----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/09c_DiffExp_2_lncRNA_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline Dataset_Label: Water_Saline ANNOTATION_FILE_DIR: /restricted/projectnb/waxmanlab/kkarri/GTF_Files1 ANNOTATION_FILE: /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt CONDITION_1_NAME: Control CONDITION_2_NAME: AFLATOXINB1 Lengths_DIR: /restricted/projectnb/waxmanlab/kkarri/GTF_Files1/lengths GENE_LENGTHS_FILE: ncRNA_genebodies_for_counting_lengths.txt COUNT_DIR: LncRNA_GeneBody_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_GeneBody DiffExp_Index: DiffExp_2e COL_SUFFIX: LncRNA_GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Sat Jun 17 13:15:55 EDT 2017 Running on node : scc-ka1 Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/09c_DiffExp_2_lncRNA_featureCounts Current job ID : 9395556 Current job name : Step_09c_DiffExp_2e Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9395556.1.linga Loading required modules... ------------------------------------------ Sample_DIR: C_M1 Sample_ID: C_M1 Description: C_M1 M_Num: M1 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: M1 ------------------------------------------ ------------------------------------------ Sample_DIR: MM_M1 Sample_ID: MM_M1 Description: MM_M1 M_Num: M1 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: MM_M2 Sample_ID: MM_M2 Description: MM_M2 M_Num: M2 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: MM_M3 Sample_ID: MM_M3 Description: MM_M3 M_Num: M3 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: M1M2M3 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 0 NUM_REP_CONDITION1: 0 ========================================================== Renaming input count files number of mapped reads (feature count summary) ========================================================== List files in Input /scratch/9395556.1.linga/Input/AFLATOXINB1: total 8 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 17 13:15 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 17 13:15 .. /scratch/9395556.1.linga/Input/Control: total 8 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 17 13:15 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 17 13:15 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Control AFLATOXINB1 0 0 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/9395556.1.linga/Input DiffExp_v2_LncRNA_GeneBody ncRNA_genebodies_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Control" [1] "AFLATOXINB1" [1] 0 [1] 0 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/9395556.1.linga/Input" [1] "DiffExp_v2_LncRNA_GeneBody" [1] "ncRNA_genebodies_for_counting_lengths.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_GeneBody_Control_AFLATOXINB1.txt AFLATOXINB1_Water_Saline_M1M2M3_vs_Control_Water_Saline_M1_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload 1 LncRNA_GeneBody ========================================================== Comparison_Info: AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R AFLATOXINB1_Water_Saline_M1M2M3_vs_Control_Water_Saline_M1_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_GeneBody'_'AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "AFLATOXINB1_Water_Saline_M1M2M3_vs_Control_Water_Saline_M1_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "LncRNA_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1" [1] "-----------------" [1] "DESeq or EdgeR job most likely failed." [1] "Quitting R now." Rscript Diff_Genes.R AFLATOXINB1_Water_Saline_M1M2M3_vs_Control_Water_Saline_M1_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_GeneBody'_'AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "AFLATOXINB1_Water_Saline_M1M2M3_vs_Control_Water_Saline_M1_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "LncRNA_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1" [1] "-----------------" [1] "DESeq or EdgeR job most likely failed." [1] "Quitting R now." #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt Down_Genes_EdgeR_LncRNA_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt LncRNA_GeneBody_Counting DiffExp_2e [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2e" [1] "-----------------" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_LncRNA_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt Up_Genes_EdgeR_LncRNA_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt LncRNA_GeneBody_Counting DiffExp_2e [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2e" [1] "-----------------" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- Comparison_Info: AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri montilab-p 0 Jun 17 13:16 /scratch/9395556.1.linga/Input/DiffExp_2e_Venn_Tables_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt -rwxr-xr-x 1 kkarri montilab-p 7706 Jun 17 13:15 /scratch/9395556.1.linga/Input/Diff_Genes.R -rwxr-xr-x 1 kkarri montilab-p 9993 Jun 17 13:15 /scratch/9395556.1.linga/Input/Venn_Diff_Genes.R -rwxr-xr-x 1 kkarri montilab-p 4968 Jun 17 13:15 /scratch/9395556.1.linga/Input/formatForSegex_ver3.R /scratch/9395556.1.linga/Input/AFLATOXINB1: total 8 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 17 13:15 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 17 13:16 .. /scratch/9395556.1.linga/Input/Control: total 8 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 17 13:15 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 17 13:16 .. ========================================================== List files in scratch total 3.5M drwxr-xr-x 3 kkarri montilab-p 4.0K Jun 17 13:16 . drwxrwxrwt. 202 root root 124K Jun 17 13:15 .. -rw-r--r-- 1 kkarri montilab-p 48 Jun 17 13:15 Condition_1.txt -rw-r--r-- 1 kkarri montilab-p 87 Jun 17 13:15 Condition_2.txt drwxr-xr-x 4 kkarri montilab-p 4.0K Jun 17 13:16 Input -rwxr-xr-x 1 kkarri montilab-p 13K Jun 17 13:15 differentialAnalysis.R -rw-r--r-- 1 kkarri montilab-p 3.3M Jun 17 13:15 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 32K drwxr-sr-x 2 kkarri waxmanlab 512 Jun 17 13:16 . drwxr-sr-x 8 kkarri waxmanlab 32K Jun 17 13:15 .. -rw-r--r-- 1 kkarri waxmanlab 0 Jun 17 13:16 DiffExp_2e_Venn_Tables_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1_featureCounts.txt ========================================================== ========================================================== Finished on : Sat Jun 17 13:16:14 EDT 2017 0 minutes and 19 seconds elapsed. ==========================================================