----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/09a_DiffExp_1_HTSeq Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G160_Samples Dataset_Label: G160 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: F_Soluble_Nuclear CONDITION_2_NAME: F_Chromatin_Pellet 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 : Thu Aug 31 00:33:59 EDT 2017 Running on node : scc-ba8 Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/09a_DiffExp_1_HTSeq Current job ID : 474639 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/474639.1.b Loading required modules... ------------------------------------------ Sample_DIR: G160_M1 Sample_ID: G160_M1 Description: Female_Soluble_Nuclear_Extract M_Num: M1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G160_M1 Sample_DIR: G160_M11 Sample_ID: G160_M11 Description: Female_Soluble_Nuclear_Extract_II M_Num: M11 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G160_M11 M_Num_Cond1_List: M1M11 ------------------------------------------ ------------------------------------------ Sample_DIR: G160_M2 Sample_ID: G160_M2 Description: Female_Chromatin_Pellet_Extract M_Num: M2 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G160_M2 Sample_DIR: G160_M22 Sample_ID: G160_M22 Description: Female_Chromatin_Pellet_Extract_II M_Num: M22 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G160_M22 M_Num_Cond2_List: M2M22 ------------------------------------------ ========================================================== 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 46209433 46209433 29167884 29167884 ========================================================== List files in Input -rw-r--r-- 1 kkarri pulmseq 249265 Aug 31 00:34 /scratch/474639.1.b/Input/F_Chromatin_Pellet0.out -rw-r--r-- 1 kkarri pulmseq 9 Aug 31 00:34 /scratch/474639.1.b/Input/F_Chromatin_Pellet0_num_mapped_reads.txt -rw-r--r-- 1 kkarri pulmseq 249265 Aug 31 00:34 /scratch/474639.1.b/Input/F_Chromatin_Pellet1.out -rw-r--r-- 1 kkarri pulmseq 9 Aug 31 00:34 /scratch/474639.1.b/Input/F_Chromatin_Pellet1_num_mapped_reads.txt -rw-r--r-- 1 kkarri pulmseq 245385 Aug 31 00:34 /scratch/474639.1.b/Input/F_Soluble_Nuclear0.out -rw-r--r-- 1 kkarri pulmseq 9 Aug 31 00:34 /scratch/474639.1.b/Input/F_Soluble_Nuclear0_num_mapped_reads.txt -rw-r--r-- 1 kkarri pulmseq 245385 Aug 31 00:34 /scratch/474639.1.b/Input/F_Soluble_Nuclear1.out -rw-r--r-- 1 kkarri pulmseq 9 Aug 31 00:34 /scratch/474639.1.b/Input/F_Soluble_Nuclear1_num_mapped_reads.txt -rw-r--r-- 1 kkarri pulmseq 300238 Aug 31 00:34 /scratch/474639.1.b/Input/Intron_Only_Regions_Lengths.txt /scratch/474639.1.b/Input/F_Chromatin_Pellet: total 8 drwxr-xr-x 2 kkarri pulmseq 4096 Aug 31 00:34 . drwxr-xr-x 4 kkarri pulmseq 4096 Aug 31 00:34 .. /scratch/474639.1.b/Input/F_Soluble_Nuclear: total 8 drwxr-xr-x 2 kkarri pulmseq 4096 Aug 31 00:34 . drwxr-xr-x 4 kkarri pulmseq 4096 Aug 31 00:34 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R F_Soluble_Nuclear F_Chromatin_Pellet 2 2 RefSeq_GeneBody.gtf /scratch/474639.1.b/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "F_Soluble_Nuclear" [1] "F_Chromatin_Pellet" [1] 2 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/474639.1.b/Input" [1] "DiffExp_v2_Intronic_Only" [1] "Intron_Only_Regions_Lengths.