----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/08a_DiffExp_1_HTSeq Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion Dataset_Label: LZ GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: Exon_Only_Regions.gtf CONDITION_1_NAME: NoInf_WT CONDITION_2_NAME: NoInf_KO 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: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri May 11 18:11:53 EDT 2018 Running on node : scc-tm1 Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/08a_DiffExp_1_HTSeq Current job ID : 6179550 Current job name : Step_08a_DiffExp_1b Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/6179550.1.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_M16 Sample_ID: LZ_M16 Description: NoInf_KO1 M_Num: M16 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M16 Sample_DIR: LZ_M17 Sample_ID: LZ_M17 Description: NoInf_KO2 M_Num: M17 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M17 Sample_DIR: LZ_M18 Sample_ID: LZ_M18 Description: NoInf_KO3 M_Num: M18 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: LZ_M18 M_Num_Cond2_List: M16M17M18 ------------------------------------------ ========================================================== 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) number of mapped reads 12477518 14799385 12279245 18780983 16794942 14882109 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291285 May 11 18:11 /scratch/6179550.1.linga/Input/Exon_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 244955 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_KO0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_KO0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245604 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_KO1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_KO1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244707 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_KO2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_KO2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246871 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_WT0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_WT0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246341 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_WT1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_WT1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245647 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_WT2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_WT2_num_mapped_reads.txt /scratch/6179550.1.linga/Input/NoInf_KO: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 11 18:11 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 11 18:11 .. /scratch/6179550.1.linga/Input/NoInf_WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 11 18:11 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 11 18:11 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R NoInf_WT NoInf_KO 3 3 Exon_Only_Regions.gtf /scratch/6179550.1.linga/Input DiffExp_v2_Exonic_Only Exon_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "NoInf_WT" [1] "NoInf_KO" [1] 3 [1] 3 [1] "Exon_Only_Regions.gtf" [1] "/scratch/6179550.1.linga/Input" [1] "DiffExp_v2_Exonic_Only" [1] "Exon_Only_Regions_Lengths.txt" load GTF file ... parse attributes ... [1] "output file is in: /scratch/6179550.1.linga/Input/DiffExp_v2_Exonic_Only_NoInf_WT_NoInf_KO.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Exonic_Only_NoInf_WT_NoInf_KO.txt NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_Exonic_Only_forSEGEXUpload 1 Exonic_Only ========================================================== Comparison_Info: NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Exonic_Only'_'NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_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_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 41 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 55 7 [1] "Check out Up_Genes_DESeq_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt!" [1] "Check out Down_Genes_DESeq_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt!" Rscript Diff_Genes.R NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Exonic_Only'_'NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_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_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 128 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 103 7 [1] "Check out Up_Genes_EdgeR_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt!" [1] "Check out Down_Genes_EdgeR_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt Down_Genes_EdgeR_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt Exonic_Only_Counting DiffExp_1b [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.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_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt Up_Genes_EdgeR_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt Exonic_Only_Counting DiffExp_1b [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.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 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 310 May 11 18:12 /scratch/6179550.1.linga/Input/DiffExp_1b_Venn_Tables_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt -rw-r--r-- 1 kkarri waxmanlab 7365581 May 11 18:12 /scratch/6179550.1.linga/Input/DiffExp_v2_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 May 11 18:11 /scratch/6179550.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 11213 May 11 18:12 /scratch/6179550.1.linga/Input/Down_Genes_DESeq_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt -rw-r--r-- 1 kkarri waxmanlab 14966 May 11 18:12 /scratch/6179550.1.linga/Input/Down_Genes_EdgeR_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt -rw-r--r-- 1 kkarri waxmanlab 291285 May 11 18:11 /scratch/6179550.1.linga/Input/Exon_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 244955 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_KO0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_KO0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245604 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_KO1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_KO1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244707 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_KO2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_KO2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 5596579 May 11 18:12 /scratch/6179550.1.linga/Input/NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 4193153 May 11 18:12 /scratch/6179550.1.linga/Input/NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 246871 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_WT0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_WT0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246341 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_WT1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_WT1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245647 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_WT2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 11 18:11 /scratch/6179550.1.linga/Input/NoInf_WT2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 4367 May 11 18:12 /scratch/6179550.1.linga/Input/Up_Genes_DESeq_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt -rw-r--r-- 1 kkarri waxmanlab 11775 May 11 18:12 /scratch/6179550.1.linga/Input/Up_Genes_EdgeR_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 May 11 18:11 /scratch/6179550.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 40334 May 11 18:12 /scratch/6179550.1.linga/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 36392 May 11 18:12 /scratch/6179550.1.linga/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 May 11 18:11 /scratch/6179550.1.linga/Input/formatForSegex_ver3.R /scratch/6179550.1.linga/Input/NoInf_KO: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 11 18:11 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 11 18:12 .. /scratch/6179550.1.linga/Input/NoInf_WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 11 18:11 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 11 18:12 .. ========================================================== List files in scratch total 19M drwx------ 3 kkarri waxmanlab 4.0K May 11 18:12 . drwxrwxrwt. 26 root root 20K May 11 18:11 .. -rw-r--r-- 1 kkarri waxmanlab 105 May 11 18:11 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 105 May 11 18:11 Condition_2.txt -rw-r--r-- 1 kkarri waxmanlab 19M May 11 18:11 Exon_Only_Regions.gtf drwxr-xr-x 4 kkarri waxmanlab 4.0K May 11 18:12 Input -rwxr-xr-x 1 kkarri waxmanlab 16K May 11 18:11 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 15M drwxr-sr-x 2 kkarri waxmanlab 32K May 11 18:12 . drwxr-sr-x 6 kkarri waxmanlab 32K May 11 18:11 .. -rw-r--r-- 1 kkarri waxmanlab 310 May 11 18:12 DiffExp_1b_Venn_Tables_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 7.1M May 11 18:12 DiffExp_v2_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 11K May 11 18:12 Down_Genes_DESeq_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 15K May 11 18:12 Down_Genes_EdgeR_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 5.4M May 11 18:12 NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 4.0M May 11 18:12 NoInf_KO_LZ_M16M17M18_vs_NoInf_WT_LZ_M13M14M15_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 4.3K May 11 18:12 Up_Genes_DESeq_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 12K May 11 18:12 Up_Genes_EdgeR_Exonic_Only_NoInf_KO_LZ_M16M17M18_NoInf_WT_LZ_M13M14M15_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 40K May 11 18:12 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 36K May 11 18:12 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_HTSeq.png ========================================================== ========================================================== Finished on : Fri May 11 18:12:51 EDT 2018 0 minutes and 58 seconds elapsed. ==========================================================