----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/test_samples/Scripts/09b_DiffExp_1_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/test_samples Dataset_Label: SRR GTF_Files_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: BCell CONDITION_2_NAME: NKcell Lengths_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/GTF_Files/lengths GENE_LENGTHS_FILE: Exon_Regions_Lengths.txt COUNT_DIR: RefSeq_Exon_GTF OUTPUT_PREFIX: DiffExp_v2_GeneBody DiffExp_Index: DiffExp_1a COL_SUFFIX: GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri Oct 19 15:30:26 EDT 2018 Running on node : scc-tl3 Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/test_samples/Scripts/09b_DiffExp_1_featureCounts Current job ID : 9032350 Current job name : Step_09b_DiffExp_1a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9032350.1.linga Loading required modules... ------------------------------------------ Sample_DIR: P3 Sample_ID: P3 Description: Bcell M_Num: P3 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: P3 Sample_DIR: P4 Sample_ID: P4 Description: Bcell M_Num: P4 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: P4 M_Num_Cond1_List: P4 ------------------------------------------ ------------------------------------------ Sample_DIR: P5 Sample_ID: P5 Description: NkCell M_Num: P5 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: P5 Sample_DIR: P6 Sample_ID: P6 Description: Nkcell M_Num: P6 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: P6 Sample_DIR: P7 Sample_ID: P7 Description: NkCell M_Num: P7 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: P7 M_Num_Cond2_List: P7 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 2 NUM_REP_CONDITION1: 2 ========================================================== Renaming input count files Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. number of mapped reads 582363 193601 179839 370759 148568 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 227904 Oct 19 15:30 /scratch/9032350.1.linga/Input/BCell0.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 15:30 /scratch/9032350.1.linga/Input/BCell0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 227047 Oct 19 15:30 /scratch/9032350.1.linga/Input/BCell1.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 15:30 /scratch/9032350.1.linga/Input/BCell1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 292936 Oct 19 15:30 /scratch/9032350.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 226592 Oct 19 15:30 /scratch/9032350.1.linga/Input/NKcell0.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 15:30 /scratch/9032350.1.linga/Input/NKcell0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 227345 Oct 19 15:30 /scratch/9032350.1.linga/Input/NKcell1.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 15:30 /scratch/9032350.1.linga/Input/NKcell1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 226630 Oct 19 15:30 /scratch/9032350.1.linga/Input/NKcell2.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 15:30 /scratch/9032350.1.linga/Input/NKcell2_num_mapped_reads.txt /scratch/9032350.1.linga/Input/BCell: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Oct 19 15:30 . drwxr-xr-x 4 kkarri waxmanlab 4096 Oct 19 15:30 .. /scratch/9032350.1.linga/Input/NKcell: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Oct 19 15:30 . drwxr-xr-x 4 kkarri waxmanlab 4096 Oct 19 15:30 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R BCell NKcell 2 3 RefSeq_GeneBody.gtf /scratch/9032350.1.linga/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "BCell" [1] "NKcell" [1] 2 [1] 3 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/9032350.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" load GTF file ... parse attributes ... [1] "output file is in: /scratch/9032350.1.linga/Input/DiffExp_v2_GeneBody_BCell_NKcell.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_BCell_NKcell.txt NKcell_SRR_P7_vs_BCell_SRR_P4_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== Comparison_Info: NKcell_SRR_P7_BCell_SRR_P4 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R NKcell_SRR_P7_vs_BCell_SRR_P4_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'NKcell_SRR_P7_BCell_SRR_P4 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "NKcell_SRR_P7_vs_BCell_SRR_P4_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "GeneBody_NKcell_SRR_P7_BCell_SRR_P4" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 0 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 0 7 [1] "Check out Up_Genes_DESeq_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt!" [1] "Check out Down_Genes_DESeq_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt!" Rscript Diff_Genes.R NKcell_SRR_P7_vs_BCell_SRR_P4_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'NKcell_SRR_P7_BCell_SRR_P4 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "NKcell_SRR_P7_vs_BCell_SRR_P4_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "GeneBody_NKcell_SRR_P7_BCell_SRR_P4" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 0 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 0 7 [1] "Check out Up_Genes_EdgeR_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt!" [1] "Check out Down_Genes_EdgeR_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt Down_Genes_EdgeR_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt GeneBody_Counting DiffExp_1a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1a" [1] "-----------------" [1] "Down.DESeq.GeneBody.HTSeq" [1] "Down.EdgeR.GeneBody.HTSeq" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt Up_Genes_EdgeR_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt GeneBody_Counting DiffExp_1a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1a" [1] "-----------------" [1] "Up.DESeq.GeneBody.HTSeq" [1] "Up.EdgeR.GeneBody.HTSeq" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- Comparison_Info: NKcell_SRR_P7_BCell_SRR_P4 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 227904 Oct 19 15:30 /scratch/9032350.1.linga/Input/BCell0.