----------------------- 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_1_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: Exon_Only_Regions.gtf CONDITION_1_NAME: WT-F-Liv_G168_G169_M1M2M3 CONDITION_2_NAME: Met-EGFKO-F-Liv_G168_G169_M4M5M6 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 : Mon Apr 15 17:30:01 EDT 2019 Running on node : scc-pe3 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/09a_DiffExp_1_HTSeq Current job ID : 5222757 Current job name : Step_09a_DiffExp_1b Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5222757.1.p Loading required modules... ------------------------------------------ Sample_DIR: G168_G169_M1 Sample_ID: G168_G169_M1 Description: WT1-Female-Liver M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M1 Sample_DIR: G168_G169_M2 Sample_ID: G168_G169_M2 Description: WT2-Female-Liver M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M2 Sample_DIR: G168_G169_M3 Sample_ID: G168_G169_M3 Description: WT3-Female-Liver M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G168_G169_M3 M_Num_Cond1_List: G169G169G169 ------------------------------------------ ------------------------------------------ Sample_DIR: G168_G169_M4 Sample_ID: G168_G169_M4 Description: Met-EGFKO1-Female-Liver M_Num: G169 Copy Condition_2 sample count files to Condition_2 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_2 sample count files to Condition_2 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_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M6 M_Num_Cond2_List: G169G169G169 ------------------------------------------ ========================================================== 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 43096139 38750304 39184895 30591403 41142742 38949776 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291285 Apr 15 17:30 /scratch/5222757.1.p/Input/Exon_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 245918 Apr 15 17:30 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M60.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 17:30 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M60_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245113 Apr 15 17:30 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M61.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 17:30 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M61_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244812 Apr 15 17:30 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M62.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 17:30 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M62_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244099 Apr 15 17:30 /scratch/5222757.1.p/Input/WT-F-Liv_G168_G169_M1M2M30.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 17:30 /scratch/5222757.1.p/Input/WT-F-Liv_G168_G169_M1M2M30_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245540 Apr 15 17:30 /scratch/5222757.1.p/Input/WT-F-Liv_G168_G169_M1M2M31.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 17:30 /scratch/5222757.1.p/Input/WT-F-Liv_G168_G169_M1M2M31_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245073 Apr 15 17:30 /scratch/5222757.1.p/Input/WT-F-Liv_G168_G169_M1M2M32.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 17:30 /scratch/5222757.1.p/Input/WT-F-Liv_G168_G169_M1M2M32_num_mapped_reads.txt /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M6: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 17:30 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 17:30 .. /scratch/5222757.1.p/Input/WT-F-Liv_G168_G169_M1M2M3: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 17:30 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 17:30 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WT-F-Liv_G168_G169_M1M2M3 Met-EGFKO-F-Liv_G168_G169_M4M5M6 3 3 Exon_Only_Regions.gtf /scratch/5222757.1.p/Input DiffExp_v2_Exonic_Only Exon_Only_Regions_Lengths.txt WARNING: ignoring environment value of R_HOME [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WT-F-Liv_G168_G169_M1M2M3" [1] "Met-EGFKO-F-Liv_G168_G169_M4M5M6" [1] 3 [1] 3 [1] "Exon_Only_Regions.gtf" [1] "/scratch/5222757.1.p/Input" [1] "DiffExp_v2_Exonic_Only" [1] "Exon_Only_Regions_Lengths.txt" [1] "sum1:106869.791852296" "sum1:100513.334056947" "sum1:103149.461444646" [4] "sum1:103510.862451296" [1] "sum2:103984.796440126" "sum2:108056.906049038" "sum2:114693.999727368" [4] "sum2:108911.900738844" load GTF file ... parse attributes ... [1] "output file is in: /scratch/5222757.1.p/Input/DiffExp_v2_Exonic_Only_WT-F-Liv_G168_G169_M1M2M3_Met-EGFKO-F-Liv_G168_G169_M4M5M6.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Exonic_Only_WT-F-Liv_G168_G169_M1M2M3_Met-EGFKO-F-Liv_G168_G169_M4M5M6.txt Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_vs_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload 1 Exonic_Only WARNING: ignoring environment value of R_HOME Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_Exonic_Only_WT-F-Liv_G168_G169_M1M2M3_Met-EGFKO-F-Liv_G168_G169_M4M5M6.txt Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_vs_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload 1 Exonic_Only WARNING: ignoring environment value of R_HOME ========================================================== Comparison_Info: Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_vs_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Exonic_Only'_'Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_vs_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_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_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 466 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 374 7 [1] "Check out Up_Genes_DESeq_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_DESeq_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt!" Rscript Diff_Genes.R Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_vs_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Exonic_Only'_'Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_vs_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_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_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 541 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 447 7 [1] "Check out Up_Genes_EdgeR_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_EdgeR_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt Down_Genes_EdgeR_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt Exonic_Only_Counting DiffExp_1b WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.