----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/08a_DiffExp_3_HTSeq Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion Dataset_Label: LZ GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: 150Inf_WT CONDITION_2_NAME: 150Inf_KO 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_3c COL_SUFFIX: Intronic_Only COUNT_PROGRAM: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Sun May 13 16:21:37 EDT 2018 Running on node : scc-ka4 Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/08a_DiffExp_3_HTSeq Current job ID : 6184866 Current job name : Step_08a_DiffExp_3c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/6184866.1.linga Loading required modules... ------------------------------------------ Sample_DIR: LZ_M27 Sample_ID: LZ_M27 Description: 150Inf_WT1 M_Num: M27 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M27 Sample_DIR: LZ_M28 Sample_ID: LZ_M28 Description: 150Inf_WT2 M_Num: M28 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M28 Sample_DIR: LZ_M29 Sample_ID: LZ_M29 Description: 150Inf_WT3 M_Num: M29 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M29 Sample_DIR: LZ_M30 Sample_ID: LZ_M30 Description: 150Inf_WT4 M_Num: M30 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M30 M_Num_Cond1_List: M27M28M29M30 ------------------------------------------ ------------------------------------------ Sample_DIR: LZ_M31 Sample_ID: LZ_M31 Description: 150Inf_KO1 M_Num: M31 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M31 Sample_DIR: LZ_M32 Sample_ID: LZ_M32 Description: 150Inf_KO2 M_Num: M32 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M32 Sample_DIR: LZ_M33 Sample_ID: LZ_M33 Description: 150Inf_KO3 M_Num: M33 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M33 Sample_DIR: LZ_M34 Sample_ID: LZ_M34 Description: 150Inf_KO4 M_Num: M34 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M34 M_Num_Cond2_List: M31M32M33M34 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 4 NUM_REP_CONDITION1: 4 ========================================================== 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) 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 13129683 17473331 15643222 17693260 17997472 14541218 15341066 11769783 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 235963 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237416 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 236784 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237245 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO3.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO3_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238121 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 236418 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237287 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 234805 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT3.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT3_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 300238 May 13 16:21 /scratch/6184866.1.linga/Input/Intron_Only_Regions_Lengths.txt /scratch/6184866.1.linga/Input/150Inf_KO: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 13 16:21 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 13 16:21 .. /scratch/6184866.1.linga/Input/150Inf_WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 13 16:21 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 13 16:21 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R 150Inf_WT 150Inf_KO 4 4 RefSeq_GeneBody.gtf /scratch/6184866.1.linga/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "150Inf_WT" [1] "150Inf_KO" [1] 4 [1] 4 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/6184866.1.linga/Input" [1] "DiffExp_v2_Intronic_Only" [1] "Intron_Only_Regions_Lengths.txt" load GTF file ... parse attributes ... [1] "output file is in: /scratch/6184866.1.linga/Input/DiffExp_v2_Intronic_Only_150Inf_WT_150Inf_KO.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_150Inf_WT_150Inf_KO.txt 150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== Comparison_Info: 150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R 150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_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_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 1 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 0 7 [1] "Check out Up_Genes_DESeq_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt!" [1] "Check out Down_Genes_DESeq_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt!" Rscript Diff_Genes.R 150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_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_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 1 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 0 7 [1] "Check out Up_Genes_EdgeR_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt!" [1] "Check out Down_Genes_EdgeR_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt Down_Genes_EdgeR_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt Intronic_Only_Counting DiffExp_3c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3c" [1] "-----------------" [1] "Down.DESeq.Intronic_Only.HTSeq" [1] "Down.EdgeR.Intronic_Only.HTSeq" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt Up_Genes_EdgeR_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt Intronic_Only_Counting DiffExp_3c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3c" [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 235963 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237416 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 236784 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237245 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO3.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_KO3_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2450985 May 13 16:24 /scratch/6184866.1.linga/Input/150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2644561 May 13 16:24 /scratch/6184866.1.linga/Input/150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 238121 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 236418 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 237287 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 234805 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT3.out -rw-r--r-- 1 kkarri waxmanlab 9 May 13 16:21 /scratch/6184866.1.linga/Input/150Inf_WT3_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 155 May 13 16:24 /scratch/6184866.1.linga/Input/DiffExp_3c_Venn_Tables_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt -rw-r--r-- 1 kkarri waxmanlab 8443306 May 13 16:24 /scratch/6184866.1.linga/Input/DiffExp_v2_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 May 13 16:21 /scratch/6184866.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 178 May 13 16:24 /scratch/6184866.1.linga/Input/Down_Genes_DESeq_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt -rw-r--r-- 1 kkarri waxmanlab 178 May 13 16:24 /scratch/6184866.1.linga/Input/Down_Genes_EdgeR_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt -rw-r--r-- 1 kkarri waxmanlab 300238 May 13 16:21 /scratch/6184866.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 241 May 13 16:24 /scratch/6184866.1.linga/Input/Up_Genes_DESeq_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt -rw-r--r-- 1 kkarri waxmanlab 246 May 13 16:24 /scratch/6184866.1.linga/Input/Up_Genes_EdgeR_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 May 13 16:21 /scratch/6184866.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 30124 May 13 16:24 /scratch/6184866.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 May 13 16:21 /scratch/6184866.1.linga/Input/formatForSegex_ver3.R /scratch/6184866.1.linga/Input/150Inf_KO: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 13 16:21 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 13 16:24 .. /scratch/6184866.1.linga/Input/150Inf_WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 13 16:21 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 13 16:24 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K May 13 16:24 . drwxrwxrwt. 53 root root 84K May 13 16:21 .. -rw-r--r-- 1 kkarri waxmanlab 133 May 13 16:21 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 133 May 13 16:21 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K May 13 16:24 Input -rw-r--r-- 1 kkarri waxmanlab 72M May 13 16:21 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 16K May 13 16:21 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 May 13 16:24 . drwxr-sr-x 7 kkarri waxmanlab 32K May 13 16:21 .. -rw-r--r-- 1 kkarri waxmanlab 2.4M May 13 16:24 150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.6M May 13 16:24 150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 155 May 13 16:24 DiffExp_3c_Venn_Tables_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 8.1M May 13 16:24 DiffExp_v2_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 178 May 13 16:24 Down_Genes_DESeq_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 178 May 13 16:24 Down_Genes_EdgeR_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 241 May 13 16:24 Up_Genes_DESeq_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 246 May 13 16:24 Up_Genes_EdgeR_Intronic_Only_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 30K May 13 16:24 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_HTSeq.png ========================================================== ========================================================== Finished on : Sun May 13 16:24:16 EDT 2018 2 minutes and 39 seconds elapsed. ==========================================================