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 15:30 /scratch/9032350.1.linga/Input/BCell0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 227047 Oct 19 15:30 /scratch/9032350.1.linga/Input/BCell1.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 15:30 /scratch/9032350.1.linga/Input/BCell1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 0 Oct 19 15:31 /scratch/9032350.1.linga/Input/DiffExp_1a_Venn_Tables_NKcell_SRR_P7_BCell_SRR_P4.txt -rw-r--r-- 1 kkarri waxmanlab 2852753 Oct 19 15:31 /scratch/9032350.1.linga/Input/DiffExp_v2_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Oct 19 15:30 /scratch/9032350.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 136 Oct 19 15:31 /scratch/9032350.1.linga/Input/Down_Genes_DESeq_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt -rw-r--r-- 1 kkarri waxmanlab 136 Oct 19 15:31 /scratch/9032350.1.linga/Input/Down_Genes_EdgeR_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt -rw-r--r-- 1 kkarri waxmanlab 292936 Oct 19 15:30 /scratch/9032350.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 226592 Oct 19 15:30 /scratch/9032350.1.linga/Input/NKcell0.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 15:30 /scratch/9032350.1.linga/Input/NKcell0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 227345 Oct 19 15:30 /scratch/9032350.1.linga/Input/NKcell1.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 15:30 /scratch/9032350.1.linga/Input/NKcell1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 226630 Oct 19 15:30 /scratch/9032350.1.linga/Input/NKcell2.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 15:30 /scratch/9032350.1.linga/Input/NKcell2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2217713 Oct 19 15:31 /scratch/9032350.1.linga/Input/NKcell_SRR_P7_vs_BCell_SRR_P4_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2047690 Oct 19 15:31 /scratch/9032350.1.linga/Input/NKcell_SRR_P7_vs_BCell_SRR_P4_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 136 Oct 19 15:31 /scratch/9032350.1.linga/Input/Up_Genes_DESeq_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt -rw-r--r-- 1 kkarri waxmanlab 136 Oct 19 15:31 /scratch/9032350.1.linga/Input/Up_Genes_EdgeR_GeneBody_NKcell_SRR_P7_BCell_SRR_P4.txt -rw-r--r-- 1 kkarri waxmanlab 4408 Oct 19 15:31 /scratch/9032350.1.linga/Input/VennDiagram2018-10-19_15-31-57.log -rwxr-xr-x 1 kkarri waxmanlab 9553 Oct 19 15:30 /scratch/9032350.1.linga/Input/Venn_Diff_Genes.R -rwxr-xr-x 1 kkarri waxmanlab 3925 Oct 19 15:30 /scratch/9032350.1.linga/Input/formatForSegex_ver3.R /scratch/9032350.1.linga/Input/BCell: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Oct 19 15:30 . drwxr-xr-x 4 kkarri waxmanlab 4096 Oct 19 15:31 .. /scratch/9032350.1.linga/Input/NKcell: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Oct 19 15:30 . drwxr-xr-x 4 kkarri waxmanlab 4096 Oct 19 15:31 .. ========================================================== List files in scratch total 73M drwx------ 3 kkarri waxmanlab 4.0K Oct 19 15:31 . drwxrwxrwt. 28 root root 132K Oct 19 15:30 .. -rw-r--r-- 1 kkarri waxmanlab 57 Oct 19 15:30 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 72 Oct 19 15:30 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Oct 19 15:31 Input -rw-r--r-- 1 kkarri waxmanlab 72M Oct 19 15:30 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 16K Oct 19 15:30 differentialAnalysis.R ========================================================== Re-naming files in OUTPUT_DIR Need to append the COUNT_PROGRAM name to all output files List files in OUTPUT_DIR total 5.1M drwxr-sr-x 2 kkarri waxmanlab 32K Oct 19 15:31 . drwxr-sr-x 6 kkarri waxmanlab 32K Oct 19 15:30 .. -rw-r--r-- 1 kkarri waxmanlab 0 Oct 19 15:31 DiffExp_1a_Venn_Tables_NKcell_SRR_P7_BCell_SRR_P4_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.8M Oct 19 15:31 DiffExp_v2_GeneBody_NKcell_SRR_P7_BCell_SRR_P4_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 136 Oct 19 15:31 Down_Genes_DESeq_GeneBody_NKcell_SRR_P7_BCell_SRR_P4_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 136 Oct 19 15:31 Down_Genes_EdgeR_GeneBody_NKcell_SRR_P7_BCell_SRR_P4_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.2M Oct 19 15:31 NKcell_SRR_P7_vs_BCell_SRR_P4_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.0M Oct 19 15:31 NKcell_SRR_P7_vs_BCell_SRR_P4_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 136 Oct 19 15:31 Up_Genes_DESeq_GeneBody_NKcell_SRR_P7_BCell_SRR_P4_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 136 Oct 19 15:31 Up_Genes_EdgeR_GeneBody_NKcell_SRR_P7_BCell_SRR_P4_featureCounts.txt ========================================================== ========================================================== Finished on : Fri Oct 19 15:31:58 EDT 2018 1 minutes and 32 seconds elapsed. ==========================================================