++++++++++++++++++
Loading read counts ...
Computing variance ...
Extracting top 25 most variable sgRNAs ...
Writing dataframe ...
Plotting heatmap ...
--------------------------------------------
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
--------------------------------------------
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 5.577
Clustering analysis completed.
**************************************************
Gene ranking ...
**************************************************
Processing sample ToxA_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA enrichment table ...
Looking for sgRNAs with significant fold change ...
Reading sgRNA counts ...
Computing accumulated fold-change scores ...
Estimating null distribution (10000 permutations)...
Plotting gene metric p-value distribution...
Writing results dataframe ...
Converting to xlsx ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 35.491
Processing sample ToxA_avg ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA enrichment table ...
Looking for sgRNAs with significant fold change ...
Reading sgRNA counts ...
Computing accumulated fold-change scores ...
Estimating null distribution (10000 permutations)...
Plotting gene metric p-value distribution...
Writing results dataframe ...
Converting to xlsx ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 35.249
Processing sample ToxA_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA enrichment table ...
Looking for sgRNAs with significant fold change ...
Reading sgRNA counts ...
Computing accumulated fold-change scores ...
Estimating null distribution (10000 permutations)...
Plotting gene metric p-value distribution...
Writing results dataframe ...
Converting to xlsx ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 35.778
Processing sample ToxB_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA enrichment table ...
Looking for sgRNAs with significant fold change ...
Reading sgRNA counts ...
Computing accumulated fold-change scores ...
Estimating null distribution (10000 permutations)...
Plotting gene metric p-value distribution...
Writing results dataframe ...
Converting to xlsx ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 31.307
Processing sample ToxB_avg ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA enrichment table ...
Looking for sgRNAs with significant fold change ...
Reading sgRNA counts ...
Computing accumulated fold-change scores ...
Estimating null distribution (10000 permutations)...
Plotting gene metric p-value distribution...
Writing results dataframe ...
Converting to xlsx ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 32.748
Processing sample ToxB_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Loading sgRNA enrichment table ...
Looking for sgRNAs with significant fold change ...
Reading sgRNA counts ...
Computing accumulated fold-change scores ...
Estimating null distribution (10000 permutations)...
Plotting gene metric p-value distribution...
Writing results dataframe ...
Converting to xlsx ...
------------------------------------------------
Script completed.
Time elapsed [secs]: 31.696
Gene ranking completed.
**************************************************
Plotting gene ranks ...
**************************************************
Processing sample ToxA_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.225
Processing sample ToxA_avg ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.285
Processing sample ToxA_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.238
Processing sample ToxB_2 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.431
Processing sample ToxB_avg ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.224
Processing sample ToxB_1 ...
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.242
Gene rank scatterplots completed.
**************************************************
Extracting top 10 ranked genes ...
**************************************************
Processing sample ToxA_1 ...
-------------------------------------------------------------------------------------
ToxA_1: Gene Ranking Results
-------------------------------------------------------------------------------------
gene SigmaFC p_value significant # sgRNAs # signif. sgRNAs
0 HBEGF 51.095414 0.0000 True 6 5
1 HAUS2 26.124261 0.0000 True 6 4
2 TAS2R4 24.002747 0.0000 True 6 4
3 DEPDC4 17.844592 0.0000 True 6 3
4 MAPK10 16.998088 0.0000 True 6 3
5 OR4P4 16.750064 0.0000 True 6 3
6 PIWIL3 16.187386 0.0001 True 6 3
7 NEURL4 15.984323 0.0001 True 6 3
8 PLEKHM2 15.626890 0.0001 True 6 3
9 KIAA2022 14.669418 0.0003 True 6 3
--------------------------------
Plotting scores: HBEGF
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.272
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.924
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.746
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.073
--------------------------------
Plotting scores: HAUS2
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.212
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.945
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.781
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.985
--------------------------------
Plotting scores: TAS2R4
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.235
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.900
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.769
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.997
--------------------------------
Plotting scores: DEPDC4
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.274
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.909
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.808
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.973
--------------------------------
Plotting scores: MAPK10
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.252
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.941
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.773
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.954
--------------------------------
Plotting scores: OR4P4
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.256
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.887
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.786
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.980
--------------------------------
Plotting scores: PIWIL3
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.234
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.938
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.792
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.981
--------------------------------
Plotting scores: NEURL4
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.236
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.890
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.792
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.940
--------------------------------
Plotting scores: PLEKHM2
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.229
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.976
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.840
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.001
--------------------------------
Plotting scores: KIAA2022
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.249
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.894
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.764
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.962
Processing sample ToxA_avg ...
