----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/09b_DiffExp_1_featureCounts 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_3h_Vehicle CONDITION_2_NAME: Male_3h_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_1b COL_SUFFIX: Exonic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri Feb 22 13:49:16 EST 2019 Running on node : scc-ka5 Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/09b_DiffExp_1_featureCounts Current job ID : 2973707 Current job name : Step_09b_DiffExp_1b Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/2973707.1.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: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. number of mapped reads 30619799 46696186 32796488 29093494 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291285 Feb 22 13:49 /scratch/2973707.1.linga/Input/Exon_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 248117 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_TCPOBOP0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 250718 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_TCPOBOP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 248433 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_Vehicle0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247749 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_Vehicle1_num_mapped_reads.txt /scratch/2973707.1.linga/Input/Male_3h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Feb 22 13:49 . drwxr-xr-x 4 kkarri waxmanlab 4096 Feb 22 13:49 .. /scratch/2973707.1.linga/Input/Male_3h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Feb 22 13:49 . drwxr-xr-x 4 kkarri waxmanlab 4096 Feb 22 13:49 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Male_3h_Vehicle Male_3h_TCPOBOP 2 2 Exon_Only_Regions.gtf /scratch/2973707.1.linga/Input DiffExp_v2_Exonic_Only Exon_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Male_3h_Vehicle" [1] "Male_3h_TCPOBOP" [1] 2 [1] 2 [1] "Exon_Only_Regions.gtf" [1] "/scratch/2973707.1.linga/Input" [1] "DiffExp_v2_Exonic_Only" [1] "Exon_Only_Regions_Lengths.txt" load GTF file ... parse attributes ... [1] "output file is in: /scratch/2973707.1.linga/Input/DiffExp_v2_Exonic_Only_Male_3h_Vehicle_Male_3h_TCPOBOP.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Exonic_Only_Male_3h_Vehicle_Male_3h_TCPOBOP.txt Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_Exonic_Only_forSEGEXUpload 1 Exonic_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_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Exonic_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_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_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] 26 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 2 7 [1] "Check out Up_Genes_DESeq_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt!" [1] "Check out Down_Genes_DESeq_Exonic_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_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Exonic_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_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_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] 80 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 29 7 [1] "Check out Up_Genes_EdgeR_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt!" [1] "Check out Down_Genes_EdgeR_Exonic_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_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt Down_Genes_EdgeR_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt Exonic_Only_Counting DiffExp_1b [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "Subtitle:" [1] "Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1b" [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_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt Up_Genes_EdgeR_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt Exonic_Only_Counting DiffExp_1b [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "Subtitle:" [1] "Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1b" [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 #---------------------------------------------------------------------------------- Comparison_Info: Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 307 Feb 22 13:50 /scratch/2973707.1.linga/Input/DiffExp_1b_Venn_Tables_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 6437585 Feb 22 13:50 /scratch/2973707.1.linga/Input/DiffExp_v2_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Feb 22 13:49 /scratch/2973707.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 324 Feb 22 13:50 /scratch/2973707.1.linga/Input/Down_Genes_DESeq_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 2893 Feb 22 13:50 /scratch/2973707.1.linga/Input/Down_Genes_EdgeR_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 291285 Feb 22 13:49 /scratch/2973707.1.linga/Input/Exon_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 248117 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_TCPOBOP0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 250718 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_TCPOBOP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2329998 Feb 22 13:50 /scratch/2973707.1.linga/Input/Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2402589 Feb 22 13:50 /scratch/2973707.1.linga/Input/Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 248433 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_Vehicle0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247749 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 13:49 /scratch/2973707.1.linga/Input/Male_3h_Vehicle1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 1954 Feb 22 13:50 /scratch/2973707.1.linga/Input/Up_Genes_DESeq_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 5802 Feb 22 13:50 /scratch/2973707.1.linga/Input/Up_Genes_EdgeR_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Feb 22 13:49 /scratch/2973707.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 33578 Feb 22 13:50 /scratch/2973707.1.linga/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 36687 Feb 22 13:50 /scratch/2973707.1.linga/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 Feb 22 13:49 /scratch/2973707.1.linga/Input/formatForSegex_ver3.R /scratch/2973707.1.linga/Input/Male_3h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Feb 22 13:49 . drwxr-xr-x 4 kkarri waxmanlab 4096 Feb 22 13:50 .. /scratch/2973707.1.linga/Input/Male_3h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Feb 22 13:49 . drwxr-xr-x 4 kkarri waxmanlab 4096 Feb 22 13:50 .. ========================================================== List files in scratch total 19M drwx------ 3 kkarri waxmanlab 4.0K Feb 22 13:50 . drwxrwxrwt. 17 root root 128K Feb 22 13:49 .. -rw-r--r-- 1 kkarri waxmanlab 101 Feb 22 13:49 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 101 Feb 22 13:49 Condition_2.txt -rw-r--r-- 1 kkarri waxmanlab 19M Feb 22 13:49 Exon_Only_Regions.gtf drwxr-xr-x 4 kkarri waxmanlab 4.0K Feb 22 13:50 Input -rwxr-xr-x 1 kkarri waxmanlab 16K Feb 22 13:49 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 Feb 22 13:50 . drwxr-sr-x 6 kkarri waxmanlab 32K Feb 22 13:50 .. -rw-r--r-- 1 kkarri waxmanlab 307 Feb 22 13:50 DiffExp_1b_Venn_Tables_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 6.2M Feb 22 13:50 DiffExp_v2_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 324 Feb 22 13:50 Down_Genes_DESeq_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.9K Feb 22 13:50 Down_Genes_EdgeR_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Feb 22 13:50 Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Feb 22 13:50 Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.0K Feb 22 13:50 Up_Genes_DESeq_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.7K Feb 22 13:50 Up_Genes_EdgeR_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 33K Feb 22 13:50 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 36K Feb 22 13:50 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Fri Feb 22 13:50:44 EST 2019 1 minutes and 28 seconds elapsed. ==========================================================