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_F_Soluble_Nuclear_F_Chromatin_Pellet.txt F_Chromatin_Pellet_G160_M2M22_vs_F_Soluble_Nuclear_G160_M1M11_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== Comparison_Info: F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R F_Chromatin_Pellet_G160_M2M22_vs_F_Soluble_Nuclear_G160_M1M11_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_Chromatin_Pellet_G160_M2M22_vs_F_Soluble_Nuclear_G160_M1M11_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_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11" [1] "-----------------" [1] "DESeq or EdgeR job most likely failed." [1] "Quitting R now." Rscript Diff_Genes.R F_Chromatin_Pellet_G160_M2M22_vs_F_Soluble_Nuclear_G160_M1M11_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_Chromatin_Pellet_G160_M2M22_vs_F_Soluble_Nuclear_G160_M1M11_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_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11" [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_Intronic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt Down_Genes_EdgeR_Intronic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt Intronic_Only_Counting DiffExp_1c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1c" [1] "-----------------" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_Intronic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt Up_Genes_EdgeR_Intronic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt Intronic_Only_Counting DiffExp_1c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1c" [1] "-----------------" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri pulmseq 0 Aug 31 00:34 /scratch/474639.1.b/Input/DiffExp_1c_Venn_Tables_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt -rwxr-xr-x 1 kkarri pulmseq 7394 Aug 31 00:34 /scratch/474639.1.b/Input/Diff_Genes.R -rw-r--r-- 1 kkarri pulmseq 249265 Aug 31 00:34 /scratch/474639.1.b/Input/F_Chromatin_Pellet0.out -rw-r--r-- 1 kkarri pulmseq 9 Aug 31 00:34 /scratch/474639.1.b/Input/F_Chromatin_Pellet0_num_mapped_reads.txt -rw-r--r-- 1 kkarri pulmseq 249265 Aug 31 00:34 /scratch/474639.1.b/Input/F_Chromatin_Pellet1.out -rw-r--r-- 1 kkarri pulmseq 9 Aug 31 00:34 /scratch/474639.1.b/Input/F_Chromatin_Pellet1_num_mapped_reads.txt -rw-r--r-- 1 kkarri pulmseq 245385 Aug 31 00:34 /scratch/474639.1.b/Input/F_Soluble_Nuclear0.out -rw-r--r-- 1 kkarri pulmseq 9 Aug 31 00:34 /scratch/474639.1.b/Input/F_Soluble_Nuclear0_num_mapped_reads.txt -rw-r--r-- 1 kkarri pulmseq 245385 Aug 31 00:34 /scratch/474639.1.b/Input/F_Soluble_Nuclear1.out -rw-r--r-- 1 kkarri pulmseq 9 Aug 31 00:34 /scratch/474639.1.b/Input/F_Soluble_Nuclear1_num_mapped_reads.txt -rw-r--r-- 1 kkarri pulmseq 300238 Aug 31 00:34 /scratch/474639.1.b/Input/Intron_Only_Regions_Lengths.txt -rwxr-xr-x 1 kkarri pulmseq 9553 Aug 31 00:34 /scratch/474639.1.b/Input/Venn_Diff_Genes.R -rwxr-xr-x 1 kkarri pulmseq 3925 Aug 31 00:34 /scratch/474639.1.b/Input/formatForSegex_ver3.R /scratch/474639.1.b/Input/F_Chromatin_Pellet: total 8 drwxr-xr-x 2 kkarri pulmseq 4096 Aug 31 00:34 . drwxr-xr-x 4 kkarri pulmseq 4096 Aug 31 00:34 .. /scratch/474639.1.b/Input/F_Soluble_Nuclear: total 8 drwxr-xr-x 2 kkarri pulmseq 4096 Aug 31 00:34 . drwxr-xr-x 4 kkarri pulmseq 4096 Aug 31 00:34 .. ========================================================== List files in scratch total 72M drwxr-xr-x 3 kkarri pulmseq 4.0K Aug 31 00:34 . drwxrwxrwt. 28 root root 20K Aug 31 00:33 .. -rw-r--r-- 1 kkarri pulmseq 132 Aug 31 00:34 Condition_1.txt -rw-r--r-- 1 kkarri pulmseq 134 Aug 31 00:34 Condition_2.txt drwxr-xr-x 4 kkarri pulmseq 4.0K Aug 31 00:34 Input -rw-r--r-- 1 kkarri pulmseq 72M Aug 31 00:34 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri pulmseq 16K Aug 31 00:34 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 Aug 31 00:34 . drwxr-sr-x 6 kkarri waxmanlab 32K Aug 31 00:34 .. -rw-r--r-- 1 kkarri waxmanlab 0 Aug 31 00:34 DiffExp_1c_Venn_Tables_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11_HTSeq.txt ========================================================== ========================================================== Finished on : Thu Aug 31 00:34:21 EDT 2017 0 minutes and 22 seconds elapsed. ==========================================================