----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/09a_DiffExp_1_HTSeq Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New Dataset_Label: G123 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: Male_3h_Vehicle CONDITION_2_NAME: Male_3h_TCPOBOP 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_1c COL_SUFFIX: Intronic_Only COUNT_PROGRAM: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Sat Dec 8 00:32:42 EST 2018 Running on node : scc-tk3 Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/09a_DiffExp_1_HTSeq Current job ID : 28800 Current job name : Step_09a_DiffExp_1c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/28800.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G123_M1 Sample_ID: G123_M1 Description: Male_3h_Vehicle_1 M_Num: M1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G123_M1 Sample_DIR: G123_M2 Sample_ID: G123_M2 Description: Male_3h_Vehicle_2 M_Num: M2 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G123_M2 M_Num_Cond1_List: M1M2 ------------------------------------------ ------------------------------------------ Sample_DIR: G123_M3 Sample_ID: G123_M3 Description: Male_3h_TCPOBOP_1 M_Num: M3 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G123_M3 Sample_DIR: G123_M4 Sample_ID: G123_M4 Description: Male_3h_TCPOBOP_2 M_Num: M4 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G123_M4 M_Num_Cond2_List: M3M4 ------------------------------------------ ========================================================== 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 30619799 46696186 32796488 29093494 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 300238 Dec 8 00:32 /scratch/28800.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 245579 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_TCPOBOP0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 248114 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_TCPOBOP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246100 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_Vehicle0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245247 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_Vehicle1_num_mapped_reads.txt /scratch/28800.1.linga/Input/Male_3h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 00:32 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 00:32 .. /scratch/28800.1.linga/Input/Male_3h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 00:32 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 00:32 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Male_3h_Vehicle Male_3h_TCPOBOP 2 2 RefSeq_GeneBody.gtf /scratch/28800.1.linga/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Male_3h_Vehicle" [1] "Male_3h_TCPOBOP" [1] 2 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/28800.1.linga/Input" [1] "DiffExp_v2_Intronic_Only" [1] "Intron_Only_Regions_Lengths.txt" load GTF file ... parse attributes ... [1] "output file is in: /scratch/28800.1.linga/Input/DiffExp_v2_Intronic_Only_Male_3h_Vehicle_Male_3h_TCPOBOP.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_Male_3h_Vehicle_Male_3h_TCPOBOP.txt Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== Comparison_Info: Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_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_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 34 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 5 7 [1] "Check out Up_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt!" [1] "Check out Down_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt!" Rscript Diff_Genes.R Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_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_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 87 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 32 7 [1] "Check out Up_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt!" [1] "Check out Down_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt Down_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt Intronic_Only_Counting DiffExp_1c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1c" [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_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt Up_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt Intronic_Only_Counting DiffExp_1c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1c" [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 319 Dec 8 00:34 /scratch/28800.1.linga/Input/DiffExp_1c_Venn_Tables_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 6441486 Dec 8 00:34 /scratch/28800.1.linga/Input/DiffExp_v2_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Dec 8 00:32 /scratch/28800.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 614 Dec 8 00:34 /scratch/28800.1.linga/Input/Down_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 3276 Dec 8 00:34 /scratch/28800.1.linga/Input/Down_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Dec 8 00:32 /scratch/28800.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 245579 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_TCPOBOP0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 248114 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_TCPOBOP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2330012 Dec 8 00:34 /scratch/28800.1.linga/Input/Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2402603 Dec 8 00:34 /scratch/28800.1.linga/Input/Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 246100 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_Vehicle0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245247 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:32 /scratch/28800.1.linga/Input/Male_3h_Vehicle1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2456 Dec 8 00:34 /scratch/28800.1.linga/Input/Up_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 6491 Dec 8 00:34 /scratch/28800.1.linga/Input/Up_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Dec 8 00:32 /scratch/28800.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 35941 Dec 8 00:34 /scratch/28800.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 37102 Dec 8 00:34 /scratch/28800.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 Dec 8 00:32 /scratch/28800.1.linga/Input/formatForSegex_ver3.R /scratch/28800.1.linga/Input/Male_3h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 00:32 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 00:34 .. /scratch/28800.1.linga/Input/Male_3h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 00:32 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 00:34 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Dec 8 00:34 . drwxrwxrwt. 17 root root 20K Dec 8 00:34 .. -rw-r--r-- 1 kkarri waxmanlab 101 Dec 8 00:32 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 101 Dec 8 00:32 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Dec 8 00:34 Input -rw-r--r-- 1 kkarri waxmanlab 72M Dec 8 00:32 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 16K Dec 8 00:32 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 11M drwxr-sr-x 2 kkarri waxmanlab 32K Dec 8 00:34 . drwxr-sr-x 6 kkarri waxmanlab 32K Dec 8 00:32 .. -rw-r--r-- 1 kkarri waxmanlab 319 Dec 8 00:34 DiffExp_1c_Venn_Tables_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 6.2M Dec 8 00:34 DiffExp_v2_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 614 Dec 8 00:34 Down_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 3.2K Dec 8 00:34 Down_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Dec 8 00:34 Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Dec 8 00:34 Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.4K Dec 8 00:34 Up_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 6.4K Dec 8 00:34 Up_Genes_EdgeR_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 36K Dec 8 00:34 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 37K Dec 8 00:34 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_HTSeq.png ========================================================== ========================================================== Finished on : Sat Dec 8 00:34:16 EST 2018 1 minutes and 34 seconds elapsed. ==========================================================