----------------------- 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: ncRNA_exon_for_counting_lengths.txt COUNT_DIR: LncRNA_Exon_Collapsed_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_ExonCollapsed DiffExp_Index: DiffExp_3d COL_SUFFIX: LncRNA_ExonCollapsed COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Mar 10 06:36:33 EDT 2020 Running on node : scc-tm1 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_3_lncRNA_featureCounts Current job ID : 3782068 Current job name : Step_08c_DiffExp_3d Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3782068.1.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 11007329 Unassigned_Ambiguity 2038956 Unassigned_MultiMapping 0 Unassigned_NoFeatures 4412272 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 12918757 Unassigned_Ambiguity 2559016 Unassigned_MultiMapping 0 Unassigned_NoFeatures 4522042 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 13170076 Unassigned_Ambiguity 2746436 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3299834 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 14594997 Unassigned_Ambiguity 3013258 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3122185 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 12159173 Unassigned_Ambiguity 2342679 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3746735 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 10921589 Unassigned_Ambiguity 1825457 Unassigned_MultiMapping 0 Unassigned_NoFeatures 5629797 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 13061811 Unassigned_Ambiguity 2817844 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3084287 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 15702613 Unassigned_Ambiguity 3509821 Unassigned_MultiMapping 0 Unassigned_NoFeatures 4664380 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 14678424 Unassigned_Ambiguity 3272630 Unassigned_MultiMapping 0 Unassigned_NoFeatures 4304999 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 11042633 Unassigned_Ambiguity 2265601 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3699572 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 12345720 Unassigned_Ambiguity 2528927 Unassigned_MultiMapping 0 Unassigned_NoFeatures 4595955 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 13594808 Unassigned_Ambiguity 2740130 Unassigned_MultiMapping 0 Unassigned_NoFeatures 4492137 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 714203 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh120.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh120.summary -rw-r--r-- 1 kkarri waxmanlab 714817 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh121.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh121.summary -rw-r--r-- 1 kkarri waxmanlab 714171 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh122.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh122.summary -rw-r--r-- 1 kkarri waxmanlab 714991 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh123.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh123.summary -rw-r--r-- 1 kkarri waxmanlab 713970 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh124.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh124.summary -rw-r--r-- 1 kkarri waxmanlab 711233 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh125.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh125.summary -rw-r--r-- 1 kkarri waxmanlab 713416 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh126.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh126.summary -rw-r--r-- 1 kkarri waxmanlab 714487 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT0.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT0.summary -rw-r--r-- 1 kkarri waxmanlab 714330 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT1.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT1.summary -rw-r--r-- 1 kkarri waxmanlab 711531 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT2.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT2.summary -rw-r--r-- 1 kkarri waxmanlab 711466 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT3.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT3.summary -rw-r--r-- 1 kkarri waxmanlab 714369 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT4.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT4.summary -rw-r--r-- 1 kkarri waxmanlab 797677 Mar 10 06:36 /scratch/3782068.1.linga/Input/ncRNA_exon_for_counting_lengths.txt /scratch/3782068.1.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/3782068.1.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/3782068.1.linga/Input DiffExp_v2_LncRNA_ExonCollapsed ncRNA_exon_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/3782068.1.linga/Input" [1] "DiffExp_v2_LncRNA_ExonCollapsed" [1] "ncRNA_exon_for_counting_lengths.txt" [1] "sum1:215876.479557005" "sum1:220616.980907883" "sum1:210675.832059615" [4] "sum1:212348.689574659" "sum1:203665.310434865" "sum1:212636.658506805" [1] "sum2:189541.275699116" "sum2:191412.876602137" "sum2:214580.781555264" [4] "sum2:234890.749418747" "sum2:207388.164710087" "sum2:171446.346723681" [7] "sum2:233049.821606524" "sum2:206044.288045079" [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/3782068.1.linga/Input/DiffExp_v2_LncRNA_ExonCollapsed_WT_Ezh12.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_ExonCollapsed_WT_Ezh12.txt Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload 1 LncRNA_ExonCollapsed Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_LncRNA_ExonCollapsed_WT_Ezh12.txt Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload 1 LncRNA_ExonCollapsed ========================================================== 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_ExonCollapsed_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_ExonCollapsed'_'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_ExonCollapsed_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 164 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 203 7 [1] "Check out Up_Genes_DESeq_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt!" Rscript Diff_Genes.R Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_ExonCollapsed'_'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_ExonCollapsed_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 167 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 236 7 [1] "Check out Up_Genes_EdgeR_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt Down_Genes_EdgeR_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt LncRNA_ExonCollapsed_Counting DiffExp_3d [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt" [1] "Subtitle:" [1] "LncRNA_ExonCollapsed_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3d" [1] "-----------------" [1] "Down.DESeq.ExonCollapsed.HTSeq" [1] "Down.EdgeR.ExonCollapsed.