----------------------- 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/09c_DiffExp_4_lncRNA_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP Dataset_Label: G168_TCPO_Env 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: WT_TCPO_D5 CONDITION_2_NAME: MetEGFKO_TCPO_D5 Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: exonic_only_gene_models_ncRNA_for_counting_lengths.txt COUNT_DIR: LncRNA_Exonic_Only_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_Exonic_Only DiffExp_Index: DiffExp_4f COL_SUFFIX: LncRNA_Exonic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Apr 22 19:56:54 EDT 2019 Running on node : scc-ka8 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/09c_DiffExp_4_lncRNA_featureCounts Current job ID : 5524868 Current job name : Step_09c_DiffExp_4f Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5524868.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G168_G169_M18 Sample_ID: G168_G169_M18 Description: WT1_TCPO_D5 M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G168_G169_M19 Sample_ID: G168_G169_M19 Description: WT2_TCPO_D5 M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G168_G169_M20 Sample_ID: G168_G169_M20 Description: WT3_TCPO_D5 M_Num: G169 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: G169G169G169 ------------------------------------------ ------------------------------------------ Sample_DIR: G168_G169_M21 Sample_ID: G168_G169_M21 Description: Met_EGFKO1_TCPO_D5 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G168_G169_M22 Sample_ID: G168_G169_M22 Description: Met_EGFKO2_TCPO_D5 M_Num: G169 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: G169G169 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 3 NUM_REP_CONDITION1: 3 ========================================================== Renaming input count files number of mapped reads (feature count summary) Status G168_G169_M21_sorted.bam Assigned 6577887 Unassigned_Ambiguity 10215 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2170781 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M22_sorted.bam Assigned 7066024 Unassigned_Ambiguity 12317 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2418987 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M18_sorted.bam Assigned 6153338 Unassigned_Ambiguity 7852 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2336853 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M19_sorted.bam Assigned 7050421 Unassigned_Ambiguity 8100 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2416478 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M20_sorted.bam Assigned 7002585 Unassigned_Ambiguity 14139 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2376280 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 710402 Apr 22 19:56 /scratch/5524868.1.linga/Input/MetEGFKO_TCPO_D50.out -rw-r--r-- 1 kkarri waxmanlab 302 Apr 22 19:56 /scratch/5524868.1.linga/Input/MetEGFKO_TCPO_D50.summary -rw-r--r-- 1 kkarri waxmanlab 711292 Apr 22 19:56 /scratch/5524868.1.linga/Input/MetEGFKO_TCPO_D51.out -rw-r--r-- 1 kkarri waxmanlab 302 Apr 22 19:56 /scratch/5524868.1.linga/Input/MetEGFKO_TCPO_D51.summary -rw-r--r-- 1 kkarri waxmanlab 710094 Apr 22 19:56 /scratch/5524868.1.linga/Input/WT_TCPO_D50.out -rw-r--r-- 1 kkarri waxmanlab 301 Apr 22 19:56 /scratch/5524868.1.linga/Input/WT_TCPO_D50.summary -rw-r--r-- 1 kkarri waxmanlab 710791 Apr 22 19:56 /scratch/5524868.1.linga/Input/WT_TCPO_D51.out -rw-r--r-- 1 kkarri waxmanlab 301 Apr 22 19:56 /scratch/5524868.1.linga/Input/WT_TCPO_D51.summary -rw-r--r-- 1 kkarri waxmanlab 710314 Apr 22 19:56 /scratch/5524868.1.linga/Input/WT_TCPO_D52.out -rw-r--r-- 1 kkarri waxmanlab 302 Apr 22 19:56 /scratch/5524868.1.linga/Input/WT_TCPO_D52.summary -rw-r--r-- 1 kkarri waxmanlab 794757 Apr 22 19:56 /scratch/5524868.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/5524868.1.linga/Input/MetEGFKO_TCPO_D5: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 19:56 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 19:56 .. /scratch/5524868.1.linga/Input/WT_TCPO_D5: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 19:56 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 19:56 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WT_TCPO_D5 MetEGFKO_TCPO_D5 3 2 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/5524868.1.linga/Input DiffExp_v2_LncRNA_Exonic_Only exonic_only_gene_models_ncRNA_for_counting_lengths.txt WARNING: ignoring environment value of R_HOME [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WT_TCPO_D5" [1] "MetEGFKO_TCPO_D5" [1] 3 [1] 2 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/5524868.1.linga/Input" [1] "DiffExp_v2_LncRNA_Exonic_Only" [1] "exonic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] "sum1:276710.125896444" "sum1:278171.187764098" "sum1:284642.394419862" [4] "sum1:279841.236026802" [1] "sum2:285290.397851684" "sum2:276921.784522986" "sum2:281106.091187335" [1] 15558 23 [1] 15558 59 [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/5524868.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_WT_TCPO_D5_MetEGFKO_TCPO_D5.