----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_3_lncRNA_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana Dataset_Label: GSE118757 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: Ezh12 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_3g COL_SUFFIX: LncRNA_Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Mar 10 06:36:32 EDT 2020 Running on node : scc-ka4 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_3_lncRNA_featureCounts Current job ID : 3782071 Current job name : Step_08c_DiffExp_3g Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3782071.1.linga Loading required modules... ------------------------------------------ Sample_DIR: WTM_1 Sample_ID: WTM_1 Description: WTM_1 M_Num: 1 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: WTM_2 Sample_ID: WTM_2 Description: WTM_2 M_Num: 2 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: WTM_3 Sample_ID: WTM_3 Description: WTM_3 M_Num: 3 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: WTF_1 Sample_ID: WTF_1 Description: WTF_1 M_Num: 1 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: WTF_2 Sample_ID: WTF_2 Description: WTF_2 M_Num: 2 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: 12312 ------------------------------------------ ------------------------------------------ Sample_DIR: Ezh12M_1 Sample_ID: Ezh12M_1 Description: Ezh12M_1 M_Num: 1 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Ezh12M_2 Sample_ID: Ezh12M_2 Description: Ezh12M_2 M_Num: 2 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Ezh12F_1 Sample_ID: Ezh12F_1 Description: Ezh12F_1 M_Num: 1 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Ezh12F_2 Sample_ID: Ezh12F_2 Description: Ezh12F_2 M_Num: 2 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Ezh12F_3 Sample_ID: Ezh12F_3 Description: Ezh12F_3 M_Num: 3 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Ezh12F_4 Sample_ID: Ezh12F_4 Description: Ezh12F_4 M_Num: 4 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Ezh12F_5 Sample_ID: Ezh12F_5 Description: Ezh12F_5 M_Num: 5 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: 1212345 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 5 NUM_REP_CONDITION1: 5 ========================================================== Renaming input count files number of mapped reads (feature count summary) Status Ezh12F_1_sorted.bam Assigned 2788075 Unassigned_Ambiguity 332727 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11106743 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12F_2_sorted.bam Assigned 2970063 Unassigned_Ambiguity 377029 Unassigned_MultiMapping 0 Unassigned_NoFeatures 12644126 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12F_3_sorted.bam Assigned 2148503 Unassigned_Ambiguity 483639 Unassigned_MultiMapping 0 Unassigned_NoFeatures 12208211 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12F_4_sorted.bam Assigned 2021184 Unassigned_Ambiguity 406076 Unassigned_MultiMapping 0 Unassigned_NoFeatures 13008798 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12F_5_sorted.bam Assigned 2217112 Unassigned_Ambiguity 391910 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11640969 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12M_1_sorted.bam Assigned 2106057 Unassigned_Ambiguity 431413 Unassigned_MultiMapping 0 Unassigned_NoFeatures 13291059 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12M_2_sorted.bam Assigned 1831983 Unassigned_Ambiguity 451834 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11889391 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status WTF_1_sorted.bam Assigned 2998711 Unassigned_Ambiguity 526122 Unassigned_MultiMapping 0 Unassigned_NoFeatures 14856921 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status WTF_2_sorted.bam Assigned 2692992 Unassigned_Ambiguity 522013 Unassigned_MultiMapping 0 Unassigned_NoFeatures 13761930 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status WTM_1_sorted.bam Assigned 1767633 Unassigned_Ambiguity 380002 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11204170 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status WTM_2_sorted.bam Assigned 1643568 Unassigned_Ambiguity 427456 Unassigned_MultiMapping 0 Unassigned_NoFeatures 13326780 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status WTM_3_sorted.bam Assigned 2868412 Unassigned_Ambiguity 481525 Unassigned_MultiMapping 0 Unassigned_NoFeatures 13065939 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 350676 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh120.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh120.summary -rw-r--r-- 1 kkarri waxmanlab 350162 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh121.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh121.summary -rw-r--r-- 1 kkarri waxmanlab 347859 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh122.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh122.summary -rw-r--r-- 1 kkarri waxmanlab 347539 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh123.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh123.summary -rw-r--r-- 1 kkarri waxmanlab 348553 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh124.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh124.summary -rw-r--r-- 1 kkarri waxmanlab 347218 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh125.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh125.summary -rw-r--r-- 1 kkarri waxmanlab 346617 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh126.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh126.summary -rw-r--r-- 1 kkarri waxmanlab 349260 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT0.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT0.summary -rw-r--r-- 1 kkarri waxmanlab 348932 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT1.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT1.summary -rw-r--r-- 1 kkarri waxmanlab 346103 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT2.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT2.summary -rw-r--r-- 1 kkarri waxmanlab 344789 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT3.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT3.summary -rw-r--r-- 1 kkarri waxmanlab 349686 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT4.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT4.summary -rw-r--r-- 1 kkarri waxmanlab 414633 Mar 10 06:36 /scratch/3782071.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3782071.1.linga/Input/Ezh12: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:36 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:36 .. /scratch/3782071.1.linga/Input/WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:36 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:36 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WT Ezh12 5 7 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/3782071.1.linga/Input DiffExp_v2_LncRNA_Intronic_Only intronic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WT" [1] "Ezh12" [1] 5 [1] 7 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/3782071.1.linga/Input" [1] "DiffExp_v2_LncRNA_Intronic_Only" [1] "intronic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] "sum1:30246.0075730227" "sum1:32515.1154566466" "sum1:25578.3688596267" [4] "sum1:24736.0558100814" "sum1:27847.1602626022" "sum1:28184.5415923959" [1] "sum2:30538.0250195355" "sum2:34636.1638009951" "sum2:42388.3381932044" [4] "sum2:43353.7642927869" "sum2:36153.5812582354" "sum2:18731.5578492683" [7] "sum2:41033.3536925232" "sum2:35262.1120152212" [1] 15558 23 [1] 15558 87 [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/3782071.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_WT_Ezh12.