----------------------- 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_2_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_D1 CONDITION_2_NAME: MetEGFKO_TCPO_D1 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_2e COL_SUFFIX: LncRNA_GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Apr 22 19:55:53 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_2_lncRNA_featureCounts Current job ID : 5524859 Current job name : Step_09c_DiffExp_2e Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5524859.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G168_G169_M7 Sample_ID: G168_G169_M7 Description: WT1_TCPO_D1 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_M8 Sample_ID: G168_G169_M8 Description: WT2_TCPO_D1 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: G169G169 ------------------------------------------ ------------------------------------------ Sample_DIR: G168_G169_M10 Sample_ID: G168_G169_M10 Description: Met_EGFKO2_TCPO_D1 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_M11 Sample_ID: G168_G169_M11 Description: Met_EGFKO3_TCPO_D1 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: 2 NUM_REP_CONDITION1: 2 ========================================================== Renaming input count files number of mapped reads (feature count summary) Status G168_G169_M10_sorted.bam Assigned 17767958 Unassigned_Ambiguity 1287057 Unassigned_MultiMapping 0 Unassigned_NoFeatures 762702 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M11_sorted.bam Assigned 20930004 Unassigned_Ambiguity 1489679 Unassigned_MultiMapping 0 Unassigned_NoFeatures 914833 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M7_sorted.bam Assigned 16991062 Unassigned_Ambiguity 1206998 Unassigned_MultiMapping 0 Unassigned_NoFeatures 797802 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M8_sorted.bam Assigned 18728586 Unassigned_Ambiguity 1294526 Unassigned_MultiMapping 0 Unassigned_NoFeatures 894193 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 717278 Apr 22 19:55 /scratch/5524859.1.linga/Input/MetEGFKO_TCPO_D10.out -rw-r--r-- 1 kkarri waxmanlab 304 Apr 22 19:55 /scratch/5524859.1.linga/Input/MetEGFKO_TCPO_D10.summary -rw-r--r-- 1 kkarri waxmanlab 718477 Apr 22 19:55 /scratch/5524859.1.linga/Input/MetEGFKO_TCPO_D11.out -rw-r--r-- 1 kkarri waxmanlab 304 Apr 22 19:55 /scratch/5524859.1.linga/Input/MetEGFKO_TCPO_D11.summary -rw-r--r-- 1 kkarri waxmanlab 716707 Apr 22 19:55 /scratch/5524859.1.linga/Input/WT_TCPO_D10.out -rw-r--r-- 1 kkarri waxmanlab 303 Apr 22 19:55 /scratch/5524859.1.linga/Input/WT_TCPO_D10.summary -rw-r--r-- 1 kkarri waxmanlab 717713 Apr 22 19:55 /scratch/5524859.1.linga/Input/WT_TCPO_D11.out -rw-r--r-- 1 kkarri waxmanlab 303 Apr 22 19:55 /scratch/5524859.1.linga/Input/WT_TCPO_D11.summary -rw-r--r-- 1 kkarri waxmanlab 815529 Apr 22 19:55 /scratch/5524859.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/5524859.1.linga/Input/MetEGFKO_TCPO_D1: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 19:55 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 19:55 .. /scratch/5524859.1.linga/Input/WT_TCPO_D1: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 19:55 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 19:55 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WT_TCPO_D1 MetEGFKO_TCPO_D1 2 2 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/5524859.1.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_D1" [1] "MetEGFKO_TCPO_D1" [1] 2 [1] 2 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/5524859.1.linga/Input" [1] "DiffExp_v2_LncRNA_GeneBody" [1] "ncRNA_genebodies_for_counting_lengths.txt" [1] "sum1:64103.6069939328" "sum1:66814.8230977837" "sum1:65459.2150458582" [1] "sum2:72651.4785677861" "sum2:69253.0129624218" "sum2:70952.2457651039" [1] 15558 23 [1] 15558 55 [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/5524859.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_WT_TCPO_D1_MetEGFKO_TCPO_D1.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_GeneBody_WT_TCPO_D1_MetEGFKO_TCPO_D1.txt MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_WT_TCPO_D1_G168_TCPO_Env_G169G169_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_D1_MetEGFKO_TCPO_D1.txt MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_WT_TCPO_D1_G168_TCPO_Env_G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload 1 LncRNA_GeneBody WARNING: ignoring environment value of R_HOME ========================================================== Comparison_Info: MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_WT_TCPO_D1_G168_TCPO_Env_G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_GeneBody'_'MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_WT_TCPO_D1_G168_TCPO_Env_G169G169_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_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 61 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 61 7 [1] "Check out Up_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt!" Rscript Diff_Genes.R MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_WT_TCPO_D1_G168_TCPO_Env_G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_GeneBody'_'MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_WT_TCPO_D1_G168_TCPO_Env_G169G169_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_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 132 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 131 7 [1] "Check out Up_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt Down_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt LncRNA_GeneBody_Counting DiffExp_2e WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2e" [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_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt Up_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt LncRNA_GeneBody_Counting DiffExp_2e WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2e" [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_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 306 Apr 22 19:57 /scratch/5524859.1.linga/Input/DiffExp_2e_Venn_Tables_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 5038460 Apr 22 19:57 /scratch/5524859.