----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/09a_DiffExp_4_HTSeq Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP Dataset_Label: G168_TCPO_Env GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: WT-TCPO-Day5_G168_G169_M18M19M20 CONDITION_2_NAME: Met-EGFKO-TCPO-Day5_G168_G169_M21M22 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_4a COL_SUFFIX: GeneBody COUNT_PROGRAM: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Apr 15 18:04:10 EDT 2019 Running on node : scc-yi3 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/09a_DiffExp_4_HTSeq Current job ID : 5222943 Current job name : Step_09a_DiffExp_4a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5222943.1.y Loading required modules... ------------------------------------------ Sample_DIR: G168_G169_M18 Sample_ID: G168_G169_M18 Description: WT1-TCPO-Day5 M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M18 Sample_DIR: G168_G169_M19 Sample_ID: G168_G169_M19 Description: WT2-TCPO-Day5 M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M19 Sample_DIR: G168_G169_M20 Sample_ID: G168_G169_M20 Description: WT3-TCPO-Day5 M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M20 M_Num_Cond1_List: G169G169G169 ------------------------------------------ ------------------------------------------ Sample_DIR: G168_G169_M21 Sample_ID: G168_G169_M21 Description: Met-EGFKO1-TCPO-Day5 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M21 Sample_DIR: G168_G169_M22 Sample_ID: G168_G169_M22 Description: Met-EGFKO2-TCPO-Day5 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M22 M_Num_Cond2_List: G169G169 ------------------------------------------ ========================================================== 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) number of mapped reads 33292201 36559934 32532256 36884316 36166860 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291522 Apr 15 18:04 /scratch/5222943.1.y/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 248579 Apr 15 18:04 /scratch/5222943.1.y/Input/Met-EGFKO-TCPO-Day5_G168_G169_M21M220.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:04 /scratch/5222943.1.y/Input/Met-EGFKO-TCPO-Day5_G168_G169_M21M220_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249697 Apr 15 18:04 /scratch/5222943.1.y/Input/Met-EGFKO-TCPO-Day5_G168_G169_M21M221.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:04 /scratch/5222943.1.y/Input/Met-EGFKO-TCPO-Day5_G168_G169_M21M221_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 248315 Apr 15 18:04 /scratch/5222943.1.y/Input/WT-TCPO-Day5_G168_G169_M18M19M200.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:04 /scratch/5222943.1.y/Input/WT-TCPO-Day5_G168_G169_M18M19M200_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249221 Apr 15 18:04 /scratch/5222943.1.y/Input/WT-TCPO-Day5_G168_G169_M18M19M201.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:04 /scratch/5222943.1.y/Input/WT-TCPO-Day5_G168_G169_M18M19M201_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 248518 Apr 15 18:04 /scratch/5222943.1.y/Input/WT-TCPO-Day5_G168_G169_M18M19M202.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:04 /scratch/5222943.1.y/Input/WT-TCPO-Day5_G168_G169_M18M19M202_num_mapped_reads.txt /scratch/5222943.1.y/Input/Met-EGFKO-TCPO-Day5_G168_G169_M21M22: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 18:04 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 18:04 .. /scratch/5222943.1.y/Input/WT-TCPO-Day5_G168_G169_M18M19M20: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 18:04 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 18:04 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WT-TCPO-Day5_G168_G169_M18M19M20 Met-EGFKO-TCPO-Day5_G168_G169_M21M22 3 2 RefSeq_GeneBody.gtf /scratch/5222943.1.y/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt WARNING: ignoring environment value of R_HOME [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WT-TCPO-Day5_G168_G169_M18M19M20" [1] "Met-EGFKO-TCPO-Day5_G168_G169_M21M22" [1] 3 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/5222943.1.y/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" [1] "sum1:225700.047615196" "sum1:225128.480992397" "sum1:232548.898426236" [4] "sum1:227792.475677943" [1] "sum2:233833.423114036" "sum2:222071.90082893" "sum2:227952.661971483" load GTF file ... parse attributes ... [1] "output file is in: /scratch/5222943.1.y/Input/DiffExp_v2_GeneBody_WT-TCPO-Day5_G168_G169_M18M19M20_Met-EGFKO-TCPO-Day5_G168_G169_M21M22.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_WT-TCPO-Day5_G168_G169_M18M19M20_Met-EGFKO-TCPO-Day5_G168_G169_M21M22.txt Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_vs_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody WARNING: ignoring environment value of R_HOME Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_GeneBody_WT-TCPO-Day5_G168_G169_M18M19M20_Met-EGFKO-TCPO-Day5_G168_G169_M21M22.txt Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_vs_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody WARNING: ignoring environment value of R_HOME ========================================================== Comparison_Info: Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_vs_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_vs_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_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_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 287 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 153 7 [1] "Check out Up_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt!" Rscript Diff_Genes.R Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_vs_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_vs_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_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_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 462 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 185 7 [1] "Check out Up_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt Down_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt GeneBody_Counting DiffExp_4a WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_4a" [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_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt Up_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt GeneBody_Counting DiffExp_4a WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_4a" [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 295 Apr 15 18:06 /scratch/5222943.1.y/Input/DiffExp_4a_Venn_Tables_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 9707980 Apr 15 18:05 /scratch/5222943.1.y/Input/DiffExp_v2_GeneBody_WT-TCPO-Day5_G168_G169_M18M19M20_Met-EGFKO-TCPO-Day5_G168_G169_M21M22.