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Intronic_Only_WT_Ezh12.txt Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload 1 LncRNA_Intronic_Only Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_LncRNA_Intronic_Only_WT_Ezh12.txt Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload 1 LncRNA_Intronic_Only ========================================================== Comparison_Info: Ezh12_GSE118757_1212345_WT_GSE118757_12312 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Intronic_Only'_'Ezh12_GSE118757_1212345_WT_GSE118757_12312 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_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_Ezh12_GSE118757_1212345_WT_GSE118757_12312" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 42 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 83 7 [1] "Check out Up_Genes_DESeq_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt!" Rscript Diff_Genes.R Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Intronic_Only'_'Ezh12_GSE118757_1212345_WT_GSE118757_12312 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_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_Ezh12_GSE118757_1212345_WT_GSE118757_12312" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 45 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 94 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt Down_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt LncRNA_Intronic_Only_Counting DiffExp_3g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3g" [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_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt Up_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt LncRNA_Intronic_Only_Counting DiffExp_3g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3g" [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: Ezh12_GSE118757_1212345_WT_GSE118757_12312 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 333 Mar 10 06:37 /scratch/3782071.1.linga/Input/DiffExp_3g_Venn_Tables_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt -rw-r--r-- 1 kkarri waxmanlab 5565392 Mar 10 06:37 /scratch/3782071.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_WT_Ezh12.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Mar 10 06:36 /scratch/3782071.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 7278 Mar 10 06:37 /scratch/3782071.1.linga/Input/Down_Genes_DESeq_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt -rw-r--r-- 1 kkarri waxmanlab 8211 Mar 10 06:37 /scratch/3782071.1.linga/Input/Down_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt -rw-r--r-- 1 kkarri waxmanlab 350676 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh120.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh120.summary -rw-r--r-- 1 kkarri waxmanlab 350162 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh121.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh121.summary -rw-r--r-- 1 kkarri waxmanlab 347859 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh122.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh122.summary -rw-r--r-- 1 kkarri waxmanlab 347539 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh123.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh123.summary -rw-r--r-- 1 kkarri waxmanlab 348553 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh124.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh124.summary -rw-r--r-- 1 kkarri waxmanlab 347218 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh125.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh125.summary -rw-r--r-- 1 kkarri waxmanlab 346617 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh126.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:36 /scratch/3782071.1.linga/Input/Ezh126.summary -rw-r--r-- 1 kkarri waxmanlab 3272711 Mar 10 06:37 /scratch/3782071.1.linga/Input/Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1732469 Mar 10 06:37 /scratch/3782071.1.linga/Input/Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 674256 Mar 10 06:37 /scratch/3782071.1.linga/Input/Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 859967 Mar 10 06:37 /scratch/3782071.1.linga/Input/Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 4501 Mar 10 06:37 /scratch/3782071.1.linga/Input/Up_Genes_DESeq_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt -rw-r--r-- 1 kkarri waxmanlab 5437 Mar 10 06:37 /scratch/3782071.1.linga/Input/Up_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Mar 10 06:36 /scratch/3782071.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 42747 Mar 10 06:37 /scratch/3782071.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 40988 Mar 10 06:37 /scratch/3782071.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 349260 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT0.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT0.summary -rw-r--r-- 1 kkarri waxmanlab 348932 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT1.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT1.summary -rw-r--r-- 1 kkarri waxmanlab 346103 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT2.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT2.summary -rw-r--r-- 1 kkarri waxmanlab 344789 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT3.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT3.summary -rw-r--r-- 1 kkarri waxmanlab 349686 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT4.out -rw-r--r-- 1 kkarri waxmanlab 296 Mar 10 06:36 /scratch/3782071.1.linga/Input/WT4.summary -rwxr-xr-x 1 kkarri waxmanlab 4968 Mar 10 06:36 /scratch/3782071.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Mar 10 06:36 /scratch/3782071.1.linga/Input/formatForSegex_ver4.R -rw-r--r-- 1 kkarri waxmanlab 414633 Mar 10 06:36 /scratch/3782071.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3782071.1.linga/Input/Ezh12: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:36 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:37 .. /scratch/3782071.1.linga/Input/WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:36 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:37 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Mar 10 06:37 . drwxrwxrwt. 13 root root 4.0K Mar 10 06:36 .. -rw-r--r-- 1 kkarri waxmanlab 123 Mar 10 06:36 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 222 Mar 10 06:36 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 10 06:37 Input -rwxr-xr-x 1 kkarri waxmanlab 15K Mar 10 06:36 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Mar 10 06:36 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 23M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 10 06:30 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 10 06:29 .. -rw-r--r-- 1 kkarri waxmanlab 333 Mar 10 06:30 DiffExp_3g_Venn_Tables_Ezh12_GSE118757_1212345_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.4M Mar 10 06:30 DiffExp_v2_LncRNA_Intronic_Only_WT_Ezh12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 7.2K Mar 10 06:30 Down_Genes_DESeq_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 8.1K Mar 10 06:30 Down_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 10 06:30 Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.7M Mar 10 06:30 Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 659K Mar 10 06:30 Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 840K Mar 10 06:30 Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.4K Mar 10 06:30 Up_Genes_DESeq_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.4K Mar 10 06:30 Up_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12_GSE118757_1212345_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 42K Mar 10 06:30 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 41K Mar 10 06:30 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Tue Mar 10 06:37:42 EDT 2020 1 minutes and 10 seconds elapsed. ==========================================================