----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/09a_DiffExp_8_HTSeq Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170 Dataset_Label: G170 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: F_Placebo_TD229 CONDITION_2_NAME: F_CPA_1cycle_TD229 Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: Intron_Only_Regions_Lengths.txt COUNT_DIR: RefSeq_Intron_GTF OUTPUT_PREFIX: DiffExp_v2_Intronic_Only DiffExp_Index: DiffExp_8c COL_SUFFIX: Intronic_Only COUNT_PROGRAM: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri Sep 6 17:15:06 EDT 2019 Running on node : scc-tk1 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/09a_DiffExp_8_HTSeq Current job ID : 9186270 Current job name : Step_09a_DiffExp_8c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9186270.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G170_M20 Sample_ID: G170_M20 Description: F_Placebo_Pool1_TD229 M_Num: M20 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G170_M20 Sample_DIR: G170_M21 Sample_ID: G170_M21 Description: F_Placebo_Pool2_TD229 M_Num: M21 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G170_M21 M_Num_Cond1_List: M20M21 ------------------------------------------ ------------------------------------------ Sample_DIR: G170_M28 Sample_ID: G170_M28 Description: F_CPA_1_cycle_Pool9_TD229 M_Num: M28 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G170_M28 Sample_DIR: G170_M29 Sample_ID: G170_M29 Description: F_CPA_1_cycle_Pool10_TD229 M_Num: M29 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G170_M29 M_Num_Cond2_List: M28M29 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 2 NUM_REP_CONDITION1: 2 ========================================================== Renaming input count files Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) number of mapped reads 43791165 42315161 44524767 45401633 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 241822 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_CPA_1cycle_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_CPA_1cycle_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 241436 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_CPA_1cycle_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_CPA_1cycle_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 239957 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_Placebo_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_Placebo_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 241413 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_Placebo_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_Placebo_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Sep 6 17:15 /scratch/9186270.1.linga/Input/Intron_Only_Regions_Lengths.txt /scratch/9186270.1.linga/Input/F_CPA_1cycle_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 6 17:15 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 6 17:15 .. /scratch/9186270.1.linga/Input/F_Placebo_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 6 17:15 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 6 17:15 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R F_Placebo_TD229 F_CPA_1cycle_TD229 2 2 RefSeq_GeneBody.gtf /scratch/9186270.1.linga/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "F_Placebo_TD229" [1] "F_CPA_1cycle_TD229" [1] 2 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/9186270.1.linga/Input" [1] "DiffExp_v2_Intronic_Only" [1] "Intron_Only_Regions_Lengths.txt" [1] "sum1:NaN" "sum1:NaN" "sum1:NaN" [1] "sum2:NaN" "sum2:NaN" "sum2:NaN" load GTF file ... parse attributes ... [1] "output file is in: /scratch/9186270.1.linga/Input/DiffExp_v2_Intronic_Only_F_Placebo_TD229_F_CPA_1cycle_TD229.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_F_Placebo_TD229_F_CPA_1cycle_TD229.txt F_CPA_1cycle_TD229_G170_M28M29_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_Intronic_Only_F_Placebo_TD229_F_CPA_1cycle_TD229.txt F_CPA_1cycle_TD229_G170_M28M29_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== Comparison_Info: F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R F_CPA_1cycle_TD229_G170_M28M29_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_CPA_1cycle_TD229_G170_M28M29_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 347 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 22 7 [1] "Check out Up_Genes_DESeq_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt!" [1] "Check out Down_Genes_DESeq_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt!" Rscript Diff_Genes.R F_CPA_1cycle_TD229_G170_M28M29_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_CPA_1cycle_TD229_G170_M28M29_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 651 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 45 7 [1] "Check out Up_Genes_EdgeR_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt!" [1] "Check out Down_Genes_EdgeR_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt Down_Genes_EdgeR_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt Intronic_Only_Counting DiffExp_8c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_8c" [1] "-----------------" [1] "Down.DESeq.Intronic_Only.HTSeq" [1] "Down.EdgeR.Intronic_Only.HTSeq" null device 1 [1] "Removing VennDiagram*.log files" [1] "Check out Venn diagram and Count.Table!" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt Up_Genes_EdgeR_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt Intronic_Only_Counting DiffExp_8c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_8c" [1] "-----------------" [1] "Up.DESeq.Intronic_Only.HTSeq" [1] "Up.EdgeR.Intronic_Only.HTSeq" null device 1 [1] "Removing VennDiagram*.log files" [1] "Check out Venn diagram and Count.Table!" