----------------------- 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_9_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: Met-EGFKO-F-Liv_G168_G169_M4M5M6 CONDITION_2_NAME: Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17 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_9b COL_SUFFIX: Exonic_Only COUNT_PROGRAM: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Apr 15 18:14:59 EDT 2019 Running on node : scc-ba4 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/09a_DiffExp_9_HTSeq Current job ID : 5223579 Current job name : Step_09a_DiffExp_9b Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5223579.1.b-long 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_M15 Sample_ID: G168_G169_M15 Description: Met-EGFKO1-TCPO-Day2 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M15 Sample_DIR: G168_G169_M16 Sample_ID: G168_G169_M16 Description: Met-EGFKO2-TCPO-Day2 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M16 Sample_DIR: G168_G169_M17 Sample_ID: G168_G169_M17 Description: Met-EGFKO3-TCPO-Day2 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G168_G169_M17 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 43895514 43259140 34527999 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291285 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Exon_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 245918 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M60.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M60_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245113 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M61.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M61_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244812 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M62.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M62_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245877 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M170.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M170_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246113 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M171.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M171_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245515 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M172.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M172_num_mapped_reads.txt /scratch/5223579.1.b-long/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M6: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 18:15 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 18:15 .. /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 18:15 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 18:15 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Met-EGFKO-F-Liv_G168_G169_M4M5M6 Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17 3 3 Exon_Only_Regions.gtf /scratch/5223579.1.b-long/Input DiffExp_v2_Exonic_Only Exon_Only_Regions_Lengths.txt WARNING: ignoring environment value of R_HOME [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Met-EGFKO-F-Liv_G168_G169_M4M5M6" [1] "Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17" [1] 3 [1] 3 [1] "Exon_Only_Regions.gtf" [1] "/scratch/5223579.1.b-long/Input" [1] "DiffExp_v2_Exonic_Only" [1] "Exon_Only_Regions_Lengths.txt" [1] "sum1:103984.796440126" "sum1:108056.906049038" "sum1:114693.999727368" [4] "sum1:108911.900738844" [1] "sum2:106116.858761807" "sum2:110991.268234586" "sum2:108744.26741031" [4] "sum2:108617.464802234" load GTF file ... parse attributes ... [1] "output file is in: /scratch/5223579.1.b-long/Input/DiffExp_v2_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17.txt Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_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_Met-EGFKO-F-Liv_G168_G169_M4M5M6_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17.txt Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload 1 Exonic_Only WARNING: ignoring environment value of R_HOME ========================================================== Comparison_Info: Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_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-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Exonic_Only'_'Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_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-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_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] 318 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 284 7 [1] "Check out Up_Genes_DESeq_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_DESeq_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt!" Rscript Diff_Genes.R Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Exonic_Only'_'Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_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-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_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] 382 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 305 7 [1] "Check out Up_Genes_EdgeR_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_EdgeR_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_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_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt Down_Genes_EdgeR_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt Exonic_Only_Counting DiffExp_9b WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_9b" [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-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt Up_Genes_EdgeR_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt Exonic_Only_Counting DiffExp_9b WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_9b" [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 18:17 /scratch/5223579.1.b-long/Input/DiffExp_9b_Venn_Tables_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 9985493 Apr 15 18:16 /scratch/5223579.1.b-long/Input/DiffExp_v2_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 65110 Apr 15 18:16 /scratch/5223579.1.b-long/Input/Down_Genes_DESeq_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 59862 Apr 15 18:16 /scratch/5223579.1.b-long/Input/Down_Genes_EdgeR_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 291285 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Exon_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 245918 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M60.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M60_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245113 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M61.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M61_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244812 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M62.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M62_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245877 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M170.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M170_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246113 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M171.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M171_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245515 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M172.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M172_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2378433 Apr 15 18:16 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2354236 Apr 15 18:16 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 2378431 Apr 15 18:16 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2354234 Apr 15 18:16 /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 23311 Apr 15 18:16 /scratch/5223579.1.b-long/Input/Up_Genes_DESeq_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 27979 Apr 15 18:16 /scratch/5223579.1.b-long/Input/Up_Genes_EdgeR_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Apr 15 18:15 /scratch/5223579.1.b-long/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 42372 Apr 15 18:16 /scratch/5223579.1.b-long/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 41504 Apr 15 18:17 /scratch/5223579.1.b-long/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 Apr 15 18:15 /scratch/5223579.1.b-long/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Apr 15 18:15 /scratch/5223579.1.b-long/Input/formatForSegex_ver4.R /scratch/5223579.1.b-long/Input/Met-EGFKO-F-Liv_G168_G169_M4M5M6: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 18:15 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 18:17 .. /scratch/5223579.1.b-long/Input/Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 15 18:15 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 15 18:17 .. ========================================================== List files in scratch total 19M drwx------ 3 kkarri waxmanlab 4.0K Apr 15 18:17 . drwxrwxrwt. 26 root root 12K Apr 15 18:14 .. -rw-r--r-- 1 kkarri waxmanlab 183 Apr 15 18:15 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 180 Apr 15 18:15 Condition_2.txt -rw-r--r-- 1 kkarri waxmanlab 19M Apr 15 18:15 Exon_Only_Regions.gtf drwxr-xr-x 4 kkarri waxmanlab 4.0K Apr 15 18:17 Input -rwxr-xr-x 1 kkarri waxmanlab 17K Apr 15 18:15 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 Apr 15 18:12 . drwxr-sr-x 5 kkarri waxmanlab 4.0K Apr 15 18:10 .. -rw-r--r-- 1 kkarri waxmanlab 312 Apr 15 18:12 DiffExp_9b_Venn_Tables_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 9.6M Apr 15 18:12 DiffExp_v2_Exonic_Only_Met-EGFKO-F-Liv_G168_G169_M4M5M6_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 64K Apr 15 18:12 Down_Genes_DESeq_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 59K Apr 15 18:12 Down_Genes_EdgeR_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Apr 15 18:12 Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Apr 15 18:12 Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Apr 15 18:12 Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_TPM_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Apr 15 18:12 Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_vs_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_DiffExp_v2_Exonic_Only_forSEGEXUpload_TPM_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 23K Apr 15 18:12 Up_Genes_DESeq_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 28K Apr 15 18:12 Up_Genes_EdgeR_Exonic_Only_Met-EGFKO-TCPO-Day2_G168_G169_M15M16M17_G168_TCPO_Env_G169G169G169_Met-EGFKO-F-Liv_G168_G169_M4M5M6_G168_TCPO_Env_G169G169G169_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 42K Apr 15 18:12 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 41K Apr 15 18:12 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_HTSeq.png ========================================================== ========================================================== Finished on : Mon Apr 15 18:17:02 EDT 2019 2 minutes and 3 seconds elapsed. ==========================================================