----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/08c_DiffExp_3_lncRNA_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion Dataset_Label: LZ ANNOTATION_FILE_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt CONDITION_1_NAME: 150Inf_WT CONDITION_2_NAME: 150Inf_KO Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: ncRNA_genebodies_for_counting_lengths.txt COUNT_DIR: LncRNA_GeneBody_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_GeneBody DiffExp_Index: DiffExp_3e COL_SUFFIX: LncRNA_GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri May 11 18:48:38 EDT 2018 Running on node : scc-kb3 Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/08c_DiffExp_3_lncRNA_featureCounts Current job ID : 6179963 Current job name : Step_08c_DiffExp_3e Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/6179963.1.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 Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: LZ_M28 Sample_ID: LZ_M28 Description: 150Inf_WT2 M_Num: M28 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: LZ_M29 Sample_ID: LZ_M29 Description: 150Inf_WT3 M_Num: M29 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: LZ_M30 Sample_ID: LZ_M30 Description: 150Inf_WT4 M_Num: M30 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder 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 Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: LZ_M32 Sample_ID: LZ_M32 Description: 150Inf_KO2 M_Num: M32 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: LZ_M33 Sample_ID: LZ_M33 Description: 150Inf_KO3 M_Num: M33 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: LZ_M34 Sample_ID: LZ_M34 Description: 150Inf_KO4 M_Num: M34 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder M_Num_Cond2_List: M31M32M33M34 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 4 NUM_REP_CONDITION1: 4 ========================================================== Renaming input count files number of mapped reads (feature count summary) Status LZ_M31_sorted.bam Assigned 11867603 Unassigned_Ambiguity 388209 Unassigned_MultiMapping 0 Unassigned_NoFeatures 873871 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M32_sorted.bam Assigned 15858244 Unassigned_Ambiguity 431170 Unassigned_MultiMapping 0 Unassigned_NoFeatures 1183917 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M33_sorted.bam Assigned 14279071 Unassigned_Ambiguity 403555 Unassigned_MultiMapping 0 Unassigned_NoFeatures 960596 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M34_sorted.bam Assigned 15984783 Unassigned_Ambiguity 601602 Unassigned_MultiMapping 0 Unassigned_NoFeatures 1106875 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M27_sorted.bam Assigned 16343524 Unassigned_Ambiguity 429766 Unassigned_MultiMapping 0 Unassigned_NoFeatures 1224182 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M28_sorted.bam Assigned 13164593 Unassigned_Ambiguity 396347 Unassigned_MultiMapping 0 Unassigned_NoFeatures 980278 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M29_sorted.bam Assigned 13846124 Unassigned_Ambiguity 493879 Unassigned_MultiMapping 0 Unassigned_NoFeatures 1001063 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M30_sorted.bam Assigned 10634012 Unassigned_Ambiguity 362769 Unassigned_MultiMapping 0 Unassigned_NoFeatures 773002 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 714006 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO0.out -rw-r--r-- 1 kkarri waxmanlab 296 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO0.summary -rw-r--r-- 1 kkarri waxmanlab 716258 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO1.out -rw-r--r-- 1 kkarri waxmanlab 297 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO1.summary -rw-r--r-- 1 kkarri waxmanlab 715602 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO2.out -rw-r--r-- 1 kkarri waxmanlab 296 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO2.summary -rw-r--r-- 1 kkarri waxmanlab 716123 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO3.out -rw-r--r-- 1 kkarri waxmanlab 297 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO3.summary -rw-r--r-- 1 kkarri waxmanlab 716474 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT0.out -rw-r--r-- 1 kkarri waxmanlab 297 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT0.summary -rw-r--r-- 1 kkarri waxmanlab 714808 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT1.out -rw-r--r-- 1 kkarri waxmanlab 296 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT1.summary -rw-r--r-- 1 kkarri waxmanlab 715277 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT2.out -rw-r--r-- 1 kkarri waxmanlab 297 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT2.summary -rw-r--r-- 1 kkarri waxmanlab 713550 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT3.out -rw-r--r-- 1 kkarri waxmanlab 296 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT3.summary -rw-r--r-- 1 kkarri waxmanlab 815529 May 11 18:48 /scratch/6179963.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/6179963.1.linga/Input/150Inf_KO: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 11 18:48 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 11 18:48 .. /scratch/6179963.1.linga/Input/150Inf_WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 11 18:48 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 11 18:48 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R 150Inf_WT 150Inf_KO 4 4 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/6179963.1.linga/Input DiffExp_v2_LncRNA_GeneBody ncRNA_genebodies_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "150Inf_WT" [1] "150Inf_KO" [1] 4 [1] 4 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/6179963.1.linga/Input" [1] "DiffExp_v2_LncRNA_GeneBody" [1] "ncRNA_genebodies_for_counting_lengths.txt" [1] 15558 23 [1] 15558 60 [1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" "chr9" [1] "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" [10] "chr19" [1] "chrX" "chrY" [1] "output file is in: /scratch/6179963.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_150Inf_WT_150Inf_KO.