----------------------- 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: ncRNA_genebodies_for_counting_lengths.txt COUNT_DIR: LncRNA_GeneBody_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_GeneBody DiffExp_Index: DiffExp_4e COL_SUFFIX: LncRNA_GeneBody 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 : 5524867 Current job name : Step_09c_DiffExp_4e Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5524867.1.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 15557342 Unassigned_Ambiguity 1035463 Unassigned_MultiMapping 0 Unassigned_NoFeatures 877256 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 17070094 Unassigned_Ambiguity 1089169 Unassigned_MultiMapping 0 Unassigned_NoFeatures 1006336 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 15110722 Unassigned_Ambiguity 929347 Unassigned_MultiMapping 0 Unassigned_NoFeatures 1045684 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 17391670 Unassigned_Ambiguity 1064535 Unassigned_MultiMapping 0 Unassigned_NoFeatures 942974 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 16888737 Unassigned_Ambiguity 1117161 Unassigned_MultiMapping 0 Unassigned_NoFeatures 974105 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 716506 Apr 22 19:56 /scratch/5524867.1.linga/Input/MetEGFKO_TCPO_D50.out -rw-r--r-- 1 kkarri waxmanlab 304 Apr 22 19:56 /scratch/5524867.1.linga/Input/MetEGFKO_TCPO_D50.summary -rw-r--r-- 1 kkarri waxmanlab 717743 Apr 22 19:56 /scratch/5524867.1.linga/Input/MetEGFKO_TCPO_D51.out -rw-r--r-- 1 kkarri waxmanlab 305 Apr 22 19:56 /scratch/5524867.1.linga/Input/MetEGFKO_TCPO_D51.summary -rw-r--r-- 1 kkarri waxmanlab 716365 Apr 22 19:56 /scratch/5524867.1.linga/Input/WT_TCPO_D50.out -rw-r--r-- 1 kkarri waxmanlab 304 Apr 22 19:56 /scratch/5524867.1.linga/Input/WT_TCPO_D50.summary -rw-r--r-- 1 kkarri waxmanlab 717096 Apr 22 19:56 /scratch/5524867.1.linga/Input/WT_TCPO_D51.out -rw-r--r-- 1 kkarri waxmanlab 304 Apr 22 19:56 /scratch/5524867.1.linga/Input/WT_TCPO_D51.summary -rw-r--r-- 1 kkarri waxmanlab 716494 Apr 22 19:56 /scratch/5524867.1.linga/Input/WT_TCPO_D52.out -rw-r--r-- 1 kkarri waxmanlab 304 Apr 22 19:56 /scratch/5524867.1.linga/Input/WT_TCPO_D52.summary -rw-r--r-- 1 kkarri waxmanlab 815529 Apr 22 19:56 /scratch/5524867.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/5524867.1.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/5524867.1.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/5524867.1.linga/Input DiffExp_v2_LncRNA_GeneBody ncRNA_genebodies_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/5524867.1.linga/Input" [1] "DiffExp_v2_LncRNA_GeneBody" [1] "ncRNA_genebodies_for_counting_lengths.txt" [1] "sum1:62231.4378802494" "sum1:61314.5118936874" "sum1:64182.9938779625" [4] "sum1:62576.3145506331" [1] "sum2:66710.5036462671" "sum2:62898.3338439229" "sum2:64804.418745095" [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/5524867.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_WT_TCPO_D5_MetEGFKO_TCPO_D5.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_GeneBody_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_GeneBody_forSEGEXUpload 1 LncRNA_GeneBody WARNING: ignoring environment value of R_HOME Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_LncRNA_GeneBody_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_GeneBody_forSEGEXUpload 1 LncRNA_GeneBody 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_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_GeneBody'_'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_GeneBody_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "LncRNA_GeneBody_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] 58 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 45 7 [1] "Check out Up_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_GeneBody_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_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_GeneBody'_'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_GeneBody_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "LncRNA_GeneBody_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] 112 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 77 7 [1] "Check out Up_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_GeneBody_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_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt Down_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt LncRNA_GeneBody_Counting DiffExp_4e WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_4e" [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_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt Up_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt LncRNA_GeneBody_Counting DiffExp_4e WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_4e" [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 #---------------------------------------------------------------------------------- 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 305 Apr 22 19:59 /scratch/5524867.1.linga/Input/DiffExp_4e_Venn_Tables_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 5594820 Apr 22 19:58 /scratch/5524867.