----------------------- 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_7_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: NoInf_WT CONDITION_2_NAME: 120Inf_KO 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_7a COL_SUFFIX: GeneBody COUNT_PROGRAM: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon May 14 12:44:58 EDT 2018 Running on node : scc-ka4 Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/08a_DiffExp_7_HTSeq Current job ID : 6187919 Current job name : Step_08a_DiffExp_7a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/6187919.1.linga Loading required modules... ------------------------------------------ Sample_DIR: LZ_M13 Sample_ID: LZ_M13 Description: NoInf_WT1 M_Num: M13 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M13 Sample_DIR: LZ_M14 Sample_ID: LZ_M14 Description: NoInf_WT2 M_Num: M14 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M14 Sample_DIR: LZ_M15 Sample_ID: LZ_M15 Description: NoInf_WT3 M_Num: M15 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M15 M_Num_Cond1_List: M13M14M15 ------------------------------------------ ------------------------------------------ Sample_DIR: LZ_M27 Sample_ID: LZ_M27 Description: 120Inf_WT1 M_Num: M27 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M27 Sample_DIR: LZ_M28 Sample_ID: LZ_M28 Description: 120Inf_WT2 M_Num: M28 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M28 Sample_DIR: LZ_M29 Sample_ID: LZ_M29 Description: 120Inf_WT3 M_Num: M29 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M29 Sample_DIR: LZ_M30 Sample_ID: LZ_M30 Description: 120Inf_WT4 M_Num: M30 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M30 M_Num_Cond2_List: M27M28M29M30 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 3 NUM_REP_CONDITION1: 3 ========================================================== 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) number of mapped reads 17997472 14541218 15341066 11769783 18780983 16794942 14882109 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 248035 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246689 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246791 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245838 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO3.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO3_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 291522 May 14 12:45 /scratch/6187919.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 248221 May 14 12:45 /scratch/6187919.1.linga/Input/NoInf_WT0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187919.1.linga/Input/NoInf_WT0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247724 May 14 12:45 /scratch/6187919.1.linga/Input/NoInf_WT1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187919.1.linga/Input/NoInf_WT1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246958 May 14 12:45 /scratch/6187919.1.linga/Input/NoInf_WT2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187919.1.linga/Input/NoInf_WT2_num_mapped_reads.txt /scratch/6187919.1.linga/Input/120Inf_KO: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 14 12:45 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 14 12:45 .. /scratch/6187919.1.linga/Input/NoInf_WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 14 12:45 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 14 12:45 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R NoInf_WT 120Inf_KO 3 4 RefSeq_GeneBody.gtf /scratch/6187919.1.linga/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "NoInf_WT" [1] "120Inf_KO" [1] 3 [1] 4 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/6187919.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" load GTF file ... parse attributes ... [1] "output file is in: /scratch/6187919.1.linga/Input/DiffExp_v2_GeneBody_NoInf_WT_120Inf_KO.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_NoInf_WT_120Inf_KO.txt 120Inf_KO_LZ_M27M28M29M30_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== Comparison_Info: 120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R 120Inf_KO_LZ_M27M28M29M30_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "120Inf_KO_LZ_M27M28M29M30_vs_NoInf_WT_LZ_M13M14M15_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_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 11 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 11 7 [1] "Check out Up_Genes_DESeq_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt!" [1] "Check out Down_Genes_DESeq_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt!" Rscript Diff_Genes.R 120Inf_KO_LZ_M27M28M29M30_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "120Inf_KO_LZ_M27M28M29M30_vs_NoInf_WT_LZ_M13M14M15_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_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 77 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 65 7 [1] "Check out Up_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt!" [1] "Check out Down_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt Down_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt GeneBody_Counting DiffExp_7a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_7a" [1] "-----------------" [1] "Down.DESeq.GeneBody.HTSeq" [1] "Down.EdgeR.GeneBody.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_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt Up_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt GeneBody_Counting DiffExp_7a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_7a" [1] "-----------------" [1] "Up.DESeq.GeneBody.HTSeq" [1] "Up.EdgeR.GeneBody.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 248035 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246689 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246791 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245838 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO3.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:45 /scratch/6187919.1.linga/Input/120Inf_KO3_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 3564011 May 14 12:48 /scratch/6187919.1.linga/Input/120Inf_KO_LZ_M27M28M29M30_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 3515617 May 14 12:48 /scratch/6187919.1.linga/Input/120Inf_KO_LZ_M27M28M29M30_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 290 May 14 12:48 /scratch/6187919.1.linga/Input/DiffExp_7a_Venn_Tables_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt -rw-r--r-- 1 kkarri waxmanlab 8591853 May 14 12:47 /scratch/6187919.1.linga/Input/DiffExp_v2_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 May 14 12:44 /scratch/6187919.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 1118 May 14 12:48 /scratch/6187919.1.linga/Input/Down_Genes_DESeq_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt -rw-r--r-- 1 kkarri waxmanlab 6095 May 14 12:48 /scratch/6187919.1.linga/Input/Down_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt -rw-r--r-- 1 kkarri waxmanlab 291522 May 14 12:45 /scratch/6187919.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 248221 May 14 12:45 /scratch/6187919.1.linga/Input/NoInf_WT0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187919.1.linga/Input/NoInf_WT0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247724 May 14 12:45 /scratch/6187919.1.linga/Input/NoInf_WT1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187919.1.linga/Input/NoInf_WT1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246958 May 14 12:45 /scratch/6187919.1.linga/Input/NoInf_WT2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187919.1.linga/Input/NoInf_WT2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 1420 May 14 12:48 /scratch/6187919.1.linga/Input/Up_Genes_DESeq_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt -rw-r--r-- 1 kkarri waxmanlab 9062 May 14 12:48 /scratch/6187919.1.linga/Input/Up_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 May 14 12:44 /scratch/6187919.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 35824 May 14 12:48 /scratch/6187919.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 33531 May 14 12:48 /scratch/6187919.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 May 14 12:44 /scratch/6187919.1.linga/Input/formatForSegex_ver3.R /scratch/6187919.1.linga/Input/120Inf_KO: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 14 12:45 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 14 12:48 .. /scratch/6187919.1.linga/Input/NoInf_WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 14 12:45 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 14 12:48 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K May 14 12:48 . drwxrwxrwt. 64 root root 84K May 14 12:47 .. -rw-r--r-- 1 kkarri waxmanlab 105 May 14 12:44 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 133 May 14 12:44 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K May 14 12:48 Input -rw-r--r-- 1 kkarri waxmanlab 72M May 14 12:44 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 16K May 14 12:44 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 13M drwxr-sr-x 2 kkarri waxmanlab 32K May 14 12:48 . drwxr-sr-x 7 kkarri waxmanlab 32K May 14 12:46 .. -rw-r--r-- 1 kkarri waxmanlab 3.4M May 14 12:48 120Inf_KO_LZ_M27M28M29M30_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 3.4M May 14 12:48 120Inf_KO_LZ_M27M28M29M30_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 290 May 14 12:48 DiffExp_7a_Venn_Tables_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 8.2M May 14 12:48 DiffExp_v2_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 1.1K May 14 12:48 Down_Genes_DESeq_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 6.0K May 14 12:48 Down_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 1.4K May 14 12:48 Up_Genes_DESeq_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 8.9K May 14 12:48 Up_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M27M28M29M30_NoInf_WT_LZ_M13M14M15_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 35K May 14 12:48 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 33K May 14 12:48 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_HTSeq.png ========================================================== ========================================================== Finished on : Mon May 14 12:48:08 EDT 2018 3 minutes and 10 seconds elapsed. ==========================================================