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_GeneBody_150Inf_WT_150Inf_KO.txt 150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload 1 LncRNA_GeneBody ========================================================== 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_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_GeneBody'_'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_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "LncRNA_GeneBody_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] 0 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 0 7 [1] "Check out Up_Genes_DESeq_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt!" Rscript Diff_Genes.R 150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_GeneBody'_'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_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "LncRNA_GeneBody_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] 0 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 2 7 [1] "Check out Up_Genes_EdgeR_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_GeneBody_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_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt Down_Genes_EdgeR_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt LncRNA_GeneBody_Counting DiffExp_3e [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3e" [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_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt Up_Genes_EdgeR_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt LncRNA_GeneBody_Counting DiffExp_3e [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3e" [1] "-----------------" [1] "Up.DESeq.GeneBody.HTSeq" [1] "Up.EdgeR.GeneBody.HTSeq" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- Comparison_Info: 150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 714006 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO0.out -rw-r--r-- 1 kkarri waxmanlab 296 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO0.summary -rw-r--r-- 1 kkarri waxmanlab 716258 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO1.out -rw-r--r-- 1 kkarri waxmanlab 297 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO1.summary -rw-r--r-- 1 kkarri waxmanlab 715602 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO2.out -rw-r--r-- 1 kkarri waxmanlab 296 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO2.summary -rw-r--r-- 1 kkarri waxmanlab 716123 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO3.out -rw-r--r-- 1 kkarri waxmanlab 297 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_KO3.summary -rw-r--r-- 1 kkarri waxmanlab 1623539 May 11 18:50 /scratch/6179963.1.linga/Input/150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1685771 May 11 18:50 /scratch/6179963.1.linga/Input/150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 716474 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT0.out -rw-r--r-- 1 kkarri waxmanlab 297 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT0.summary -rw-r--r-- 1 kkarri waxmanlab 714808 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT1.out -rw-r--r-- 1 kkarri waxmanlab 296 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT1.summary -rw-r--r-- 1 kkarri waxmanlab 715277 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT2.out -rw-r--r-- 1 kkarri waxmanlab 297 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT2.summary -rw-r--r-- 1 kkarri waxmanlab 713550 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT3.out -rw-r--r-- 1 kkarri waxmanlab 296 May 11 18:48 /scratch/6179963.1.linga/Input/150Inf_WT3.summary -rw-r--r-- 1 kkarri waxmanlab 151 May 11 18:50 /scratch/6179963.1.linga/Input/DiffExp_3e_Venn_Tables_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt -rw-r--r-- 1 kkarri waxmanlab 5401420 May 11 18:50 /scratch/6179963.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 May 11 18:48 /scratch/6179963.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 192 May 11 18:50 /scratch/6179963.1.linga/Input/Down_Genes_DESeq_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt -rw-r--r-- 1 kkarri waxmanlab 336 May 11 18:50 /scratch/6179963.1.linga/Input/Down_Genes_EdgeR_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt -rw-r--r-- 1 kkarri waxmanlab 192 May 11 18:50 /scratch/6179963.1.linga/Input/Up_Genes_DESeq_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt -rw-r--r-- 1 kkarri waxmanlab 192 May 11 18:50 /scratch/6179963.1.linga/Input/Up_Genes_EdgeR_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30.txt -rw-r--r-- 1 kkarri waxmanlab 2204 May 11 18:50 /scratch/6179963.1.linga/Input/VennDiagram2018-05-11_18-50-27.log -rwxr-xr-x 1 kkarri waxmanlab 9993 May 11 18:48 /scratch/6179963.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 32308 May 11 18:50 /scratch/6179963.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 4968 May 11 18:48 /scratch/6179963.1.linga/Input/formatForSegex_ver3.R -rw-r--r-- 1 kkarri waxmanlab 815529 May 11 18:48 /scratch/6179963.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/6179963.1.linga/Input/150Inf_KO: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 11 18:48 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 11 18:50 .. /scratch/6179963.1.linga/Input/150Inf_WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 11 18:48 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 11 18:50 .. ========================================================== List files in scratch total 3.5M drwx------ 3 kkarri waxmanlab 4.0K May 11 18:50 . drwxrwxrwt. 55 root root 112K May 11 18:48 .. -rw-r--r-- 1 kkarri waxmanlab 133 May 11 18:48 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 133 May 11 18:48 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K May 11 18:50 Input -rwxr-xr-x 1 kkarri waxmanlab 13K May 11 18:48 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M May 11 18:48 ncRNA_output_filtered_final_gene.txt ========================================================== Re-naming files in OUTPUT_DIR Need to append the COUNT_PROGRAM name to all output files List files in OUTPUT_DIR total 7.1M drwxr-sr-x 2 kkarri waxmanlab 32K May 11 18:50 . drwxr-sr-x 7 kkarri waxmanlab 32K May 11 18:48 .. -rw-r--r-- 1 kkarri waxmanlab 1.6M May 11 18:50 150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.7M May 11 18:50 150Inf_KO_LZ_M31M32M33M34_vs_150Inf_WT_LZ_M27M28M29M30_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 151 May 11 18:50 DiffExp_3e_Venn_Tables_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.2M May 11 18:50 DiffExp_v2_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 192 May 11 18:50 Down_Genes_DESeq_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 336 May 11 18:50 Down_Genes_EdgeR_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 192 May 11 18:50 Up_Genes_DESeq_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 192 May 11 18:50 Up_Genes_EdgeR_LncRNA_GeneBody_150Inf_KO_LZ_M31M32M33M34_150Inf_WT_LZ_M27M28M29M30_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 32K May 11 18:50 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Fri May 11 18:50:28 EDT 2018 1 minutes and 50 seconds elapsed. ==========================================================