----------------------- 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_5_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_KO 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_5a COL_SUFFIX: GeneBody COUNT_PROGRAM: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon May 14 12:44:58 EDT 2018 Running on node : scc-kb1 Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/08a_DiffExp_5_HTSeq Current job ID : 6187913 Current job name : Step_08a_DiffExp_5a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/6187913.1.linga Loading required modules... ------------------------------------------ Sample_DIR: LZ_M16 Sample_ID: LZ_M16 Description: NoInf_KO1 M_Num: M16 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M16 Sample_DIR: LZ_M17 Sample_ID: LZ_M17 Description: NoInf_KO2 M_Num: M17 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M17 Sample_DIR: LZ_M18 Sample_ID: LZ_M18 Description: NoInf_KO3 M_Num: M18 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: LZ_M18 M_Num_Cond1_List: M16M17M18 ------------------------------------------ ------------------------------------------ Sample_DIR: LZ_M31 Sample_ID: LZ_M31 Description: 120Inf_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: 120Inf_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: 120Inf_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: 120Inf_KO3 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: 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 13129683 17473331 15643222 17693260 12477518 14799385 12279245 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 245851 May 14 12:45 /scratch/6187913.1.linga/Input/120Inf_KO0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187913.1.linga/Input/120Inf_KO0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247883 May 14 12:45 /scratch/6187913.1.linga/Input/120Inf_KO1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187913.1.linga/Input/120Inf_KO1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247447 May 14 12:45 /scratch/6187913.1.linga/Input/120Inf_KO2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187913.1.linga/Input/120Inf_KO2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247886 May 14 12:45 /scratch/6187913.1.linga/Input/120Inf_KO3.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:45 /scratch/6187913.1.linga/Input/120Inf_KO3_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 291522 May 14 12:45 /scratch/6187913.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 246264 May 14 12:45 /scratch/6187913.1.linga/Input/NoInf_KO0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187913.1.linga/Input/NoInf_KO0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246926 May 14 12:45 /scratch/6187913.1.linga/Input/NoInf_KO1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187913.1.linga/Input/NoInf_KO1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246038 May 14 12:45 /scratch/6187913.1.linga/Input/NoInf_KO2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187913.1.linga/Input/NoInf_KO2_num_mapped_reads.txt /scratch/6187913.1.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/6187913.1.linga/Input/NoInf_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 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R NoInf_KO 120Inf_KO 3 4 RefSeq_GeneBody.gtf /scratch/6187913.1.linga/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "NoInf_KO" [1] "120Inf_KO" [1] 3 [1] 4 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/6187913.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" load GTF file ... parse attributes ... [1] "output file is in: /scratch/6187913.1.linga/Input/DiffExp_v2_GeneBody_NoInf_KO_120Inf_KO.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_NoInf_KO_120Inf_KO.txt 120Inf_KO_LZ_M31M32M33M34_vs_NoInf_KO_LZ_M16M17M18_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== Comparison_Info: 120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R 120Inf_KO_LZ_M31M32M33M34_vs_NoInf_KO_LZ_M16M17M18_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "120Inf_KO_LZ_M31M32M33M34_vs_NoInf_KO_LZ_M16M17M18_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_M31M32M33M34_NoInf_KO_LZ_M16M17M18" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 48 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 22 7 [1] "Check out Up_Genes_DESeq_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt!" [1] "Check out Down_Genes_DESeq_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt!" Rscript Diff_Genes.R 120Inf_KO_LZ_M31M32M33M34_vs_NoInf_KO_LZ_M16M17M18_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "120Inf_KO_LZ_M31M32M33M34_vs_NoInf_KO_LZ_M16M17M18_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_M31M32M33M34_NoInf_KO_LZ_M16M17M18" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 129 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 90 7 [1] "Check out Up_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt!" [1] "Check out Down_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt Down_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt GeneBody_Counting