-------------------------------------------------------------------------------------
ToxA_avg: Gene Ranking Results
-------------------------------------------------------------------------------------
gene SigmaFC p_value significant # sgRNAs # signif. sgRNAs
0 HBEGF 35.190429 0.0000 True 6 4
1 DEPDC4 17.296658 0.0001 True 6 3
2 MAPK10 16.825627 0.0002 True 6 3
3 OR4P4 16.217397 0.0002 True 6 3
4 HAUS2 16.087863 0.0002 True 6 3
5 PIWIL3 15.952012 0.0003 True 6 3
6 NEURL4 15.762875 0.0003 True 6 3
7 PLEKHM2 15.610037 0.0003 True 6 3
8 TAS2R4 14.830866 0.0003 True 6 3
9 PQLC2 14.410042 0.0004 True 6 3
--------------------------------
Plotting scores: HBEGF
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.238
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.869
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.745
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.974
--------------------------------
Plotting scores: DEPDC4
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.254
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.902
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.726
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.972
--------------------------------
Plotting scores: MAPK10
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.232
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.907
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.775
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.002
--------------------------------
Plotting scores: OR4P4
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.221
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.919
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.755
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.956
--------------------------------
Plotting scores: HAUS2
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.326
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.892
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.763
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.976
--------------------------------
Plotting scores: PIWIL3
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.223
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.917
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.734
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.968
--------------------------------
Plotting scores: NEURL4
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.271
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.865
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.770
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.951
--------------------------------
Plotting scores: PLEKHM2
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.232
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.887
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.767
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.981
--------------------------------
Plotting scores: TAS2R4
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.331
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.940
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.761
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.971
--------------------------------
Plotting scores: PQLC2
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.220
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.927
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.750
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.952
Processing sample ToxA_2 ...
-------------------------------------------------------------------------------------
ToxA_2: Gene Ranking Results
-------------------------------------------------------------------------------------
gene SigmaFC p_value significant # sgRNAs # signif. sgRNAs
0 HBEGF 32.830661 0.0000 True 6 4
1 ZMYM3 22.927139 0.0000 True 6 4
2 ERC2 16.783328 0.0000 True 6 3
3 DEPDC4 16.568228 0.0000 True 6 3
4 MAPK10 16.455196 0.0000 True 6 3
5 PIWIL3 15.671846 0.0000 True 6 3
6 OR4P4 15.576698 0.0000 True 6 3
7 PLEKHM2 15.462160 0.0001 True 6 3
8 BCR 15.375051 0.0001 True 6 3
9 HAUS2 15.230957 0.0001 True 6 3
--------------------------------
Plotting scores: HBEGF
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.231
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.868
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.753
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.888
--------------------------------
Plotting scores: ZMYM3
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.240
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.910
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.740
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.938
--------------------------------
Plotting scores: ERC2
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.240
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.852
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.762
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.945
--------------------------------
Plotting scores: DEPDC4
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.294
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.902
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.734
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.995
--------------------------------
Plotting scores: MAPK10
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.228
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.853
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.750
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.894
--------------------------------
Plotting scores: PIWIL3
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.514
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.859
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.737
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.947
--------------------------------
Plotting scores: OR4P4
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.202
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.855
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.739
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.913
--------------------------------
Plotting scores: PLEKHM2
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.231
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.876
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.751
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.950
--------------------------------
Plotting scores: BCR
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.233
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.874
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.732
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.923
--------------------------------
Plotting scores: HAUS2
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.204
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.878
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.726
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.936
Processing sample ToxB_2 ...
