----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/09b_DiffExp_4_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: Female_27h_Vehicle CONDITION_2_NAME: Female_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_4a COL_SUFFIX: GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Sat Dec 8 01:07:57 EST 2018 Running on node : scc-ka6 Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/09b_DiffExp_4_featureCounts Current job ID : 29149 Current job name : Step_09b_DiffExp_4a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/29149.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G123_M13 Sample_ID: G123_M13 Description: Female_27h_Vehicle_1 M_Num: M13 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G123_M13 Sample_DIR: G123_M14 Sample_ID: G123_M14 Description: Female_27h_Vehicle_2 M_Num: M14 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G123_M14 M_Num_Cond1_List: M13M14 ------------------------------------------ ------------------------------------------ Sample_DIR: G123_M15 Sample_ID: G123_M15 Description: Female_27h_TCPOBOP_1 M_Num: M15 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G123_M15 Sample_DIR: G123_M16 Sample_ID: G123_M16 Description: Female_27h_TCPOBOP_2 M_Num: M16 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G123_M16 M_Num_Cond2_List: M15M16 ------------------------------------------ ========================================================== 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 29753135 41817847 35844361 26909698 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291522 Dec 8 01:07 /scratch/29149.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 249787 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_TCPOBOP0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 251944 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_TCPOBOP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 251029 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_Vehicle0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249376 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_Vehicle1_num_mapped_reads.txt /scratch/29149.1.linga/Input/Female_27h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 01:07 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 01:07 .. /scratch/29149.1.linga/Input/Female_27h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 01:07 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 01:07 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Female_27h_Vehicle Female_27h_TCPOBOP 2 2 RefSeq_GeneBody.gtf /scratch/29149.1.linga/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Female_27h_Vehicle" [1] "Female_27h_TCPOBOP" [1] 2 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/29149.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" load GTF file ... parse attributes ... [1] "output file is in: /scratch/29149.1.linga/Input/DiffExp_v2_GeneBody_Female_27h_Vehicle_Female_27h_TCPOBOP.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_Female_27h_Vehicle_Female_27h_TCPOBOP.txt Female_27h_TCPOBOP_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== Comparison_Info: Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Female_27h_TCPOBOP_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Female_27h_TCPOBOP_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_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_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 243 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 167 7 [1] "Check out Up_Genes_DESeq_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt!" [1] "Check out Down_Genes_DESeq_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt!" Rscript Diff_Genes.R Female_27h_TCPOBOP_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Female_27h_TCPOBOP_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_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_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 459 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 303 7 [1] "Check out Up_Genes_EdgeR_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt!" [1] "Check out Down_Genes_EdgeR_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt Down_Genes_EdgeR_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt GeneBody_Counting DiffExp_4a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_4a" [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_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt Up_Genes_EdgeR_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt GeneBody_Counting DiffExp_4a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_4a" [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: Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 296 Dec 8 01:10 /scratch/29149.1.linga/Input/DiffExp_4a_Venn_Tables_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt -rw-r--r-- 1 kkarri waxmanlab 6996216 Dec 8 01:10 /scratch/29149.1.linga/Input/DiffExp_v2_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Dec 8 01:07 /scratch/29149.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 20325 Dec 8 01:10 /scratch/29149.1.linga/Input/Down_Genes_DESeq_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt -rw-r--r-- 1 kkarri waxmanlab 38000 Dec 8 01:10 /scratch/29149.1.linga/Input/Down_Genes_EdgeR_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt -rw-r--r-- 1 kkarri waxmanlab 291522 Dec 8 01:07 /scratch/29149.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 249787 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_TCPOBOP0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 251944 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_TCPOBOP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2354180 Dec 8 01:10 /scratch/29149.1.linga/Input/Female_27h_TCPOBOP_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2378377 Dec 8 01:10 /scratch/29149.1.linga/Input/Female_27h_TCPOBOP_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 251029 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_Vehicle0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249376 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 9 Dec 8 01:07 /scratch/29149.1.linga/Input/Female_27h_Vehicle1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 17396 Dec 8 01:10 /scratch/29149.1.linga/Input/Up_Genes_DESeq_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt -rw-r--r-- 1 kkarri waxmanlab 34106 Dec 8 01:10 /scratch/29149.1.linga/Input/Up_Genes_EdgeR_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Dec 8 01:07 /scratch/29149.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 40915 Dec 8 01:10 /scratch/29149.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 39275 Dec 8 01:10 /scratch/29149.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 Dec 8 01:07 /scratch/29149.1.linga/Input/formatForSegex_ver3.R /scratch/29149.1.linga/Input/Female_27h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 01:07 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 01:10 .. /scratch/29149.1.linga/Input/Female_27h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 01:07 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 01:10 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Dec 8 01:10 . drwxrwxrwt. 36 root root 92K Dec 8 01:07 .. -rw-r--r-- 1 kkarri waxmanlab 111 Dec 8 01:07 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 111 Dec 8 01:07 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Dec 8 01:10 Input -rw-r--r-- 1 kkarri waxmanlab 72M Dec 8 01:07 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 16K Dec 8 01:07 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 01:10 . drwxr-sr-x 6 kkarri waxmanlab 32K Dec 8 01:07 .. -rw-r--r-- 1 kkarri waxmanlab 296 Dec 8 01:10 DiffExp_4a_Venn_Tables_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 6.7M Dec 8 01:10 DiffExp_v2_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 20K Dec 8 01:10 Down_Genes_DESeq_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 38K Dec 8 01:10 Down_Genes_EdgeR_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Dec 8 01:10 Female_27h_TCPOBOP_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Dec 8 01:10 Female_27h_TCPOBOP_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 17K Dec 8 01:10 Up_Genes_DESeq_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 34K Dec 8 01:10 Up_Genes_EdgeR_GeneBody_Female_27h_TCPOBOP_G123_M15M16_Female_27h_Vehicle_G123_M13M14_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 40K Dec 8 01:10 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 39K Dec 8 01:10 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Sat Dec 8 01:10:23 EST 2018 2 minutes and 26 seconds elapsed. ==========================================================