----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/09b_DiffExp_2_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline Dataset_Label: Water_Saline GTF_Files_DIR: /restricted/projectnb/waxmanlab/kkarri/GTF_Files1 ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: Control CONDITION_2_NAME: AFLATOXINB1 Lengths_DIR: /restricted/projectnb/waxmanlab/kkarri/GTF_Files1/lengths GENE_LENGTHS_FILE: Intron_Only_Regions_Lengths.txt COUNT_DIR: RefSeq_Intron_GTF OUTPUT_PREFIX: DiffExp_v2_Intronic_Only DiffExp_Index: DiffExp_2c COL_SUFFIX: Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri Jun 23 15:56:39 EDT 2017 Running on node : scc-ka8 Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/09b_DiffExp_2_featureCounts Current job ID : 9535015 Current job name : Step_09b_DiffExp_2c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9535015.1.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 calculate mapped reads: C_M1 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 calculate mapped reads: MM_M1 Sample_DIR: MM_M2 Sample_ID: MM_M2 Description: MM_M2 M_Num: M2 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: MM_M2 Sample_DIR: MM_M3 Sample_ID: MM_M3 Description: MM_M3 M_Num: M3 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: MM_M3 M_Num_Cond2_List: M1M2M3 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 0 NUM_REP_CONDITION1: 0 ========================================================== Renaming input count files Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. number of mapped reads ========================================================== List files in Input /scratch/9535015.1.linga/Input/AFLATOXINB1: total 20 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 23 15:56 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 23 15:56 .. -rw-r--r-- 1 kkarri montilab-p 9 Jun 23 15:56 MM_M1_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 23 15:56 MM_M2_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 23 15:56 MM_M3_num_mapped_reads.txt /scratch/9535015.1.linga/Input/Control: total 12 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 23 15:56 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 23 15:56 .. -rw-r--r-- 1 kkarri montilab-p 10 Jun 23 15:56 C_M1_num_mapped_reads.txt ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Control AFLATOXINB1 0 0 RefSeq_GeneBody.gtf /scratch/9535015.1.linga/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Control" [1] "AFLATOXINB1" [1] 0 [1] 0 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/9535015.1.linga/Input" [1] "DiffExp_v2_Intronic_Only" [1] "Intron_Only_Regions_Lengths.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_Control_AFLATOXINB1.txt AFLATOXINB1_Water_Saline_M1M2M3_vs_Control_Water_Saline_M1_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== 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_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'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_Intronic_Only_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "Intronic_Only_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_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'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_Intronic_Only_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "Intronic_Only_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_Intronic_Only_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt Down_Genes_EdgeR_Intronic_Only_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt Intronic_Only_Counting DiffExp_2c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2c" [1] "-----------------" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_Intronic_Only_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt Up_Genes_EdgeR_Intronic_Only_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt Intronic_Only_Counting DiffExp_2c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2c" [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 23 15:57 /scratch/9535015.1.linga/Input/DiffExp_2c_Venn_Tables_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt -rwxr-xr-x 1 kkarri montilab-p 7394 Jun 23 15:56 /scratch/9535015.1.linga/Input/Diff_Genes.R -rwxr-xr-x 1 kkarri montilab-p 9553 Jun 23 15:56 /scratch/9535015.1.linga/Input/Venn_Diff_Genes.R -rwxr-xr-x 1 kkarri montilab-p 3925 Jun 23 15:56 /scratch/9535015.1.linga/Input/formatForSegex_ver3.R /scratch/9535015.1.linga/Input/AFLATOXINB1: total 20 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 23 15:56 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 23 15:57 .. -rw-r--r-- 1 kkarri montilab-p 9 Jun 23 15:56 MM_M1_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 23 15:56 MM_M2_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 23 15:56 MM_M3_num_mapped_reads.txt /scratch/9535015.1.linga/Input/Control: total 12 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 23 15:56 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 23 15:57 .. -rw-r--r-- 1 kkarri montilab-p 10 Jun 23 15:56 C_M1_num_mapped_reads.txt ========================================================== List files in scratch total 41M drwxr-xr-x 3 kkarri montilab-p 4.0K Jun 23 15:57 . drwxrwxrwt. 168 root root 72K Jun 23 15:56 .. -rw-r--r-- 1 kkarri montilab-p 48 Jun 23 15:56 Condition_1.txt -rw-r--r-- 1 kkarri montilab-p 87 Jun 23 15:56 Condition_2.txt drwxr-xr-x 4 kkarri montilab-p 4.0K Jun 23 15:57 Input -rwx------ 1 kkarri montilab-p 41M Jun 23 15:56 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri montilab-p 16K Jun 23 15:56 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 32K drwxr-sr-x 2 kkarri waxmanlab 512 Jun 23 15:57 . drwxr-sr-x 6 kkarri waxmanlab 32K Jun 23 15:56 .. -rw-r--r-- 1 kkarri waxmanlab 0 Jun 23 15:57 DiffExp_2c_Venn_Tables_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1_featureCounts.txt ========================================================== ========================================================== Finished on : Fri Jun 23 15:57:14 EDT 2017 0 minutes and 35 seconds elapsed. ==========================================================