----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/09a_DiffExp_2_HTSeq Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New Dataset_Label: G123 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: Exon_Only_Regions.gtf CONDITION_1_NAME: Male_27h_Vehicle CONDITION_2_NAME: Male_27h_TCPOBOP Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: Exon_Only_Regions_Lengths.txt COUNT_DIR: RefSeq_Exon_Only_GTF OUTPUT_PREFIX: DiffExp_v2_Exonic_Only DiffExp_Index: DiffExp_2b COL_SUFFIX: Exonic_Only COUNT_PROGRAM: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Sat Dec 8 00:37:49 EST 2018 Running on node : scc-tk4 Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/09a_DiffExp_2_HTSeq Current job ID : 28802 Current job name : Step_09a_DiffExp_2b Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/28802.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G123_M5 Sample_ID: G123_M5 Description: Male_27h_Vehicle_1 M_Num: M5 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G123_M5 Sample_DIR: G123_M6 Sample_ID: G123_M6 Description: Male_27h_Vehicle_2 M_Num: M6 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G123_M6 M_Num_Cond1_List: M5M6 ------------------------------------------ ------------------------------------------ Sample_DIR: G123_M7 Sample_ID: G123_M7 Description: Male_27h_TCPOBOP_1 M_Num: M7 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G123_M7 Sample_DIR: G123_M8 Sample_ID: G123_M8 Description: Male_27h_TCPOBOP_2 M_Num: M8 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G123_M8 M_Num_Cond2_List: M7M8 ------------------------------------------ ========================================================== 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 34313514 32110871 29383190 40788463 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291285 Dec 8 00:37 /scratch/28802.1.linga/Input/Exon_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 248845 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_TCPOBOP0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 248476 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_TCPOBOP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247930 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_Vehicle0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 250157 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_Vehicle1_num_mapped_reads.txt /scratch/28802.1.linga/Input/Male_27h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 00:37 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 00:37 .. /scratch/28802.1.linga/Input/Male_27h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 00:37 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 00:37 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Male_27h_Vehicle Male_27h_TCPOBOP 2 2 Exon_Only_Regions.gtf /scratch/28802.1.linga/Input DiffExp_v2_Exonic_Only Exon_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Male_27h_Vehicle" [1] "Male_27h_TCPOBOP" [1] 2 [1] 2 [1] "Exon_Only_Regions.gtf" [1] "/scratch/28802.1.linga/Input" [1] "DiffExp_v2_Exonic_Only" [1] "Exon_Only_Regions_Lengths.txt" load GTF file ... parse attributes ... [1] "output file is in: /scratch/28802.1.linga/Input/DiffExp_v2_Exonic_Only_Male_27h_Vehicle_Male_27h_TCPOBOP.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Exonic_Only_Male_27h_Vehicle_Male_27h_TCPOBOP.txt Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_Exonic_Only_forSEGEXUpload 1 Exonic_Only ========================================================== Comparison_Info: Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Exonic_Only'_'Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 230 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 59 7 [1] "Check out Up_Genes_DESeq_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt!" [1] "Check out Down_Genes_DESeq_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt!" Rscript Diff_Genes.R Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Exonic_Only'_'Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 457 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 156 7 [1] "Check out Up_Genes_EdgeR_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt!" [1] "Check out Down_Genes_EdgeR_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt Down_Genes_EdgeR_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt Exonic_Only_Counting DiffExp_2b [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "Subtitle:" [1] "Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2b" [1] "-----------------" [1] "Down.DESeq.Exonic_Only.HTSeq" [1] "Down.EdgeR.Exonic_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_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt Up_Genes_EdgeR_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt Exonic_Only_Counting DiffExp_2b [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "Subtitle:" [1] "Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2b" [1] "-----------------" [1] "Up.DESeq.Exonic_Only.HTSeq" [1] "Up.EdgeR.Exonic_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 312 Dec 8 00:38 /scratch/28802.1.linga/Input/DiffExp_2b_Venn_Tables_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 6392829 Dec 8 00:38 /scratch/28802.1.linga/Input/DiffExp_v2_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Dec 8 00:37 /scratch/28802.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 8079 Dec 8 00:38 /scratch/28802.1.linga/Input/Down_Genes_DESeq_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 20592 Dec 8 00:38 /scratch/28802.1.linga/Input/Down_Genes_EdgeR_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 291285 Dec 8 00:37 /scratch/28802.1.linga/Input/Exon_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 248845 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_TCPOBOP0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 248476 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_TCPOBOP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2330000 Dec 8 00:38 /scratch/28802.1.linga/Input/Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2354197 Dec 8 00:38 /scratch/28802.1.linga/Input/Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 247930 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_Vehicle0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 250157 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:37 /scratch/28802.1.linga/Input/Male_27h_Vehicle1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 16467 Dec 8 00:38 /scratch/28802.1.linga/Input/Up_Genes_DESeq_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 32984 Dec 8 00:38 /scratch/28802.1.linga/Input/Up_Genes_EdgeR_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Dec 8 00:37 /scratch/28802.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 39105 Dec 8 00:38 /scratch/28802.1.linga/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 38953 Dec 8 00:38 /scratch/28802.1.linga/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 Dec 8 00:37 /scratch/28802.1.linga/Input/formatForSegex_ver3.R /scratch/28802.1.linga/Input/Male_27h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 00:37 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 00:38 .. /scratch/28802.1.linga/Input/Male_27h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 00:37 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 00:38 .. ========================================================== List files in scratch total 19M drwx------ 3 kkarri waxmanlab 4.0K Dec 8 00:38 . drwxrwxrwt. 13 root root 52K Dec 8 00:38 .. -rw-r--r-- 1 kkarri waxmanlab 103 Dec 8 00:37 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 103 Dec 8 00:37 Condition_2.txt -rw-r--r-- 1 kkarri waxmanlab 19M Dec 8 00:37 Exon_Only_Regions.gtf drwxr-xr-x 4 kkarri waxmanlab 4.0K Dec 8 00:38 Input -rwxr-xr-x 1 kkarri waxmanlab 16K Dec 8 00:37 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 9.1M drwxr-sr-x 2 kkarri waxmanlab 32K Dec 8 00:38 . drwxr-sr-x 6 kkarri waxmanlab 32K Dec 8 00:37 .. -rw-r--r-- 1 kkarri waxmanlab 312 Dec 8 00:38 DiffExp_2b_Venn_Tables_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 6.1M Dec 8 00:38 DiffExp_v2_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 7.9K Dec 8 00:38 Down_Genes_DESeq_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 21K Dec 8 00:38 Down_Genes_EdgeR_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Dec 8 00:38 Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Dec 8 00:38 Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 17K Dec 8 00:38 Up_Genes_DESeq_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 33K Dec 8 00:38 Up_Genes_EdgeR_Exonic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 39K Dec 8 00:38 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 39K Dec 8 00:38 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_HTSeq.png ========================================================== ========================================================== Finished on : Sat Dec 8 00:38:47 EST 2018 0 minutes and 58 seconds elapsed. ==========================================================