----------------------- 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_6_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: M2WT CONDITION_2_NAME: M2Ezh12 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_6g COL_SUFFIX: LncRNA_Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Mar 10 06:22:42 EDT 2020 Running on node : scc-tm3 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_6_lncRNA_featureCounts Current job ID : 3782053 Current job name : Step_08c_DiffExp_6g Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3782053.1.linga Loading required modules... ------------------------------------------ Sample_DIR: M2WTM_1 Sample_ID: M2WTM_1 Description: M2WTM_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: M2WTM_2 Sample_ID: M2WTM_2 Description: M2WTM_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: M2WTF_1 Sample_ID: M2WTF_1 Description: M2WTF_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: M2WTF_2 Sample_ID: M2WTF_2 Description: M2WTF_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: 1212 ------------------------------------------ ------------------------------------------ Sample_DIR: M2Ezh12M_1 Sample_ID: M2Ezh12M_1 Description: M2Ezh12M_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: M2Ezh12M_2 Sample_ID: M2Ezh12M_2 Description: M2Ezh12M_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: M2Ezh12M_3 Sample_ID: M2Ezh12M_3 Description: M2Ezh12M_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: M2Ezh12F_1 Sample_ID: M2Ezh12F_1 Description: M2Ezh12F_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: M2Ezh12F_2 Sample_ID: M2Ezh12F_2 Description: M2Ezh12F_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: M2Ezh12F_3 Sample_ID: M2Ezh12F_3 Description: M2Ezh12F_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 M_Num_Cond2_List: 123123 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 4 NUM_REP_CONDITION1: 4 ========================================================== Renaming input count files number of mapped reads (feature count summary) Status M2Ezh12F_1_sorted.bam Assigned 4391940 Unassigned_Ambiguity 825558 Unassigned_MultiMapping 0 Unassigned_NoFeatures 24952168 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2Ezh12F_2_sorted.bam Assigned 2235682 Unassigned_Ambiguity 468006 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11711307 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2Ezh12F_3_sorted.bam Assigned 1455874 Unassigned_Ambiguity 419175 Unassigned_MultiMapping 0 Unassigned_NoFeatures 10750534 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2Ezh12M_1_sorted.bam Assigned 2623543 Unassigned_Ambiguity 447397 Unassigned_MultiMapping 0 Unassigned_NoFeatures 10749292 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2Ezh12M_2_sorted.bam Assigned 2323792 Unassigned_Ambiguity 534847 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11072122 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2Ezh12M_3_sorted.bam Assigned 980171 Unassigned_Ambiguity 249058 Unassigned_MultiMapping 0 Unassigned_NoFeatures 6070043 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2WTF_1_sorted.bam Assigned 2301679 Unassigned_Ambiguity 610124 Unassigned_MultiMapping 0 Unassigned_NoFeatures 12856265 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2WTF_2_sorted.bam Assigned 2224366 Unassigned_Ambiguity 625016 Unassigned_MultiMapping 0 Unassigned_NoFeatures 12374278 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2WTM_1_sorted.bam Assigned 1341939 Unassigned_Ambiguity 833454 Unassigned_MultiMapping 0 Unassigned_NoFeatures 10493073 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status M2WTM_2_sorted.bam Assigned 1394741 Unassigned_Ambiguity 822479 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11310168 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 352988 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh120.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh120.summary -rw-r--r-- 1 kkarri waxmanlab 349472 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh121.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh121.summary -rw-r--r-- 1 kkarri waxmanlab 345882 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh122.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh122.summary -rw-r--r-- 1 kkarri waxmanlab 350995 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh123.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh123.summary -rw-r--r-- 1 kkarri waxmanlab 349322 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh124.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh124.summary -rw-r--r-- 1 kkarri waxmanlab 344514 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh125.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh125.summary -rw-r--r-- 1 kkarri waxmanlab 347874 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT0.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT0.summary -rw-r--r-- 1 kkarri waxmanlab 348095 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT1.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT1.summary -rw-r--r-- 1 kkarri waxmanlab 344068 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT2.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT2.summary -rw-r--r-- 1 kkarri waxmanlab 344017 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT3.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT3.summary -rw-r--r-- 1 kkarri waxmanlab 414633 Mar 10 06:22 /scratch/3782053.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3782053.1.linga/Input/M2Ezh12: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:22 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:22 .. /scratch/3782053.1.linga/Input/M2WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:22 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:22 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R M2WT M2Ezh12 4 6 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/3782053.1.linga/Input DiffExp_v2_LncRNA_Intronic_Only intronic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "M2WT" [1] "M2Ezh12" [1] 4 [1] 6 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/3782053.1.linga/Input" [1] "DiffExp_v2_LncRNA_Intronic_Only" [1] "intronic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] "sum1:26375.8029728786" "sum1:29642.4687450495" "sum1:31177.0918087022" [4] "sum1:27305.8564091849" "sum1:28625.3049839538" [1] "sum2:25526.5836955502" "sum2:27086.211296228" "sum2:27216.7269236359" [4] "sum2:28628.3949938226" "sum2:22836.5738084052" "sum2:25832.6520029308" [7] "sum2:26187.8571200955" [1] 15558 23 [1] 15558 79 [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/3782053.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_M2WT_M2Ezh12.