----------------------- 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_9_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: M2WT 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_9d COL_SUFFIX: LncRNA_ExonCollapsed COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Mar 10 14:06:43 EDT 2020 Running on node : scc-kb8 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_9_lncRNA_featureCounts Current job ID : 3784417 Current job name : Step_08c_DiffExp_9d Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3784417.1.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: M2WTM_1 Sample_ID: M2WTM_1 Description: M2WTM_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: M2WTM_2 Sample_ID: M2WTM_2 Description: M2WTM_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: M2WTF_1 Sample_ID: M2WTF_1 Description: M2WTF_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: M2WTF_2 Sample_ID: M2WTF_2 Description: M2WTF_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 M_Num_Cond2_List: 1212 ------------------------------------------ ========================================================== 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 M2WTF_1_sorted.bam Assigned 12750429 Unassigned_Ambiguity 2568599 Unassigned_MultiMapping 0 Unassigned_NoFeatures 4882301 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 12795935 Unassigned_Ambiguity 2601097 Unassigned_MultiMapping 0 Unassigned_NoFeatures 4243136 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 11264959 Unassigned_Ambiguity 2073434 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3060164 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 11619484 Unassigned_Ambiguity 2106529 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3406460 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 713095 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT0.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT0.summary -rw-r--r-- 1 kkarri waxmanlab 713331 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT1.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT1.summary -rw-r--r-- 1 kkarri waxmanlab 711067 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT2.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT2.summary -rw-r--r-- 1 kkarri waxmanlab 711008 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT3.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT3.summary -rw-r--r-- 1 kkarri waxmanlab 714487 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT0.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT0.summary -rw-r--r-- 1 kkarri waxmanlab 714330 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT1.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT1.summary -rw-r--r-- 1 kkarri waxmanlab 711531 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT2.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT2.summary -rw-r--r-- 1 kkarri waxmanlab 711466 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT3.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT3.summary -rw-r--r-- 1 kkarri waxmanlab 714369 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT4.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT4.summary -rw-r--r-- 1 kkarri waxmanlab 797677 Mar 10 14:06 /scratch/3784417.1.linga/Input/ncRNA_exon_for_counting_lengths.txt /scratch/3784417.1.linga/Input/M2WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:06 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:06 .. /scratch/3784417.1.linga/Input/WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:06 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:06 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WT M2WT 5 4 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/3784417.1.linga/Input DiffExp_v2_LncRNA_ExonCollapsed ncRNA_exon_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WT" [1] "M2WT" [1] 5 [1] 4 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/3784417.1.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] "sum2:195632.684277759" "sum2:200237.878479036" "sum2:209382.181742634" [4] "sum2:204600.449567589" "sum2:202463.298516754" [1] 15558 23 [1] 15558 75 [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/3784417.1.linga/Input/DiffExp_v2_LncRNA_ExonCollapsed_WT_M2WT.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_ExonCollapsed_WT_M2WT.txt M2WT_GSE118757_1212_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_M2WT.txt M2WT_GSE118757_1212_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload 1 LncRNA_ExonCollapsed ========================================================== Comparison_Info: M2WT_GSE118757_1212_WT_GSE118757_12312 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R M2WT_GSE118757_1212_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_ExonCollapsed'_'M2WT_GSE118757_1212_WT_GSE118757_12312 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2WT_GSE118757_1212_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_M2WT_GSE118757_1212_WT_GSE118757_12312" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 310 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 476 7 [1] "Check out Up_Genes_DESeq_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt!" Rscript Diff_Genes.R M2WT_GSE118757_1212_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_ExonCollapsed'_'M2WT_GSE118757_1212_WT_GSE118757_12312 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2WT_GSE118757_1212_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_M2WT_GSE118757_1212_WT_GSE118757_12312" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 346 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 537 7 [1] "Check out Up_Genes_EdgeR_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt Down_Genes_EdgeR_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt LncRNA_ExonCollapsed_Counting DiffExp_9d [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt" [1] "Subtitle:" [1] "LncRNA_ExonCollapsed_Counting" [1] "DiffExp_Index:" [1] "DiffExp_9d" [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_M2WT_GSE118757_1212_WT_GSE118757_12312.txt Up_Genes_EdgeR_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt LncRNA_ExonCollapsed_Counting DiffExp_9d [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt" [1] "Subtitle:" [1] "LncRNA_ExonCollapsed_Counting" [1] "DiffExp_Index:" [1] "DiffExp_9d" [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: M2WT_GSE118757_1212_WT_GSE118757_12312 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 338 Mar 10 14:08 /scratch/3784417.1.linga/Input/DiffExp_9d_Venn_Tables_M2WT_GSE118757_1212_WT_GSE118757_12312.txt -rw-r--r-- 1 kkarri waxmanlab 7877154 Mar 10 14:07 /scratch/3784417.1.linga/Input/DiffExp_v2_LncRNA_ExonCollapsed_WT_M2WT.