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Apr 15 18:04 /scratch/5222943.1.y/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 31853 Apr 15 18:05 /scratch/5222943.1.y/Input/Down_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 30891 Apr 15 18:05 /scratch/5222943.1.y/Input/Down_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 291522 Apr 15 18:04 /scratch/5222943.1.y/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 248579 Apr 15 18:04 /scratch/5222943.1.y/Input/Met-EGFKO-TCPO-Day5_G168_G169_M21M220.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:04 /scratch/5222943.1.y/Input/Met-EGFKO-TCPO-Day5_G168_G169_M21M220_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249697 Apr 15 18:04 /scratch/5222943.1.y/Input/Met-EGFKO-TCPO-Day5_G168_G169_M21M221.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:04 /scratch/5222943.1.y/Input/Met-EGFKO-TCPO-Day5_G168_G169_M21M221_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2402606 Apr 15 18:05 /scratch/5222943.1.y/Input/Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_vs_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 7121021 Apr 15 18:05 /scratch/5222943.1.y/Input/Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_vs_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 2378407 Apr 15 18:05 /scratch/5222943.1.y/Input/Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_vs_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 7096822 Apr 15 18:05 /scratch/5222943.1.y/Input/Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_vs_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 20698 Apr 15 18:05 /scratch/5222943.1.y/Input/Up_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 121963 Apr 15 18:05 /scratch/5222943.1.y/Input/Up_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Apr 15 18:04 /scratch/5222943.1.y/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 42964 Apr 15 18:05 /scratch/5222943.1.y/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 40897 Apr 15 18:06 /scratch/5222943.1.y/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 248315 Apr 15 18:04 /scratch/5222943.1.y/Input/WT-TCPO-Day5_G168_G169_M18M19M200.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:04 /scratch/5222943.1.y/Input/WT-TCPO-Day5_G168_G169_M18M19M200_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249221 Apr 15 18:04 /scratch/5222943.1.y/Input/WT-TCPO-Day5_G168_G169_M18M19M201.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:04 /scratch/5222943.1.y/Input/WT-TCPO-Day5_G168_G169_M18M19M201_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 248518 Apr 15 18:04 /scratch/5222943.1.y/Input/WT-TCPO-Day5_G168_G169_M18M19M202.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:04 /scratch/5222943.1.y/Input/WT-TCPO-Day5_G168_G169_M18M19M202_num_mapped_reads.txt -rwxr-xr-x 1 kkarri waxmanlab 3925 Apr 15 18:04 /scratch/5222943.1.y/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Apr 15 18:04 /scratch/5222943.1.y/Input/formatForSegex_ver4.R /scratch/5222943.1.y/Input/Met-EGFKO-TCPO-Day5_G168_G169_M21M22: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 18:04 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 18:06 .. /scratch/5222943.1.y/Input/WT-TCPO-Day5_G168_G169_M18M19M20: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 18:04 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 18:06 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Apr 15 18:06 . drwxrwxrwt. 30 root root 4.0K Apr 15 18:04 .. -rw-r--r-- 1 kkarri waxmanlab 159 Apr 15 18:04 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 131 Apr 15 18:04 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Apr 15 18:06 Input -rw-r--r-- 1 kkarri waxmanlab 72M Apr 15 18:04 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K Apr 15 18:04 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 48M drwxr-sr-x 2 kkarri waxmanlab 4.0K Apr 15 18:01 . drwxr-sr-x 6 kkarri waxmanlab 4.0K Apr 15 17:59 .. -rw-r--r-- 1 kkarri waxmanlab 295 Apr 15 18:01 DiffExp_4a_Venn_Tables_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 9.3M Apr 15 18:01 DiffExp_v2_GeneBody_WT-TCPO-Day5_G168_G169_M18M19M20_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 32K Apr 15 18:01 Down_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 31K Apr 15 18:01 Down_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Apr 15 18:01 Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_vs_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 6.8M Apr 15 18:01 Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_vs_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Apr 15 18:01 Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_vs_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 6.8M Apr 15 18:01 Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_vs_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 21K Apr 15 18:01 Up_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 120K Apr 15 18:01 Up_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day5_G168_G169_M21M22_G168_TCPO_Env_G169G169_WT-TCPO-Day5_G168_G169_M18M19M20_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 42K Apr 15 18:01 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 40K Apr 15 18:01 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_HTSeq.png ========================================================== ========================================================== Finished on : Mon Apr 15 18:06:15 EDT 2019 2 minutes and 5 seconds elapsed. ==========================================================