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Intronic_Only_M2WT_M2Ezh12.txt M2Ezh12_GSE118757_123123_vs_M2WT_GSE118757_1212_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_M2WT_M2Ezh12.txt M2Ezh12_GSE118757_123123_vs_M2WT_GSE118757_1212_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload 1 LncRNA_Intronic_Only ========================================================== Comparison_Info: M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R M2Ezh12_GSE118757_123123_vs_M2WT_GSE118757_1212_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Intronic_Only'_'M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2Ezh12_GSE118757_123123_vs_M2WT_GSE118757_1212_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_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212" [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] 90 7 [1] "Check out Up_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt!" Rscript Diff_Genes.R M2Ezh12_GSE118757_123123_vs_M2WT_GSE118757_1212_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Intronic_Only'_'M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2Ezh12_GSE118757_123123_vs_M2WT_GSE118757_1212_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_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212" [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] 107 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt LncRNA_Intronic_Only_Counting DiffExp_6g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_6g" [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_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt LncRNA_Intronic_Only_Counting DiffExp_6g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_6g" [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: M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 335 Mar 10 06:23 /scratch/3782053.1.linga/Input/DiffExp_6g_Venn_Tables_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt -rw-r--r-- 1 kkarri waxmanlab 5036457 Mar 10 06:23 /scratch/3782053.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_M2WT_M2Ezh12.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Mar 10 06:22 /scratch/3782053.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 9652 Mar 10 06:23 /scratch/3782053.1.linga/Input/Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt -rw-r--r-- 1 kkarri waxmanlab 11328 Mar 10 06:23 /scratch/3782053.1.linga/Input/Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt -rw-r--r-- 1 kkarri waxmanlab 352988 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh120.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh120.summary -rw-r--r-- 1 kkarri waxmanlab 349472 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh121.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh121.summary -rw-r--r-- 1 kkarri waxmanlab 345882 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh122.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh122.summary -rw-r--r-- 1 kkarri waxmanlab 350995 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh123.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh123.summary -rw-r--r-- 1 kkarri waxmanlab 349322 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh124.out -rw-r--r-- 1 kkarri waxmanlab 301 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh124.summary -rw-r--r-- 1 kkarri waxmanlab 344514 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh125.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2Ezh125.summary -rw-r--r-- 1 kkarri waxmanlab 2043633 Mar 10 06:23 /scratch/3782053.1.linga/Input/M2Ezh12_GSE118757_123123_vs_M2WT_GSE118757_1212_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2105865 Mar 10 06:23 /scratch/3782053.1.linga/Input/M2Ezh12_GSE118757_123123_vs_M2WT_GSE118757_1212_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 872416 Mar 10 06:23 /scratch/3782053.1.linga/Input/M2Ezh12_GSE118757_123123_vs_M2WT_GSE118757_1212_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1259204 Mar 10 06:23 /scratch/3782053.1.linga/Input/M2Ezh12_GSE118757_123123_vs_M2WT_GSE118757_1212_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 347874 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT0.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT0.summary -rw-r--r-- 1 kkarri waxmanlab 348095 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT1.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT1.summary -rw-r--r-- 1 kkarri waxmanlab 344068 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT2.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT2.summary -rw-r--r-- 1 kkarri waxmanlab 344017 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT3.out -rw-r--r-- 1 kkarri waxmanlab 298 Mar 10 06:22 /scratch/3782053.1.linga/Input/M2WT3.summary -rw-r--r-- 1 kkarri waxmanlab 5552 Mar 10 06:23 /scratch/3782053.1.linga/Input/Up_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt -rw-r--r-- 1 kkarri waxmanlab 7641 Mar 10 06:23 /scratch/3782053.1.linga/Input/Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Mar 10 06:22 /scratch/3782053.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 44470 Mar 10 06:23 /scratch/3782053.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 41101 Mar 10 06:23 /scratch/3782053.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 4968 Mar 10 06:22 /scratch/3782053.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Mar 10 06:22 /scratch/3782053.1.linga/Input/formatForSegex_ver4.R -rw-r--r-- 1 kkarri waxmanlab 414633 Mar 10 06:22 /scratch/3782053.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3782053.1.linga/Input/M2Ezh12: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:22 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:23 .. /scratch/3782053.1.linga/Input/M2WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 06:22 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 06:23 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Mar 10 06:23 . drwxrwxrwt. 16 root root 4.0K Mar 10 06:22 .. -rw-r--r-- 1 kkarri waxmanlab 129 Mar 10 06:22 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 231 Mar 10 06:22 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 10 06:23 Input -rwxr-xr-x 1 kkarri waxmanlab 15K Mar 10 06:22 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Mar 10 06:22 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-xr-x 2 kkarri waxmanlab 4.0K Mar 10 06:15 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 10 06:15 .. -rw-r--r-- 1 kkarri waxmanlab 335 Mar 10 06:15 DiffExp_6g_Venn_Tables_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.9M Mar 10 06:15 DiffExp_v2_LncRNA_Intronic_Only_M2WT_M2Ezh12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 9.5K Mar 10 06:15 Down_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 12K Mar 10 06:15 Down_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.0M Mar 10 06:15 M2Ezh12_GSE118757_123123_vs_M2WT_GSE118757_1212_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.1M Mar 10 06:15 M2Ezh12_GSE118757_123123_vs_M2WT_GSE118757_1212_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 852K Mar 10 06:15 M2Ezh12_GSE118757_123123_vs_M2WT_GSE118757_1212_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.3M Mar 10 06:15 M2Ezh12_GSE118757_123123_vs_M2WT_GSE118757_1212_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.5K Mar 10 06:15 Up_Genes_DESeq_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 7.5K Mar 10 06:15 Up_Genes_EdgeR_LncRNA_Intronic_Only_M2Ezh12_GSE118757_123123_M2WT_GSE118757_1212_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 44K Mar 10 06:15 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 41K Mar 10 06:15 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Tue Mar 10 06:23:25 EDT 2020 0 minutes and 43 seconds elapsed. ==========================================================