-------------------------------------------------------------------------------------
ToxB_2: Gene Ranking Results
-------------------------------------------------------------------------------------
gene SigmaFC p_value significant # sgRNAs # signif. sgRNAs
0 HBEGF 22.971139 0.0000 True 6 4
1 PIP5K1B 14.333257 0.0000 True 6 3
2 CPSF3L 9.177657 0.0001 True 6 2
3 PCDHB1 7.765885 0.0005 True 6 2
4 HELT 7.576019 0.0005 True 6 2
5 SLC35G6 7.372092 0.0005 True 6 2
6 HMGN4 7.220548 0.0005 True 6 2
7 LRRC8C 7.082370 0.0005 True 6 2
8 CSGALNACT1 7.073043 0.0005 True 6 2
9 COL20A1 6.912073 0.0005 True 6 2
--------------------------------
Plotting scores: HBEGF
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.197
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.858
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.694
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.927
--------------------------------
Plotting scores: PIP5K1B
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.254
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.924
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.817
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.010
--------------------------------
Plotting scores: CPSF3L
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.261
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.981
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.783
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.991
--------------------------------
Plotting scores: PCDHB1
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.276
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.926
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.795
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.984
--------------------------------
Plotting scores: HELT
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.255
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.943
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.811
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.979
--------------------------------
Plotting scores: SLC35G6
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.245
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.932
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.841
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.973
--------------------------------
Plotting scores: HMGN4
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.234
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.915
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.783
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.037
--------------------------------
Plotting scores: LRRC8C
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.252
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.911
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.807
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.956
--------------------------------
Plotting scores: CSGALNACT1
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.249
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.957
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.768
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.999
--------------------------------
Plotting scores: COL20A1
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.247
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.892
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.790
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.989
Processing sample ToxB_avg ...
-------------------------------------------------------------------------------------
ToxB_avg: Gene Ranking Results
-------------------------------------------------------------------------------------
gene SigmaFC p_value significant # sgRNAs # signif. sgRNAs
0 HBEGF 23.648165 0.0000 True 6 4
1 PIP5K1B 14.074874 0.0000 True 6 3
2 CPSF3L 9.268806 0.0001 True 6 2
3 XKRX 7.943433 0.0002 True 6 2
4 HELT 7.538944 0.0003 True 6 2
5 SLC35G6 7.484568 0.0003 True 6 2
6 HMGN4 7.206569 0.0004 True 6 2
7 LRRC8C 7.068008 0.0004 True 6 2
8 CSGALNACT1 6.918520 0.0004 True 6 2
9 GALNT16 6.762275 0.0004 True 6 2
--------------------------------
Plotting scores: HBEGF
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.228
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.901
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.771
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.961
--------------------------------
Plotting scores: PIP5K1B
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.253
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.894
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.792
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.005
--------------------------------
Plotting scores: CPSF3L
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.306
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.889
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.790
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.990
--------------------------------
Plotting scores: XKRX
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.296
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.021
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.796
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.973
--------------------------------
Plotting scores: HELT
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.298
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.890
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.733
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.959
--------------------------------
Plotting scores: SLC35G6
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.269
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.924
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.761
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.972
--------------------------------
Plotting scores: HMGN4
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.259
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.923
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.803
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.146
--------------------------------
Plotting scores: LRRC8C
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.577
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.072
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.128
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.176
--------------------------------
Plotting scores: CSGALNACT1
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.256
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.909
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.820
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 3.007
--------------------------------
Plotting scores: GALNT16
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.246
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.867
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.771
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.994
Processing sample ToxB_1 ...