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_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt Up_Genes_EdgeR_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt LncRNA_ExonCollapsed_Counting DiffExp_3d [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt" [1] "Subtitle:" [1] "LncRNA_ExonCollapsed_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3d" [1] "-----------------" [1] "Up.DESeq.ExonCollapsed.HTSeq" [1] "Up.EdgeR.ExonCollapsed.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 338 Mar 10 06:37 /scratch/3782068.1.linga/Input/DiffExp_3d_Venn_Tables_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt -rw-r--r-- 1 kkarri waxmanlab 9454777 Mar 10 06:37 /scratch/3782068.1.linga/Input/DiffExp_v2_LncRNA_ExonCollapsed_WT_Ezh12.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Mar 10 06:36 /scratch/3782068.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 24643 Mar 10 06:37 /scratch/3782068.1.linga/Input/Down_Genes_DESeq_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt -rw-r--r-- 1 kkarri waxmanlab 47968 Mar 10 06:37 /scratch/3782068.1.linga/Input/Down_Genes_EdgeR_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt -rw-r--r-- 1 kkarri waxmanlab 714203 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh120.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh120.summary -rw-r--r-- 1 kkarri waxmanlab 714817 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh121.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh121.summary -rw-r--r-- 1 kkarri waxmanlab 714171 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh122.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh122.summary -rw-r--r-- 1 kkarri waxmanlab 714991 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh123.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh123.summary -rw-r--r-- 1 kkarri waxmanlab 713970 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh124.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh124.summary -rw-r--r-- 1 kkarri waxmanlab 711233 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh125.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh125.summary -rw-r--r-- 1 kkarri waxmanlab 713416 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh126.out -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 06:36 /scratch/3782068.1.linga/Input/Ezh126.summary -rw-r--r-- 1 kkarri waxmanlab 1716911 Mar 10 06:37 /scratch/3782068.1.linga/Input/Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1748027 Mar 10 06:37 /scratch/3782068.1.linga/Input/Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 1032779 Mar 10 06:37 /scratch/3782068.1.linga/Input/Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1153790 Mar 10 06:37 /scratch/3782068.1.linga/Input/Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 13462 Mar 10 06:37 /scratch/3782068.1.linga/Input/Up_Genes_DESeq_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt -rw-r--r-- 1 kkarri waxmanlab 13886 Mar 10 06:37 /scratch/3782068.1.linga/Input/Up_Genes_EdgeR_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Mar 10 06:36 /scratch/3782068.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 45126 Mar 10 06:37 /scratch/3782068.1.linga/Input/Venn_Down.DESeq.ExonCollapsed.HTSeq.Down.EdgeR.ExonCollapsed.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 43451 Mar 10 06:37 /scratch/3782068.1.linga/Input/Venn_Up.DESeq.ExonCollapsed.HTSeq.Up.EdgeR.ExonCollapsed.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 714487 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT0.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT0.summary -rw-r--r-- 1 kkarri waxmanlab 714330 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT1.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT1.summary -rw-r--r-- 1 kkarri waxmanlab 711531 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT2.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT2.summary -rw-r--r-- 1 kkarri waxmanlab 711466 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT3.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT3.summary -rw-r--r-- 1 kkarri waxmanlab 714369 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT4.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 06:36 /scratch/3782068.1.linga/Input/WT4.summary -rwxr-xr-x 1 kkarri waxmanlab 4968 Mar 10 06:36 /scratch/3782068.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Mar 10 06:36 /scratch/3782068.1.linga/Input/formatForSegex_ver4.R -rw-r--r-- 1 kkarri waxmanlab 797677 Mar 10 06:36 /scratch/3782068.1.linga/Input/ncRNA_exon_for_counting_lengths.txt /scratch/3782068.1.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/3782068.1.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. 21 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 26M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 10 06:29 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 10 06:29 .. -rw-r--r-- 1 kkarri waxmanlab 338 Mar 10 06:29 DiffExp_3d_Venn_Tables_Ezh12_GSE118757_1212345_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 9.1M Mar 10 06:29 DiffExp_v2_LncRNA_ExonCollapsed_WT_Ezh12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 25K Mar 10 06:29 Down_Genes_DESeq_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 47K Mar 10 06:29 Down_Genes_EdgeR_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.7M Mar 10 06:29 Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.7M Mar 10 06:29 Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1009K Mar 10 06:29 Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.2M Mar 10 06:29 Ezh12_GSE118757_1212345_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 14K Mar 10 06:29 Up_Genes_DESeq_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 14K Mar 10 06:29 Up_Genes_EdgeR_LncRNA_ExonCollapsed_Ezh12_GSE118757_1212345_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 45K Mar 10 06:29 Venn_Down.DESeq.ExonCollapsed.HTSeq.Down.EdgeR.ExonCollapsed.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 43K Mar 10 06:29 Venn_Up.DESeq.ExonCollapsed.HTSeq.Up.EdgeR.ExonCollapsed.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Tue Mar 10 06:37:34 EDT 2020 1 minutes and 1 seconds elapsed. ==========================================================