----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/08c_DiffExp_1_lncRNA_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation Dataset_Label: LZ 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 CONDITION_2_NAME: KcO Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: intronic_only_gene_models_ncRNA_for_counting_lengths.txt COUNT_DIR: LncRNA_Intronic_Only_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_Intronic_Only DiffExp_Index: DiffExp_1g COL_SUFFIX: LncRNA_Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed May 9 20:23:52 EDT 2018 Running on node : scc-kb6 Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/08c_DiffExp_1_lncRNA_featureCounts Current job ID : 6139633 Current job name : Step_08c_DiffExp_1g Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/6139633.1.linga Loading required modules... ------------------------------------------ Sample_DIR: LZ_M1 Sample_ID: LZ_M1 Description: WT1 M_Num: M1 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: LZ_M2 Sample_ID: LZ_M2 Description: WT2 M_Num: M2 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: LZ_M3 Sample_ID: LZ_M3 Description: WT3 M_Num: M3 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: LZ_M4 Sample_ID: LZ_M4 Description: WT4 M_Num: M4 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: LZ_M5 Sample_ID: LZ_M5 Description: WT5 M_Num: M5 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: LZ_M6 Sample_ID: LZ_M6 Description: WT6 M_Num: M6 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: Sample_ID: Description: M_Num: 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: M1M2M3M4M5M6 ------------------------------------------ ------------------------------------------ Sample_DIR: LZ_M7 Sample_ID: LZ_M7 Description: KO1 M_Num: M7 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: LZ_M8 Sample_ID: LZ_M8 Description: KO2 M_Num: M8 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: LZ_M9 Sample_ID: LZ_M9 Description: KO3 M_Num: M9 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: LZ_M10 Sample_ID: LZ_M10 Description: KO4 M_Num: M10 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: LZ_M11 Sample_ID: LZ_M11 Description: KO5 M_Num: M11 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: LZ_M12 Sample_ID: LZ_M12 Description: KO6 M_Num: M12 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Sample_ID: Description: M_Num: 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: M7M8M9M10M11M12 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 6 NUM_REP_CONDITION1: 6 ========================================================== Renaming input count files number of mapped reads (feature count summary) Status LZ_M10_sorted.bam Assigned 1121083 Unassigned_Ambiguity 193471 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11024271 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M11_sorted.bam Assigned 892650 Unassigned_Ambiguity 164603 Unassigned_MultiMapping 0 Unassigned_NoFeatures 8753206 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M12_sorted.bam Assigned 862259 Unassigned_Ambiguity 148211 Unassigned_MultiMapping 0 Unassigned_NoFeatures 8305458 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M7_sorted.bam Assigned 1095027 Unassigned_Ambiguity 173479 Unassigned_MultiMapping 0 Unassigned_NoFeatures 10769877 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M8_sorted.bam Assigned 1048641 Unassigned_Ambiguity 162428 Unassigned_MultiMapping 0 Unassigned_NoFeatures 9226358 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M9_sorted.bam Assigned 1222746 Unassigned_Ambiguity 184935 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11033017 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M1_sorted.bam Assigned 1050020 Unassigned_Ambiguity 252976 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11409861 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M2_sorted.bam Assigned 1287524 Unassigned_Ambiguity 193707 Unassigned_MultiMapping 0 Unassigned_NoFeatures 12186363 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M3_sorted.bam Assigned 1058510 Unassigned_Ambiguity 206560 Unassigned_MultiMapping 0 Unassigned_NoFeatures 10066146 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M4_sorted.bam Assigned 926665 Unassigned_Ambiguity 202284 Unassigned_MultiMapping 0 Unassigned_NoFeatures 9816360 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M5_sorted.bam Assigned 947126 Unassigned_Ambiguity 151889 Unassigned_MultiMapping 0 Unassigned_NoFeatures 9387019 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status LZ_M6_sorted.bam Assigned 927146 Unassigned_Ambiguity 163444 Unassigned_MultiMapping 0 Unassigned_NoFeatures 9474905 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 345539 May 9 20:23 /scratch/6139633.1.linga/Input/KcO0.out -rw-r--r-- 1 kkarri waxmanlab 297 May 9 20:23 /scratch/6139633.1.linga/Input/KcO0.summary -rw-r--r-- 1 kkarri waxmanlab 343282 May 9 20:23 /scratch/6139633.1.linga/Input/KcO1.out -rw-r--r-- 1 kkarri waxmanlab 295 May 9 20:23 /scratch/6139633.1.linga/Input/KcO1.summary -rw-r--r-- 1 kkarri waxmanlab 344177 May 9 20:23 /scratch/6139633.1.linga/Input/KcO2.out -rw-r--r-- 1 kkarri waxmanlab 295 May 9 20:23 /scratch/6139633.1.linga/Input/KcO2.summary -rw-r--r-- 1 kkarri waxmanlab 344907 May 9 20:23 /scratch/6139633.1.linga/Input/KcO3.out -rw-r--r-- 1 kkarri waxmanlab 296 May 9 20:23 /scratch/6139633.1.linga/Input/KcO3.summary -rw-r--r-- 1 kkarri waxmanlab 344089 May 9 20:23 /scratch/6139633.1.linga/Input/KcO4.out -rw-r--r-- 1 kkarri waxmanlab 295 May 9 20:23 /scratch/6139633.1.linga/Input/KcO4.summary -rw-r--r-- 1 kkarri waxmanlab 345320 May 9 20:23 /scratch/6139633.1.linga/Input/KcO5.out -rw-r--r-- 1 kkarri waxmanlab 296 May 9 20:23 /scratch/6139633.1.linga/Input/KcO5.summary -rw-r--r-- 1 kkarri waxmanlab 344713 May 9 20:23 /scratch/6139633.1.linga/Input/WT0.out -rw-r--r-- 1 kkarri waxmanlab 296 May 9 20:23 /scratch/6139633.1.linga/Input/WT0.summary -rw-r--r-- 1 kkarri waxmanlab 346001 May 9 20:23 /scratch/6139633.1.linga/Input/WT1.out -rw-r--r-- 1 kkarri waxmanlab 296 May 9 20:23 /scratch/6139633.1.linga/Input/WT1.summary -rw-r--r-- 1 kkarri waxmanlab 344743 May 9 20:23 /scratch/6139633.1.linga/Input/WT2.out -rw-r--r-- 1 kkarri waxmanlab 296 May 9 20:23 /scratch/6139633.1.linga/Input/WT2.summary -rw-r--r-- 1 kkarri waxmanlab 343623 May 9 20:23 /scratch/6139633.1.linga/Input/WT3.out -rw-r--r-- 1 kkarri waxmanlab 294 May 9 20:23 /scratch/6139633.1.linga/Input/WT3.summary -rw-r--r-- 1 kkarri waxmanlab 344124 May 9 20:23 /scratch/6139633.1.linga/Input/WT4.out -rw-r--r-- 1 kkarri waxmanlab 294 May 9 20:23 /scratch/6139633.1.linga/Input/WT4.summary -rw-r--r-- 1 kkarri waxmanlab 344457 May 9 20:23 /scratch/6139633.1.linga/Input/WT5.out -rw-r--r-- 1 kkarri waxmanlab 294 May 9 20:23 /scratch/6139633.1.linga/Input/WT5.summary -rw-r--r-- 1 kkarri waxmanlab 414633 May 9 20:23 /scratch/6139633.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/6139633.1.linga/Input/KcO: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 9 20:23 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 9 20:23 .. /scratch/6139633.1.linga/Input/WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 9 20:23 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 9 20:23 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WT KcO 6 6 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/6139633.1.linga/Input DiffExp_v2_LncRNA_Intronic_Only intronic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WT" [1] "KcO" [1] 6 [1] 6 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/6139633.1.linga/Input" [1] "DiffExp_v2_LncRNA_Intronic_Only" [1] "intronic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] 15558 23 [1] 15558 72 [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/6139633.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_WT_KcO.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Intronic_Only_WT_KcO.txt KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload 1 LncRNA_Intronic_Only ========================================================== Comparison_Info: KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Intronic_Only'_'KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_LncRNA_Intronic_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_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 1 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 9 7 [1] "Check out Up_Genes_DESeq_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt!" Rscript Diff_Genes.R KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Intronic_Only'_'KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_LncRNA_Intronic_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_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 1 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 13 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt Down_Genes_EdgeR_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt LncRNA_Intronic_Only_Counting DiffExp_1g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1g" [1] "-----------------" [1] "Down.DESeq.Intronic_Only.HTSeq" [1] "Down.EdgeR.Intronic_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_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt Up_Genes_EdgeR_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt LncRNA_Intronic_Only_Counting DiffExp_1g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1g" [1] "-----------------" [1] "Up.DESeq.Intronic_Only.HTSeq" [1] "Up.EdgeR.Intronic_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: KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 329 May 9 20:25 /scratch/6139633.1.linga/Input/DiffExp_1g_Venn_Tables_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 4471325 May 9 20:25 /scratch/6139633.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 May 9 20:23 /scratch/6139633.