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_WT_TCPO_D1_MetEGFKO_TCPO_D1.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Apr 22 19:55 /scratch/5524859.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 7403 Apr 22 19:57 /scratch/5524859.1.linga/Input/Down_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 18551 Apr 22 19:57 /scratch/5524859.1.linga/Input/Down_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 717278 Apr 22 19:55 /scratch/5524859.1.linga/Input/MetEGFKO_TCPO_D10.out -rw-r--r-- 1 kkarri waxmanlab 304 Apr 22 19:55 /scratch/5524859.1.linga/Input/MetEGFKO_TCPO_D10.summary -rw-r--r-- 1 kkarri waxmanlab 718477 Apr 22 19:55 /scratch/5524859.1.linga/Input/MetEGFKO_TCPO_D11.out -rw-r--r-- 1 kkarri waxmanlab 304 Apr 22 19:55 /scratch/5524859.1.linga/Input/MetEGFKO_TCPO_D11.summary -rw-r--r-- 1 kkarri waxmanlab 2245867 Apr 22 19:57 /scratch/5524859.1.linga/Input/MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_WT_TCPO_D1_G168_TCPO_Env_G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2603701 Apr 22 19:57 /scratch/5524859.1.linga/Input/MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_WT_TCPO_D1_G168_TCPO_Env_G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 1173926 Apr 22 19:57 /scratch/5524859.1.linga/Input/MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_WT_TCPO_D1_G168_TCPO_Env_G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1975342 Apr 22 19:57 /scratch/5524859.1.linga/Input/MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_WT_TCPO_D1_G168_TCPO_Env_G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 6779 Apr 22 19:57 /scratch/5524859.1.linga/Input/Up_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 16162 Apr 22 19:57 /scratch/5524859.1.linga/Input/Up_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Apr 22 19:55 /scratch/5524859.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 42393 Apr 22 19:57 /scratch/5524859.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 40060 Apr 22 19:57 /scratch/5524859.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 716707 Apr 22 19:55 /scratch/5524859.1.linga/Input/WT_TCPO_D10.out -rw-r--r-- 1 kkarri waxmanlab 303 Apr 22 19:55 /scratch/5524859.1.linga/Input/WT_TCPO_D10.summary -rw-r--r-- 1 kkarri waxmanlab 717713 Apr 22 19:55 /scratch/5524859.1.linga/Input/WT_TCPO_D11.out -rw-r--r-- 1 kkarri waxmanlab 303 Apr 22 19:55 /scratch/5524859.1.linga/Input/WT_TCPO_D11.summary -rwxr-xr-x 1 kkarri waxmanlab 4968 Apr 22 19:55 /scratch/5524859.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Apr 22 19:55 /scratch/5524859.1.linga/Input/formatForSegex_ver4.R -rw-r--r-- 1 kkarri waxmanlab 815529 Apr 22 19:55 /scratch/5524859.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/5524859.1.linga/Input/MetEGFKO_TCPO_D1: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 19:55 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 19:57 .. /scratch/5524859.1.linga/Input/WT_TCPO_D1: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 19:55 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 19:57 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Apr 22 19:57 . drwxrwxrwt. 63 root root 72K Apr 22 19:57 .. -rw-r--r-- 1 kkarri waxmanlab 109 Apr 22 19:55 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 127 Apr 22 19:55 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Apr 22 19:57 Input -rwxr-xr-x 1 kkarri waxmanlab 15K Apr 22 19:55 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Apr 22 19:55 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 19:52 . drwxr-sr-x 7 kkarri waxmanlab 4.0K Apr 22 19:51 .. -rw-r--r-- 1 kkarri waxmanlab 306 Apr 22 19:52 DiffExp_2e_Venn_Tables_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.9M Apr 22 19:52 DiffExp_v2_LncRNA_GeneBody_WT_TCPO_D1_MetEGFKO_TCPO_D1_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 7.3K Apr 22 19:52 Down_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 19K Apr 22 19:52 Down_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.2M Apr 22 19:52 MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_WT_TCPO_D1_G168_TCPO_Env_G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.5M Apr 22 19:52 MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_WT_TCPO_D1_G168_TCPO_Env_G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.2M Apr 22 19:52 MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_WT_TCPO_D1_G168_TCPO_Env_G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.9M Apr 22 19:52 MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_vs_WT_TCPO_D1_G168_TCPO_Env_G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 6.7K Apr 22 19:52 Up_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 16K Apr 22 19:52 Up_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D1_G168_TCPO_Env_G169G169_WT_TCPO_D1_G168_TCPO_Env_G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 42K Apr 22 19:52 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 40K Apr 22 19:52 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Apr 22 19:58:04 EDT 2019 2 minutes and 11 seconds elapsed. ==========================================================