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 323 Sep 6 17:17 /scratch/9186270.1.linga/Input/DiffExp_8c_Venn_Tables_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 7482594 Sep 6 17:16 /scratch/9186270.1.linga/Input/DiffExp_v2_Intronic_Only_F_Placebo_TD229_F_CPA_1cycle_TD229.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Sep 6 17:15 /scratch/9186270.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 1895 Sep 6 17:16 /scratch/9186270.1.linga/Input/Down_Genes_DESeq_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 4125 Sep 6 17:16 /scratch/9186270.1.linga/Input/Down_Genes_EdgeR_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 241822 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_CPA_1cycle_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_CPA_1cycle_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 241436 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_CPA_1cycle_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_CPA_1cycle_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 3031728 Sep 6 17:16 /scratch/9186270.1.linga/Input/F_CPA_1cycle_TD229_G170_M28M29_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 3588259 Sep 6 17:16 /scratch/9186270.1.linga/Input/F_CPA_1cycle_TD229_G170_M28M29_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 2354210 Sep 6 17:16 /scratch/9186270.1.linga/Input/F_CPA_1cycle_TD229_G170_M28M29_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2910741 Sep 6 17:16 /scratch/9186270.1.linga/Input/F_CPA_1cycle_TD229_G170_M28M29_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 239957 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_Placebo_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_Placebo_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 241413 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_Placebo_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:15 /scratch/9186270.1.linga/Input/F_Placebo_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Sep 6 17:15 /scratch/9186270.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 34022 Sep 6 17:16 /scratch/9186270.1.linga/Input/Up_Genes_DESeq_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 79417 Sep 6 17:16 /scratch/9186270.1.linga/Input/Up_Genes_EdgeR_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Sep 6 17:15 /scratch/9186270.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 41195 Sep 6 17:17 /scratch/9186270.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 40246 Sep 6 17:17 /scratch/9186270.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 Sep 6 17:15 /scratch/9186270.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Sep 6 17:15 /scratch/9186270.1.linga/Input/formatForSegex_ver4.R /scratch/9186270.1.linga/Input/F_CPA_1cycle_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 6 17:15 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 6 17:17 .. /scratch/9186270.1.linga/Input/F_Placebo_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 6 17:15 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 6 17:17 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Sep 6 17:17 . drwxrwxrwt. 14 root root 4.0K Sep 6 17:15 .. -rw-r--r-- 1 kkarri waxmanlab 113 Sep 6 17:15 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 122 Sep 6 17:15 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Sep 6 17:17 Input -rw-r--r-- 1 kkarri waxmanlab 72M Sep 6 17:15 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K Sep 6 17:15 differentialAnalysis.R ========================================================== Re-naming files in OUTPUT_DIR Need to append the COUNT_PROGRAM name to all output files List files in OUTPUT_DIR total 30M drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 6 17:11 . drwxr-xr-x 6 kkarri waxmanlab 4.0K Sep 6 17:09 .. -rw-r--r-- 1 kkarri waxmanlab 323 Sep 6 17:11 DiffExp_8c_Venn_Tables_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 7.2M Sep 6 17:11 DiffExp_v2_Intronic_Only_F_Placebo_TD229_F_CPA_1cycle_TD229_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 1.9K Sep 6 17:11 Down_Genes_DESeq_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 4.1K Sep 6 17:11 Down_Genes_EdgeR_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.9M Sep 6 17:11 F_CPA_1cycle_TD229_G170_M28M29_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 3.5M Sep 6 17:11 F_CPA_1cycle_TD229_G170_M28M29_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Sep 6 17:11 F_CPA_1cycle_TD229_G170_M28M29_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.8M Sep 6 17:11 F_CPA_1cycle_TD229_G170_M28M29_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 34K Sep 6 17:11 Up_Genes_DESeq_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 78K Sep 6 17:11 Up_Genes_EdgeR_Intronic_Only_F_CPA_1cycle_TD229_G170_M28M29_F_Placebo_TD229_G170_M20M21_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 41K Sep 6 17:11 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 40K Sep 6 17:11 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_HTSeq.png ========================================================== ========================================================== Finished on : Fri Sep 6 17:17:16 EDT 2019 2 minutes and 10 seconds elapsed. ==========================================================