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 1073 May 9 20:25 /scratch/6139633.1.linga/Input/Down_Genes_DESeq_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 1531 May 9 20:25 /scratch/6139633.1.linga/Input/Down_Genes_EdgeR_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 345539 May 9 20:23 /scratch/6139633.1.linga/Input/KcO0.out -rw-r--r-- 1 kkarri waxmanlab 297 May 9 20:23 /scratch/6139633.1.linga/Input/KcO0.summary -rw-r--r-- 1 kkarri waxmanlab 343282 May 9 20:23 /scratch/6139633.1.linga/Input/KcO1.out -rw-r--r-- 1 kkarri waxmanlab 295 May 9 20:23 /scratch/6139633.1.linga/Input/KcO1.summary -rw-r--r-- 1 kkarri waxmanlab 344177 May 9 20:23 /scratch/6139633.1.linga/Input/KcO2.out -rw-r--r-- 1 kkarri waxmanlab 295 May 9 20:23 /scratch/6139633.1.linga/Input/KcO2.summary -rw-r--r-- 1 kkarri waxmanlab 344907 May 9 20:23 /scratch/6139633.1.linga/Input/KcO3.out -rw-r--r-- 1 kkarri waxmanlab 296 May 9 20:23 /scratch/6139633.1.linga/Input/KcO3.summary -rw-r--r-- 1 kkarri waxmanlab 344089 May 9 20:23 /scratch/6139633.1.linga/Input/KcO4.out -rw-r--r-- 1 kkarri waxmanlab 295 May 9 20:23 /scratch/6139633.1.linga/Input/KcO4.summary -rw-r--r-- 1 kkarri waxmanlab 345320 May 9 20:23 /scratch/6139633.1.linga/Input/KcO5.out -rw-r--r-- 1 kkarri waxmanlab 296 May 9 20:23 /scratch/6139633.1.linga/Input/KcO5.summary -rw-r--r-- 1 kkarri waxmanlab 1872489 May 9 20:25 /scratch/6139633.1.linga/Input/KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1996953 May 9 20:25 /scratch/6139633.1.linga/Input/KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 292 May 9 20:25 /scratch/6139633.1.linga/Input/Up_Genes_DESeq_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 294 May 9 20:25 /scratch/6139633.1.linga/Input/Up_Genes_EdgeR_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 May 9 20:23 /scratch/6139633.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 41951 May 9 20:25 /scratch/6139633.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 31172 May 9 20:25 /scratch/6139633.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 344713 May 9 20:23 /scratch/6139633.1.linga/Input/WT0.out -rw-r--r-- 1 kkarri waxmanlab 296 May 9 20:23 /scratch/6139633.1.linga/Input/WT0.summary -rw-r--r-- 1 kkarri waxmanlab 346001 May 9 20:23 /scratch/6139633.1.linga/Input/WT1.out -rw-r--r-- 1 kkarri waxmanlab 296 May 9 20:23 /scratch/6139633.1.linga/Input/WT1.summary -rw-r--r-- 1 kkarri waxmanlab 344743 May 9 20:23 /scratch/6139633.1.linga/Input/WT2.out -rw-r--r-- 1 kkarri waxmanlab 296 May 9 20:23 /scratch/6139633.1.linga/Input/WT2.summary -rw-r--r-- 1 kkarri waxmanlab 343623 May 9 20:23 /scratch/6139633.1.linga/Input/WT3.out -rw-r--r-- 1 kkarri waxmanlab 294 May 9 20:23 /scratch/6139633.1.linga/Input/WT3.summary -rw-r--r-- 1 kkarri waxmanlab 344124 May 9 20:23 /scratch/6139633.1.linga/Input/WT4.out -rw-r--r-- 1 kkarri waxmanlab 294 May 9 20:23 /scratch/6139633.1.linga/Input/WT4.summary -rw-r--r-- 1 kkarri waxmanlab 344457 May 9 20:23 /scratch/6139633.1.linga/Input/WT5.out -rw-r--r-- 1 kkarri waxmanlab 294 May 9 20:23 /scratch/6139633.1.linga/Input/WT5.summary -rwxr-xr-x 1 kkarri waxmanlab 4968 May 9 20:23 /scratch/6139633.1.linga/Input/formatForSegex_ver3.R -rw-r--r-- 1 kkarri waxmanlab 414633 May 9 20:23 /scratch/6139633.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/6139633.1.linga/Input/KcO: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 9 20:23 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 9 20:25 .. /scratch/6139633.1.linga/Input/WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 May 9 20:23 . drwxr-xr-x 4 kkarri waxmanlab 4096 May 9 20:25 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K May 9 20:25 . drwxrwxrwt. 51 root root 84K May 9 20:25 .. -rw-r--r-- 1 kkarri waxmanlab 132 May 9 20:23 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 138 May 9 20:23 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K May 9 20:25 Input -rwxr-xr-x 1 kkarri waxmanlab 13K May 9 20:23 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M May 9 20:23 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 6.1M drwxr-sr-x 2 kkarri waxmanlab 32K May 9 20:25 . drwxr-sr-x 7 kkarri waxmanlab 32K May 9 20:23 .. -rw-r--r-- 1 kkarri waxmanlab 329 May 9 20:25 DiffExp_1g_Venn_Tables_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.3M May 9 20:25 DiffExp_v2_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.1K May 9 20:25 Down_Genes_DESeq_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.5K May 9 20:25 Down_Genes_EdgeR_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.8M May 9 20:25 KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.0M May 9 20:25 KcO_LZ_M7M8M9M10M11M12_vs_WT_LZ_M1M2M3M4M5M6_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 292 May 9 20:25 Up_Genes_DESeq_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 294 May 9 20:25 Up_Genes_EdgeR_LncRNA_Intronic_Only_KcO_LZ_M7M8M9M10M11M12_WT_LZ_M1M2M3M4M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 41K May 9 20:25 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 31K May 9 20:25 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Wed May 9 20:25:26 EDT 2018 1 minutes and 34 seconds elapsed. ==========================================================