----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/09b_DiffExp_2_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New Dataset_Label: G123 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: Male_27h_Vehicle CONDITION_2_NAME: Male_27h_TCPOBOP Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: Exon_Regions_Lengths.txt COUNT_DIR: RefSeq_Exon_GTF OUTPUT_PREFIX: DiffExp_v2_GeneBody DiffExp_Index: DiffExp_2a COL_SUFFIX: GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Sat Dec 8 00:59:00 EST 2018 Running on node : scc-ka6 Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/09b_DiffExp_2_featureCounts Current job ID : 29142 Current job name : Step_09b_DiffExp_2a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/29142.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G123_M5 Sample_ID: G123_M5 Description: Male_27h_Vehicle_1 M_Num: M5 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G123_M5 Sample_DIR: G123_M6 Sample_ID: G123_M6 Description: Male_27h_Vehicle_2 M_Num: M6 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G123_M6 M_Num_Cond1_List: M5M6 ------------------------------------------ ------------------------------------------ Sample_DIR: G123_M7 Sample_ID: G123_M7 Description: Male_27h_TCPOBOP_1 M_Num: M7 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G123_M7 Sample_DIR: G123_M8 Sample_ID: G123_M8 Description: Male_27h_TCPOBOP_2 M_Num: M8 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G123_M8 M_Num_Cond2_List: M7M8 ------------------------------------------ ========================================================== 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. number of mapped reads 34313514 32110871 29383190 40788463 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291522 Dec 8 00:59 /scratch/29142.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 250594 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_TCPOBOP0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 250180 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_TCPOBOP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249575 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_Vehicle0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 251933 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_Vehicle1_num_mapped_reads.txt /scratch/29142.1.linga/Input/Male_27h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 00:59 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 00:59 .. /scratch/29142.1.linga/Input/Male_27h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 00:59 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 00:59 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Male_27h_Vehicle Male_27h_TCPOBOP 2 2 RefSeq_GeneBody.gtf /scratch/29142.1.linga/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Male_27h_Vehicle" [1] "Male_27h_TCPOBOP" [1] 2 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/29142.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" load GTF file ... parse attributes ... [1] "output file is in: /scratch/29142.1.linga/Input/DiffExp_v2_GeneBody_Male_27h_Vehicle_Male_27h_TCPOBOP.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_Male_27h_Vehicle_Male_27h_TCPOBOP.txt Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== Comparison_Info: Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_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_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 251 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 67 7 [1] "Check out Up_Genes_DESeq_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt!" [1] "Check out Down_Genes_DESeq_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt!" Rscript Diff_Genes.R Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_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_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 478 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 170 7 [1] "Check out Up_Genes_EdgeR_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt!" [1] "Check out Down_Genes_EdgeR_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt Down_Genes_EdgeR_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt GeneBody_Counting DiffExp_2a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2a" [1] "-----------------" [1] "Down.DESeq.GeneBody.HTSeq" [1] "Down.EdgeR.GeneBody.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_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt Up_Genes_EdgeR_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt GeneBody_Counting DiffExp_2a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2a" [1] "-----------------" [1] "Up.DESeq.GeneBody.HTSeq" [1] "Up.EdgeR.GeneBody.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: Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 295 Dec 8 01:01 /scratch/29142.1.linga/Input/DiffExp_2a_Venn_Tables_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 7043022 Dec 8 01:01 /scratch/29142.1.linga/Input/DiffExp_v2_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Dec 8 00:59 /scratch/29142.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 9457 Dec 8 01:01 /scratch/29142.1.linga/Input/Down_Genes_DESeq_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 22247 Dec 8 01:01 /scratch/29142.1.linga/Input/Down_Genes_EdgeR_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 291522 Dec 8 00:59 /scratch/29142.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 250594 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_TCPOBOP0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 250180 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_TCPOBOP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2329979 Dec 8 01:01 /scratch/29142.1.linga/Input/Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2354176 Dec 8 01:01 /scratch/29142.1.linga/Input/Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 249575 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_Vehicle0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 251933 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 00:59 /scratch/29142.1.linga/Input/Male_27h_Vehicle1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 17953 Dec 8 01:01 /scratch/29142.1.linga/Input/Up_Genes_DESeq_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 34514 Dec 8 01:01 /scratch/29142.1.linga/Input/Up_Genes_EdgeR_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Dec 8 00:59 /scratch/29142.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 39029 Dec 8 01:01 /scratch/29142.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 39056 Dec 8 01:01 /scratch/29142.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 Dec 8 00:59 /scratch/29142.1.linga/Input/formatForSegex_ver3.R /scratch/29142.1.linga/Input/Male_27h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 00:59 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 01:01 .. /scratch/29142.1.linga/Input/Male_27h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 00:59 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 01:01 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Dec 8 01:01 . drwxrwxrwt. 36 root root 92K Dec 8 00:58 .. -rw-r--r-- 1 kkarri waxmanlab 103 Dec 8 00:59 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 103 Dec 8 00:59 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Dec 8 01:01 Input -rw-r--r-- 1 kkarri waxmanlab 72M Dec 8 00:59 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 16K Dec 8 00:59 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 11M drwxr-sr-x 2 kkarri waxmanlab 32K Dec 8 01:01 . drwxr-sr-x 6 kkarri waxmanlab 32K Dec 8 00:59 .. -rw-r--r-- 1 kkarri waxmanlab 295 Dec 8 01:01 DiffExp_2a_Venn_Tables_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 6.8M Dec 8 01:01 DiffExp_v2_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 9.3K Dec 8 01:01 Down_Genes_DESeq_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 22K Dec 8 01:01 Down_Genes_EdgeR_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Dec 8 01:01 Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Dec 8 01:01 Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 18K Dec 8 01:01 Up_Genes_DESeq_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 34K Dec 8 01:01 Up_Genes_EdgeR_GeneBody_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 39K Dec 8 01:01 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 39K Dec 8 01:01 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Sat Dec 8 01:01:29 EST 2018 2 minutes and 29 seconds elapsed. ==========================================================