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_WT_TCPO_D5_MetEGFKO_TCPO_D5.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Apr 22 19:56 /scratch/5524867.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 5226 Apr 22 19:58 /scratch/5524867.1.linga/Input/Down_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 8505 Apr 22 19:58 /scratch/5524867.1.linga/Input/Down_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 716506 Apr 22 19:56 /scratch/5524867.1.linga/Input/MetEGFKO_TCPO_D50.out -rw-r--r-- 1 kkarri waxmanlab 304 Apr 22 19:56 /scratch/5524867.1.linga/Input/MetEGFKO_TCPO_D50.summary -rw-r--r-- 1 kkarri waxmanlab 717743 Apr 22 19:56 /scratch/5524867.1.linga/Input/MetEGFKO_TCPO_D51.out -rw-r--r-- 1 kkarri waxmanlab 305 Apr 22 19:56 /scratch/5524867.1.linga/Input/MetEGFKO_TCPO_D51.summary -rw-r--r-- 1 kkarri waxmanlab 2665933 Apr 22 19:58 /scratch/5524867.1.linga/Input/MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2945977 Apr 22 19:58 /scratch/5524867.1.linga/Input/MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 1373613 Apr 22 19:58 /scratch/5524867.1.linga/Input/MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2299009 Apr 22 19:58 /scratch/5524867.1.linga/Input/MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 8252 Apr 22 19:58 /scratch/5524867.1.linga/Input/Up_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 18005 Apr 22 19:58 /scratch/5524867.1.linga/Input/Up_Genes_EdgeR_LncRNA_GeneBody_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/5524867.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 42491 Apr 22 19:59 /scratch/5524867.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 41309 Apr 22 19:59 /scratch/5524867.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 716365 Apr 22 19:56 /scratch/5524867.1.linga/Input/WT_TCPO_D50.out -rw-r--r-- 1 kkarri waxmanlab 304 Apr 22 19:56 /scratch/5524867.1.linga/Input/WT_TCPO_D50.summary -rw-r--r-- 1 kkarri waxmanlab 717096 Apr 22 19:56 /scratch/5524867.1.linga/Input/WT_TCPO_D51.out -rw-r--r-- 1 kkarri waxmanlab 304 Apr 22 19:56 /scratch/5524867.1.linga/Input/WT_TCPO_D51.summary -rw-r--r-- 1 kkarri waxmanlab 716494 Apr 22 19:56 /scratch/5524867.1.linga/Input/WT_TCPO_D52.out -rw-r--r-- 1 kkarri waxmanlab 304 Apr 22 19:56 /scratch/5524867.1.linga/Input/WT_TCPO_D52.summary -rwxr-xr-x 1 kkarri waxmanlab 4968 Apr 22 19:56 /scratch/5524867.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Apr 22 19:56 /scratch/5524867.1.linga/Input/formatForSegex_ver4.R -rw-r--r-- 1 kkarri waxmanlab 815529 Apr 22 19:56 /scratch/5524867.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/5524867.1.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 19:59 .. /scratch/5524867.1.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 19:59 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Apr 22 19:59 . drwxrwxrwt. 56 root root 72K Apr 22 19:59 .. -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 19:59 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 29M drwxr-sr-x 2 kkarri waxmanlab 4.0K Apr 22 19:54 . drwxr-sr-x 7 kkarri waxmanlab 4.0K Apr 22 19:51 .. -rw-r--r-- 1 kkarri waxmanlab 305 Apr 22 19:53 DiffExp_4e_Venn_Tables_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.4M Apr 22 19:53 DiffExp_v2_LncRNA_GeneBody_WT_TCPO_D5_MetEGFKO_TCPO_D5_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.2K Apr 22 19:53 Down_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 8.4K Apr 22 19:53 Down_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.6M Apr 22 19:53 MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.9M Apr 22 19:53 MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.4M Apr 22 19:53 MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.2M Apr 22 19:53 MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_vs_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 8.1K Apr 22 19:53 Up_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D5_G168_TCPO_Env_G169G169_WT_TCPO_D5_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 18K Apr 22 19:53 Up_Genes_EdgeR_LncRNA_GeneBody_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.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 41K Apr 22 19:53 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Apr 22 19:59:44 EDT 2019 2 minutes and 50 seconds elapsed. ==========================================================