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Exonic_Only_WT_TCPO_D5_MetEGFKO_TCPO_D5.txt MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload 1 LncRNA_Exonic_Only WARNING: ignoring environment value of R_HOME Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_LncRNA_Exonic_Only_WT_TCPO_D5_MetEGFKO_TCPO_D5.txt MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload 1 LncRNA_Exonic_Only WARNING: ignoring environment value of R_HOME ========================================================== Comparison_Info: MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Exonic_Only'_'MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_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] "LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 32 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 18 7 [1] "Check out Up_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt!" Rscript Diff_Genes.R MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Exonic_Only'_'MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_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] "LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 70 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 37 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt Down_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt LncRNA_Exonic_Only_Counting DiffExp_4f WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_4f" [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_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt Up_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt LncRNA_Exonic_Only_Counting DiffExp_4f WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_4f" [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 #---------------------------------------------------------------------------------- Comparison_Info: MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 322 Apr 22 19:58 /scratch/5524868.1.linga/Input/DiffExp_4f_Venn_Tables_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 4942814 Apr 22 19:58 /scratch/5524868.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_WT_TCPO_D5_MetEGFKO_TCPO_D5.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Apr 22 19:56 /scratch/5524868.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 1757 Apr 22 19:58 /scratch/5524868.1.linga/Input/Down_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 3751 Apr 22 19:58 /scratch/5524868.1.linga/Input/Down_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 710402 Apr 22 19:56 /scratch/5524868.1.linga/Input/MetEGFKO_TCPO_D50.out -rw-r--r-- 1 kkarri waxmanlab 302 Apr 22 19:56 /scratch/5524868.1.linga/Input/MetEGFKO_TCPO_D50.summary -rw-r--r-- 1 kkarri waxmanlab 711292 Apr 22 19:56 /scratch/5524868.1.linga/Input/MetEGFKO_TCPO_D51.out -rw-r--r-- 1 kkarri waxmanlab 302 Apr 22 19:56 /scratch/5524868.1.linga/Input/MetEGFKO_TCPO_D51.summary -rw-r--r-- 1 kkarri waxmanlab 1732474 Apr 22 19:58 /scratch/5524868.1.linga/Input/MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2619280 Apr 22 19:58 /scratch/5524868.1.linga/Input/MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 906117 Apr 22 19:58 /scratch/5524868.1.linga/Input/MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2028200 Apr 22 19:58 /scratch/5524868.1.linga/Input/MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 2920 Apr 22 19:58 /scratch/5524868.1.linga/Input/Up_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 10246 Apr 22 19:58 /scratch/5524868.1.linga/Input/Up_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Apr 22 19:56 /scratch/5524868.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 42430 Apr 22 19:58 /scratch/5524868.1.linga/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 40705 Apr 22 19:58 /scratch/5524868.1.linga/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 710094 Apr 22 19:56 /scratch/5524868.1.linga/Input/WT_TCPO_D50.out -rw-r--r-- 1 kkarri waxmanlab 301 Apr 22 19:56 /scratch/5524868.1.linga/Input/WT_TCPO_D50.summary -rw-r--r-- 1 kkarri waxmanlab 710791 Apr 22 19:56 /scratch/5524868.1.linga/Input/WT_TCPO_D51.out -rw-r--r-- 1 kkarri waxmanlab 301 Apr 22 19:56 /scratch/5524868.1.linga/Input/WT_TCPO_D51.summary -rw-r--r-- 1 kkarri waxmanlab 710314 Apr 22 19:56 /scratch/5524868.1.linga/Input/WT_TCPO_D52.out -rw-r--r-- 1 kkarri waxmanlab 302 Apr 22 19:56 /scratch/5524868.1.linga/Input/WT_TCPO_D52.summary -rw-r--r-- 1 kkarri waxmanlab 794757 Apr 22 19:56 /scratch/5524868.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt -rwxr-xr-x 1 kkarri waxmanlab 4968 Apr 22 19:56 /scratch/5524868.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Apr 22 19:56 /scratch/5524868.1.linga/Input/formatForSegex_ver4.R /scratch/5524868.1.linga/Input/MetEGFKO_TCPO_D5: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 19:56 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 19:58 .. /scratch/5524868.1.linga/Input/WT_TCPO_D5: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 19:56 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 19:58 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Apr 22 19:58 . drwxrwxrwt. 58 root root 72K Apr 22 19:58 .. -rw-r--r-- 1 kkarri waxmanlab 153 Apr 22 19:56 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 127 Apr 22 19:56 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Apr 22 19:58 Input -rwxr-xr-x 1 kkarri waxmanlab 15K Apr 22 19:56 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Apr 22 19:56 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 26M drwxr-sr-x 2 kkarri waxmanlab 4.0K Apr 22 19:53 . drwxr-sr-x 7 kkarri waxmanlab 4.0K Apr 22 19:51 .. -rw-r--r-- 1 kkarri waxmanlab 322 Apr 22 19:53 DiffExp_4f_Venn_Tables_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.8M Apr 22 19:53 DiffExp_v2_LncRNA_Exonic_Only_WT_TCPO_D5_MetEGFKO_TCPO_D5_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.8K Apr 22 19:53 Down_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.7K Apr 22 19:53 Down_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.7M Apr 22 19:53 MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.5M Apr 22 19:53 MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 885K Apr 22 19:53 MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.0M Apr 22 19:53 MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.9K Apr 22 19:53 Up_Genes_DESeq_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 11K Apr 22 19:53 Up_Genes_EdgeR_LncRNA_Exonic_Only_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 42K Apr 22 19:53 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 40K Apr 22 19:53 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Apr 22 19:59:08 EDT 2019 2 minutes and 14 seconds elapsed. ==========================================================