----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/09b_DiffExp_2_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_Env Dataset_Label: G123 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.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_Regions_Lengths.txt COUNT_DIR: RefSeq_Exon_GTF OUTPUT_PREFIX: DiffExp_v2_GeneBody DiffExp_Index: DiffExp_2a COL_SUFFIX: GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed Dec 19 16:44:20 EST 2018 Running on node : scc-tk3 Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/09b_DiffExp_2_featureCounts Current job ID : 391929 Current job name : Step_09b_DiffExp_2a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/391929.1.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: 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 34313260 32110941 29382937 40788664 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291522 Dec 19 16:44 /scratch/391929.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 0 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_TCPOBOP0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 0 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_TCPOBOP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 0 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_Vehicle0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 0 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_Vehicle1_num_mapped_reads.txt /scratch/391929.1.linga/Input/Male_27h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 19 16:44 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 19 16:44 .. /scratch/391929.1.linga/Input/Male_27h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 19 16:44 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 19 16:44 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Male_27h_Vehicle Male_27h_TCPOBOP 2 2 RefSeq_GeneBody.gtf /scratch/391929.1.linga/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Male_27h_Vehicle" [1] "Male_27h_TCPOBOP" [1] 2 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/391929.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_Male_27h_Vehicle_Male_27h_TCPOBOP.txt Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== 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_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'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_GeneBody_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6" [1] "-----------------" [1] "DESeq or EdgeR job most likely failed." [1] "Quitting R now." Rscript Diff_Genes.R Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'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_GeneBody_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6" [1] "-----------------" [1] "DESeq or EdgeR job most likely failed." [1] "Quitting R now." #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt Down_Genes_EdgeR_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt GeneBody_Counting DiffExp_2a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2a" [1] "-----------------" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt Up_Genes_EdgeR_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt GeneBody_Counting DiffExp_2a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2a" [1] "-----------------" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- Comparison_Info: Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 0 Dec 19 16:44 /scratch/391929.1.linga/Input/DiffExp_2a_Venn_Tables_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Dec 19 16:44 /scratch/391929.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 291522 Dec 19 16:44 /scratch/391929.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 0 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_TCPOBOP0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 0 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_TCPOBOP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 0 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_Vehicle0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 0 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 19 16:44 /scratch/391929.1.linga/Input/Male_27h_Vehicle1_num_mapped_reads.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Dec 19 16:44 /scratch/391929.1.linga/Input/Venn_Diff_Genes.R -rwxr-xr-x 1 kkarri waxmanlab 3925 Dec 19 16:44 /scratch/391929.1.linga/Input/formatForSegex_ver3.R /scratch/391929.1.linga/Input/Male_27h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 19 16:44 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 19 16:44 .. /scratch/391929.1.linga/Input/Male_27h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 19 16:44 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 19 16:44 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Dec 19 16:44 . drwxrwxrwt. 11 root root 20K Dec 19 16:44 .. -rw-r--r-- 1 kkarri waxmanlab 103 Dec 19 16:44 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 103 Dec 19 16:44 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Dec 19 16:44 Input -rw-r--r-- 1 kkarri waxmanlab 72M Dec 19 16:44 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 16K Dec 19 16:44 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 32K drwxr-sr-x 2 kkarri waxmanlab 512 Dec 19 16:44 . drwxr-sr-x 6 kkarri waxmanlab 32K Dec 19 16:44 .. -rw-r--r-- 1 kkarri waxmanlab 0 Dec 19 16:44 DiffExp_2a_Venn_Tables_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_featureCounts.txt ========================================================== ========================================================== Finished on : Wed Dec 19 16:44:39 EST 2018 0 minutes and 19 seconds elapsed. ==========================================================