----------------------- 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_8_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: Met-EGFKO-F-Liv_G168_G169_M4M5M6 CONDITION_2_NAME: Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11 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_8a COL_SUFFIX: GeneBody COUNT_PROGRAM: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon May 6 13:42:18 EDT 2019 Running on node : scc-ka2 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/09a_DiffExp_8_HTSeq Current job ID : 5891741 Current job name : Step_09a_DiffExp_8a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5891741.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G168_G169_M4 Sample_ID: G168_G169_M4 Description: Met-EGFKO1-Female-Liver M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M4 Sample_DIR: G168_G169_M5 Sample_ID: G168_G169_M5 Description: Met-EGFKO2-Female-Liver M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M5 Sample_DIR: G168_G169_M6 Sample_ID: G168_G169_M6 Description: Met-EGFKO3-Female-Liver M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M6 M_Num_Cond1_List: G169G169G169 ------------------------------------------ ------------------------------------------ Sample_DIR: G168_G169_M10 Sample_ID: G168_G169_M10 Description: Met-EGFKO2-TCPO-Day1 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M10 Sample_DIR: G168_G169_M11 Sample_ID: G168_G169_M11 Description: Met-EGFKO3-TCPO-Day1 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M11 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 43161323 38784376 39214060 37757460 44387098 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291522 May 6 13:42 /scratch/5891741.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 250117 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M60.out -rw-r--r-- 1 kkarri waxmanlab 9 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M60_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249269 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M61.out -rw-r--r-- 1 kkarri waxmanlab 9 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M61_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 248769 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M62.out -rw-r--r-- 1 kkarri waxmanlab 9 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M62_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249116 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-TCPO-Day1_G168_G169_M9M10M110.out -rw-r--r-- 1 kkarri waxmanlab 9 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-TCPO-Day1_G168_G169_M9M10M110_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249923 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-TCPO-Day1_G168_G169_M9M10M111.out -rw-r--r-- 1 kkarri waxmanlab 9 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-TCPO-Day1_G168_G169_M9M10M111_num_mapped_reads.txt /scratch/5891741.1.linga/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M6: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 6 13:42 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 6 13:42 .. /scratch/5891741.1.linga/Input/Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 6 13:42 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 6 13:42 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Met-EGFKO-F-Liv_G168_G169_M4M5M6 Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11 3 2 RefSeq_GeneBody.gtf /scratch/5891741.1.linga/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Met-EGFKO-F-Liv_G168_G169_M4M5M6" [1] "Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11" [1] 3 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/5891741.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" [1] "sum1:227570.16940439" "sum1:235906.700466977" "sum1:245709.592022732" [4] "sum1:236395.487298033" [1] "sum2:249012.584913976" "sum2:239439.352921733" "sum2:244225.968917854" load GTF file ... parse attributes ... [1] "output file is in: /scratch/5891741.1.linga/Input/DiffExp_v2_GeneBody_Met-EGFKO-F-Liv_G168_G169_M4M5M6_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_Met-EGFKO-F-Liv_G168_G169_M4M5M6_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11.txt Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_GeneBody_Met-EGFKO-F-Liv_G168_G169_M4M5M6_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11.txt Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== Comparison_Info: Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_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-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 273 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 190 7 [1] "Check out Up_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt!" Rscript Diff_Genes.R Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_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-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 431 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 297 7 [1] "Check out Up_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_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-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt Down_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt GeneBody_Counting DiffExp_8a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_8a" [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-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt Up_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt GeneBody_Counting DiffExp_8a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_8a" [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 296 May 6 13:44 /scratch/5891741.1.linga/Input/DiffExp_8a_Venn_Tables_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 9794481 May 6 13:44 /scratch/5891741.1.linga/Input/DiffExp_v2_GeneBody_Met-EGFKO-F-Liv_G168_G169_M4M5M6_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 May 6 13:42 /scratch/5891741.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 37531 May 6 13:44 /scratch/5891741.1.linga/Input/Down_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 51442 May 6 13:44 /scratch/5891741.1.linga/Input/Down_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 291522 May 6 13:42 /scratch/5891741.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 250117 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M60.out -rw-r--r-- 1 kkarri waxmanlab 9 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M60_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249269 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M61.out -rw-r--r-- 1 kkarri waxmanlab 9 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M61_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 248769 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M62.out -rw-r--r-- 1 kkarri waxmanlab 9 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M62_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249116 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-TCPO-Day1_G168_G169_M9M10M110.out -rw-r--r-- 1 kkarri waxmanlab 9 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-TCPO-Day1_G168_G169_M9M10M110_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249923 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-TCPO-Day1_G168_G169_M9M10M111.out -rw-r--r-- 1 kkarri waxmanlab 9 May 6 13:42 /scratch/5891741.1.linga/Input/Met-EGFKO-TCPO-Day1_G168_G169_M9M10M111_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2378411 May 6 13:44 /scratch/5891741.1.linga/Input/Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2426805 May 6 13:44 /scratch/5891741.1.linga/Input/Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 2354212 May 6 13:44 /scratch/5891741.1.linga/Input/Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2402606 May 6 13:44 /scratch/5891741.1.linga/Input/Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 20109 May 6 13:44 /scratch/5891741.1.linga/Input/Up_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 32057 May 6 13:44 /scratch/5891741.1.linga/Input/Up_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 May 6 13:42 /scratch/5891741.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 40346 May 6 13:44 /scratch/5891741.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 39751 May 6 13:44 /scratch/5891741.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 May 6 13:42 /scratch/5891741.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 May 6 13:42 /scratch/5891741.1.linga/Input/formatForSegex_ver4.R /scratch/5891741.1.linga/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M6: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 6 13:42 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 6 13:44 .. /scratch/5891741.1.linga/Input/Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 6 13:42 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 6 13:44 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K May 6 13:44 . drwxrwxrwt. 59 root root 116K May 6 13:42 .. -rw-r--r-- 1 kkarri waxmanlab 183 May 6 13:42 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 131 May 6 13:42 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K May 6 13:44 Input -rw-r--r-- 1 kkarri waxmanlab 72M May 6 13:42 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K May 6 13:42 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 30M drwxr-sr-x 2 kkarri waxmanlab 4.0K May 6 13:38 . drwxr-sr-x 6 kkarri waxmanlab 4.0K May 6 13:36 .. -rw-r--r-- 1 kkarri waxmanlab 296 May 6 13:38 DiffExp_8a_Venn_Tables_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 9.4M May 6 13:38 DiffExp_v2_GeneBody_Met-EGFKO-F-Liv_G168_G169_M4M5M6_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 37K May 6 13:38 Down_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 51K May 6 13:38 Down_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M May 6 13:38 Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.4M May 6 13:38 Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M May 6 13:38 Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M May 6 13:38 Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 20K May 6 13:38 Up_Genes_DESeq_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 32K May 6 13:38 Up_Genes_EdgeR_GeneBody_Met-EGFKO-TCPO-Day1_G168_G169_M9M10M11_G168_TCPO_Env_G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 40K May 6 13:38 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 39K May 6 13:38 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_HTSeq.png ========================================================== ========================================================== Finished on : Mon May 6 13:44:41 EDT 2019 2 minutes and 23 seconds elapsed. ==========================================================