DiffExp_5a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_5a" [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_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt Up_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt GeneBody_Counting DiffExp_5a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_5a" [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 245851 May 14 12:45 /scratch/6187913.1.linga/Input/120Inf_KO0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187913.1.linga/Input/120Inf_KO0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247883 May 14 12:45 /scratch/6187913.1.linga/Input/120Inf_KO1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187913.1.linga/Input/120Inf_KO1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247447 May 14 12:45 /scratch/6187913.1.linga/Input/120Inf_KO2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187913.1.linga/Input/120Inf_KO2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247886 May 14 12:45 /scratch/6187913.1.linga/Input/120Inf_KO3.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:45 /scratch/6187913.1.linga/Input/120Inf_KO3_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 3176859 May 14 12:47 /scratch/6187913.1.linga/Input/120Inf_KO_LZ_M31M32M33M34_vs_NoInf_KO_LZ_M16M17M18_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 3055874 May 14 12:47 /scratch/6187913.1.linga/Input/120Inf_KO_LZ_M31M32M33M34_vs_NoInf_KO_LZ_M16M17M18_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 291 May 14 12:47 /scratch/6187913.1.linga/Input/DiffExp_5a_Venn_Tables_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt -rw-r--r-- 1 kkarri waxmanlab 8591198 May 14 12:47 /scratch/6187913.1.linga/Input/DiffExp_v2_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 May 14 12:44 /scratch/6187913.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 2361 May 14 12:47 /scratch/6187913.1.linga/Input/Down_Genes_DESeq_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt -rw-r--r-- 1 kkarri waxmanlab 9034 May 14 12:47 /scratch/6187913.1.linga/Input/Down_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt -rw-r--r-- 1 kkarri waxmanlab 291522 May 14 12:45 /scratch/6187913.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 246264 May 14 12:45 /scratch/6187913.1.linga/Input/NoInf_KO0.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187913.1.linga/Input/NoInf_KO0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246926 May 14 12:45 /scratch/6187913.1.linga/Input/NoInf_KO1.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187913.1.linga/Input/NoInf_KO1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246038 May 14 12:45 /scratch/6187913.1.linga/Input/NoInf_KO2.out -rw-r--r-- 1 kkarri waxmanlab 9 May 14 12:44 /scratch/6187913.1.linga/Input/NoInf_KO2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 4531 May 14 12:47 /scratch/6187913.1.linga/Input/Up_Genes_DESeq_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt -rw-r--r-- 1 kkarri waxmanlab 11931 May 14 12:47 /scratch/6187913.1.linga/Input/Up_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 May 14 12:44 /scratch/6187913.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 37274 May 14 12:47 /scratch/6187913.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 36854 May 14 12:47 /scratch/6187913.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 May 14 12:44 /scratch/6187913.1.linga/Input/formatForSegex_ver3.R /scratch/6187913.1.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 12:47 .. /scratch/6187913.1.linga/Input/NoInf_KO: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 14 12:45 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 14 12:47 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K May 14 12:47 . drwxrwxrwt. 55 root root 180K 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 12:47 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 11M drwxr-sr-x 2 kkarri waxmanlab 32K May 14 12:47 . drwxr-sr-x 7 kkarri waxmanlab 32K May 14 12:44 .. -rw-r--r-- 1 kkarri waxmanlab 3.1M May 14 12:47 120Inf_KO_LZ_M31M32M33M34_vs_NoInf_KO_LZ_M16M17M18_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 3.0M May 14 12:47 120Inf_KO_LZ_M31M32M33M34_vs_NoInf_KO_LZ_M16M17M18_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 291 May 14 12:47 DiffExp_5a_Venn_Tables_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 8.2M May 14 12:47 DiffExp_v2_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.4K May 14 12:47 Down_Genes_DESeq_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 8.9K May 14 12:47 Down_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 4.5K May 14 12:47 Up_Genes_DESeq_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 12K May 14 12:47 Up_Genes_EdgeR_GeneBody_120Inf_KO_LZ_M31M32M33M34_NoInf_KO_LZ_M16M17M18_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 37K May 14 12:47 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 36K May 14 12:47 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_HTSeq.png ========================================================== ========================================================== Finished on : Mon May 14 12:47:56 EDT 2018 2 minutes and 58 seconds elapsed. ==========================================================