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_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt Up_Genes_EdgeR_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt Exonic_Only_Counting DiffExp_1b WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.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 312 Apr 15 17:31 /scratch/5222757.1.p/Input/DiffExp_1b_Venn_Tables_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 9917006 Apr 15 17:31 /scratch/5222757.1.p/Input/DiffExp_v2_Exonic_Only_WT-F-Liv_G168_G169_M1M2M3_Met-EGFKO-F-Liv_G168_G169_M4M5M6.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Apr 15 17:30 /scratch/5222757.1.p/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 77464 Apr 15 17:31 /scratch/5222757.1.p/Input/Down_Genes_DESeq_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 76513 Apr 15 17:31 /scratch/5222757.1.p/Input/Down_Genes_EdgeR_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 291285 Apr 15 17:30 /scratch/5222757.1.p/Input/Exon_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 245918 Apr 15 17:30 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M60.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 17:30 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M60_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245113 Apr 15 17:30 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M61.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 17:30 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M61_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244812 Apr 15 17:30 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M62.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 17:30 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M62_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2378419 Apr 15 17:31 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_vs_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 6322530 Apr 15 17:31 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_vs_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 2378417 Apr 15 17:31 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_vs_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 6322528 Apr 15 17:31 /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_vs_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 33965 Apr 15 17:31 /scratch/5222757.1.p/Input/Up_Genes_DESeq_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 127078 Apr 15 17:31 /scratch/5222757.1.p/Input/Up_Genes_EdgeR_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Apr 15 17:30 /scratch/5222757.1.p/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 41864 Apr 15 17:31 /scratch/5222757.1.p/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 39125 Apr 15 17:31 /scratch/5222757.1.p/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 244099 Apr 15 17:30 /scratch/5222757.1.p/Input/WT-F-Liv_G168_G169_M1M2M30.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 17:30 /scratch/5222757.1.p/Input/WT-F-Liv_G168_G169_M1M2M30_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245540 Apr 15 17:30 /scratch/5222757.1.p/Input/WT-F-Liv_G168_G169_M1M2M31.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 17:30 /scratch/5222757.1.p/Input/WT-F-Liv_G168_G169_M1M2M31_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245073 Apr 15 17:30 /scratch/5222757.1.p/Input/WT-F-Liv_G168_G169_M1M2M32.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 17:30 /scratch/5222757.1.p/Input/WT-F-Liv_G168_G169_M1M2M32_num_mapped_reads.txt -rwxr-xr-x 1 kkarri waxmanlab 3925 Apr 15 17:30 /scratch/5222757.1.p/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Apr 15 17:30 /scratch/5222757.1.p/Input/formatForSegex_ver4.R /scratch/5222757.1.p/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M6: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 17:30 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 17:31 .. /scratch/5222757.1.p/Input/WT-F-Liv_G168_G169_M1M2M3: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 17:30 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 17:31 .. ========================================================== List files in scratch total 19M drwx------ 3 kkarri waxmanlab 4.0K Apr 15 17:31 . drwxrwxrwt. 18 root root 4.0K Apr 15 17:30 .. -rw-r--r-- 1 kkarri waxmanlab 162 Apr 15 17:30 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 183 Apr 15 17:30 Condition_2.txt -rw-r--r-- 1 kkarri waxmanlab 19M Apr 15 17:30 Exon_Only_Regions.gtf drwxr-xr-x 4 kkarri waxmanlab 4.0K Apr 15 17:31 Input -rwxr-xr-x 1 kkarri waxmanlab 17K Apr 15 17:30 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 17:27 . drwxr-sr-x 6 kkarri waxmanlab 4.0K Apr 15 17:25 .. -rw-r--r-- 1 kkarri waxmanlab 312 Apr 15 17:27 DiffExp_1b_Venn_Tables_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 9.5M Apr 15 17:26 DiffExp_v2_Exonic_Only_WT-F-Liv_G168_G169_M1M2M3_Met-EGFKO-F-Liv_G168_G169_M4M5M6_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 76K Apr 15 17:26 Down_Genes_DESeq_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 75K Apr 15 17:26 Down_Genes_EdgeR_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Apr 15 17:26 Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_vs_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 6.1M Apr 15 17:26 Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_vs_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Apr 15 17:26 Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_vs_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_TPM_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 6.1M Apr 15 17:26 Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_vs_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_TPM_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 34K Apr 15 17:26 Up_Genes_DESeq_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 125K Apr 15 17:26 Up_Genes_EdgeR_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_WT-F-Liv_G168_G169_M1M2M3_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 41K Apr 15 17:26 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 39K Apr 15 17:26 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_HTSeq.png ========================================================== ========================================================== Finished on : Mon Apr 15 17:31:53 EDT 2019 1 minutes and 52 seconds elapsed. ==========================================================