-------------------------------------------------------------------------------------
ToxB_1: Gene Ranking Results
-------------------------------------------------------------------------------------
gene SigmaFC p_value significant # sgRNAs # signif. sgRNAs
0 HBEGF 24.259481 0.0000 True 6 4
1 CPSF3L 9.353068 0.0001 True 6 2
2 XKRX 8.088081 0.0002 True 6 2
3 SLC35G6 7.584759 0.0002 True 6 2
4 HELT 7.499230 0.0002 True 6 2
5 PIP5K1B 7.462428 0.0002 True 6 2
6 HMGN4 7.192288 0.0002 True 6 2
7 GALNT16 7.055044 0.0002 True 6 2
8 LRRC8C 7.053209 0.0002 True 6 2
9 CSGALNACT1 6.743691 0.0003 True 6 2
--------------------------------
Plotting scores: HBEGF
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.244
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.920
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.745
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.909
--------------------------------
Plotting scores: CPSF3L
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.232
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.892
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.775
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.979
--------------------------------
Plotting scores: XKRX
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.229
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.939
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.780
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.919
--------------------------------
Plotting scores: SLC35G6
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.227
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.891
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.799
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.955
--------------------------------
Plotting scores: HELT
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.221
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.923
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.742
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.942
--------------------------------
Plotting scores: PIP5K1B
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.222
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.905
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.773
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.958
--------------------------------
Plotting scores: HMGN4
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.223
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.924
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.707
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.972
--------------------------------
Plotting scores: GALNT16
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.236
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.873
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.765
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.955
--------------------------------
Plotting scores: LRRC8C
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.228
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.906
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.740
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.973
--------------------------------
Plotting scores: CSGALNACT1
--------------------------------
++++++++++++++++++++++++++++++++++++++++++++++++
Reading gene ranking data....
Plotting SigmaFC scores ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.226
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Computing fold-change z-scores ...
Generating z-score plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.885
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log transformation ...
Generating volcano plot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.809
++++++++++++++++++++++++++++++++++++++++++++++++
Reading sgRNA read counts ...
Log10 transformation ...
Generating scatterplot ...
------------------------------------------------
Script completed.
Time elapsed (Total) [secs]: 2.920
**************************************************
PinAPL-Py completed.
Time elapsed [mins]: 44.166
*** RUN FINISHED SUCCESSFULLY ***
LOADING RESULTS PAGE. PLEASE REFRESH PERIODICALLY...
# Required
ScreenType: 'enrichment'