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Mar 10 14:06 /scratch/3784417.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 42584 Mar 10 14:08 /scratch/3784417.1.linga/Input/Down_Genes_DESeq_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt -rw-r--r-- 1 kkarri waxmanlab 48567 Mar 10 14:08 /scratch/3784417.1.linga/Input/Down_Genes_EdgeR_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt -rw-r--r-- 1 kkarri waxmanlab 713095 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT0.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT0.summary -rw-r--r-- 1 kkarri waxmanlab 713331 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT1.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT1.summary -rw-r--r-- 1 kkarri waxmanlab 711067 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT2.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT2.summary -rw-r--r-- 1 kkarri waxmanlab 711008 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT3.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 10 14:06 /scratch/3784417.1.linga/Input/M2WT3.summary -rw-r--r-- 1 kkarri waxmanlab 1794700 Mar 10 14:07 /scratch/3784417.1.linga/Input/M2WT_GSE118757_1212_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1810258 Mar 10 14:07 /scratch/3784417.1.linga/Input/M2WT_GSE118757_1212_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 1008218 Mar 10 14:08 /scratch/3784417.1.linga/Input/M2WT_GSE118757_1212_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1126103 Mar 10 14:08 /scratch/3784417.1.linga/Input/M2WT_GSE118757_1212_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 48838 Mar 10 14:08 /scratch/3784417.1.linga/Input/Up_Genes_DESeq_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt -rw-r--r-- 1 kkarri waxmanlab 90130 Mar 10 14:08 /scratch/3784417.1.linga/Input/Up_Genes_EdgeR_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Mar 10 14:06 /scratch/3784417.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 43315 Mar 10 14:08 /scratch/3784417.1.linga/Input/Venn_Down.DESeq.ExonCollapsed.HTSeq.Down.EdgeR.ExonCollapsed.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 41275 Mar 10 14:08 /scratch/3784417.1.linga/Input/Venn_Up.DESeq.ExonCollapsed.HTSeq.Up.EdgeR.ExonCollapsed.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 714487 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT0.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT0.summary -rw-r--r-- 1 kkarri waxmanlab 714330 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT1.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT1.summary -rw-r--r-- 1 kkarri waxmanlab 711531 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT2.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT2.summary -rw-r--r-- 1 kkarri waxmanlab 711466 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT3.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT3.summary -rw-r--r-- 1 kkarri waxmanlab 714369 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT4.out -rw-r--r-- 1 kkarri waxmanlab 297 Mar 10 14:06 /scratch/3784417.1.linga/Input/WT4.summary -rwxr-xr-x 1 kkarri waxmanlab 4968 Mar 10 14:06 /scratch/3784417.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Mar 10 14:06 /scratch/3784417.1.linga/Input/formatForSegex_ver4.R -rw-r--r-- 1 kkarri waxmanlab 797677 Mar 10 14:06 /scratch/3784417.1.linga/Input/ncRNA_exon_for_counting_lengths.txt /scratch/3784417.1.linga/Input/M2WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:06 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:08 .. /scratch/3784417.1.linga/Input/WT: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:06 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:08 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Mar 10 14:08 . drwxrwxrwt. 25 root root 4.0K Mar 10 14:08 .. -rw-r--r-- 1 kkarri waxmanlab 123 Mar 10 14:06 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 129 Mar 10 14:06 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 10 14:08 Input -rwxr-xr-x 1 kkarri waxmanlab 15K Mar 10 14:06 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Mar 10 14:06 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 14:00 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 10 13:59 .. -rw-r--r-- 1 kkarri waxmanlab 338 Mar 10 14:00 DiffExp_9d_Venn_Tables_M2WT_GSE118757_1212_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 7.6M Mar 10 14:00 DiffExp_v2_LncRNA_ExonCollapsed_WT_M2WT_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 42K Mar 10 14:00 Down_Genes_DESeq_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 48K Mar 10 14:00 Down_Genes_EdgeR_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.8M Mar 10 14:00 M2WT_GSE118757_1212_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.8M Mar 10 14:00 M2WT_GSE118757_1212_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 985K Mar 10 14:00 M2WT_GSE118757_1212_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.1M Mar 10 14:00 M2WT_GSE118757_1212_vs_WT_GSE118757_12312_DiffExp_v2_LncRNA_ExonCollapsed_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 48K Mar 10 14:00 Up_Genes_DESeq_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 89K Mar 10 14:00 Up_Genes_EdgeR_LncRNA_ExonCollapsed_M2WT_GSE118757_1212_WT_GSE118757_12312_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 43K Mar 10 14:00 Venn_Down.DESeq.ExonCollapsed.HTSeq.Down.EdgeR.ExonCollapsed.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 41K Mar 10 14:00 Venn_Up.DESeq.ExonCollapsed.HTSeq.Up.EdgeR.ExonCollapsed.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Tue Mar 10 14:08:09 EDT 2020 1 minutes and 26 seconds elapsed. ==========================================================