LibFilename: 'GeCKOv21_Human.tsv'
# Library Parameters
seq_5_end: 'TCTTGTGGAAAGGACGAAACACCN'
NonTargetPrefix: 'NonTargeting'
NumGuidesPerGene: 6
# Gene Ranking
GeneMetric: 'SigmaFC'
Np: 10000
alpha_g: 0.01
thr_STARS: 10
IncludeGeneRankCombination: False
w_SigmaFC: [0,1,2,3,4,5,6]
# sgRNA Ranking
padj: 'Sidak'
alpha_s: 0.01
ClusterBy: 'variance'
TopN: 25
# Read Counting
Normalization: 'cpm'
Cutoff: 0
RoundCount: False
repl_avg: 'median'
# Alignment
sgRNALength: 20
CutErrorTol: 0.1
AS_min: 40
Theta: 2
L_bw: 11
N_bw: 1
i_bw: 'S,1,0.75'
AlnOutput: 'Delete'
keepCutReads: False
R_min: 20
# Plotting
ShowNonTargets: True
scatter_annotate: False
TransparencyLevel: 0.05
dotsize: 10
dpi: 300
HitListFormat: 'xlsx'
AutoHighlight: True
IncludeDensityPlots: True
p_overdisp: 0.05
PrintHighlights: false
FCmin_SigmaFC: 0
delta: 1
logbase: 10
width_p: 800
height_p: 800
fontsize_p: 14
marginsize: 10
max_q: 95
svg: True
WorkingDir: '/workingdir/'
DataDir: '/workingdir/Data/'
TempDataDir: '/workingdir/TempData/'
LibDir: '/workingdir/Library/'
IndexDir: '/workingdir/Library/Bowtie2_Index/'
ScriptsDir: '/opt/PinAPL-Py/Scripts/'
AlignDir: '/workingdir/Alignments/'
AnalysisDir: '/workingdir/Analysis/'
TrimLogDir: '/workingdir/Analysis/01_Alignment_Results/Read_Trimming/'
sgRNARanksDir: '/workingdir/Analysis/02_sgRNA-Ranking_Results/sgRNA_Rankings/'
GeneDir: '/workingdir/Analysis/03_GeneRanking_Results/Gene_Rankings'
ControlDir: '/workingdir/Analysis/02_sgRNA-Ranking_Results/ControlSample_Analysis/'
HeatDir: '/workingdir/Analysis/02_sgRNA-Ranking_Results/Heatmap/'
AlnQCDir: '/workingdir/Analysis/01_Alignment_Results/Alignment_Statistics/'
sgRNAReadCountDir: '/workingdir/Analysis/01_Alignment_Results/ReadCounts_per_sgRNA/'
GeneReadCountDir: '/workingdir/Analysis/01_Alignment_Results/ReadCounts_per_Gene/'
CountQCDir: '/workingdir/Analysis/02_sgRNA-Ranking_Results/ReadCount_Distribution/'
ScatterDir: '/workingdir/Analysis/02_sgRNA-Ranking_Results/sgRNA_Scatterplots/'
DensityDir: '/workingdir/Analysis/02_sgRNA-Ranking_Results/sgRNA_Densities/'
GenePlotDir: '/workingdir/Analysis/03_GeneRanking_Results/GeneScore_Scatterplots/'
HiLiteDir: '/workingdir/Analysis/02_sgRNA-Ranking_Results/ReadCount_Scatterplots/Highlighted_Genes/'
CorrelDir: '/workingdir/Analysis/02_sgRNA-Ranking_Results/Replicate_Correlation/'
HiLiteDir2: '/workingdir/Analysis/02_sgRNA-Ranking_Results/Replicate_Correlation/Highlighted_Genes/'
EffDir: '/workingdir/Analysis/03_GeneRanking_Results/sgRNA_Efficacy/'
DepthDir: '/workingdir/Analysis/01_Alignment_Results/Read_Depth/'
SeqQCDir: '/workingdir/Analysis/01_Alignment_Results/Sequence_Quality/'
pvalDir_sgRNA: '/workingdir/Analysis/02_sgRNA-Ranking_Results/p-value_Distribution/'
pvalDir_genes: '/workingdir/Analysis/03_GeneRanking_Results/p-value_Distribution/'
LogFileDir: '/workingdir/Analysis/00_Log_File/'
zScoreDir_sgRNA: '/workingdir/Analysis/02_sgRNA-Ranking_Results/sgRNA_z-Scores/'
VolcanoDir_sgRNA: '/workingdir/Analysis/02_sgRNA-Ranking_Results/sgRNA_VolcanoPlots/'
bw2Dir: '/usr/bin/'
CutAdaptDir: '/root/.local/bin/'
STARSDir: '/opt/PinAPL-Py/Scripts/STARS_mod/'
SanityScript: 'CheckCharacters'
IndexScript: 'BuildLibraryIndex'
LoaderScript: 'LoadDataSheet'
ReadDepthScript: 'PlotNumReads'
SeqQCScript: 'CheckSequenceQuality'
TrimScript: 'TrimReads'
AlignScript: 'AlignReads'
ClassifyScript: 'GetReadCounts'
CutoffScript: 'ApplyCutoff'
CleanUpScript: 'RemoveTempOutput'
NormalizeScript: 'NormalizeReadCounts'
AverageCountsScript: 'AverageCounts'
StatsScript: 'AnalyzeReadCounts'
ControlScript: 'AnalyzeControl'
sgRNARankScript: 'RanksgRNAs'
zFCScript: 'PlotFCz'
vFCScript: 'PlotFCvolcano'
GeneRankScript: 'RankGenes'
GenePlotScript: 'PlotGeneScores'
CombineScript: 'CombineGeneRanks'
ScatterScript: 'PlotCounts'
DensityScript: 'PlotDensity'
ReplicateScript: 'PlotReplicates'
ClusterScript: 'PlotHeatmap'
ExtractTop10Script: 'ExtractTop10Genes'
| Filename | Sample Name |
|---|---|
| Control_R1_S14_L008_R1_001_x.fastq.gz | Control_1 |
| Control_R2_S15_L008_R1_001_x.fastq.gz | Control_2 |
| ToxA_R1_98_S2_L008_R1_001_x.fastq.gz | ToxA_1 |
| ToxA_R2_S2_L005_R1_001_x.fastq.gz | ToxA_2 |
| ToxB_R1_98_S4_L008_R1_001_x.fastq.gz | ToxB_1 |
| ToxB_R2_S4_L005_R1_001_x.fastq.gz | ToxB_2 |