----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/09a_DiffExp_2_HTSeq Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline Dataset_Label: IP_Saline GTF_Files_DIR: /restricted/projectnb/waxmanlab/kkarri/GTF_Files1 ANNOTATION_FILE: Exon_Only_Regions.gtf CONDITION_1_NAME: Control CONDITION_2_NAME: N-NITROSODIMETHYLAMINE Lengths_DIR: /restricted/projectnb/waxmanlab/kkarri/GTF_Files1/lengths GENE_LENGTHS_FILE: Exon_Only_Regions_Lengths.txt COUNT_DIR: RefSeq_Exon_Only_GTF OUTPUT_PREFIX: DiffExp_v2_Exonic_Only DiffExp_Index: DiffExp_2b COL_SUFFIX: Exonic_Only COUNT_PROGRAM: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Thu Jun 22 17:01:04 EDT 2017 Running on node : scc-ka6 Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/09a_DiffExp_2_HTSeq Current job ID : 9501415 Current job name : Step_09a_DiffExp_2b Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9501415.1.linga Loading required modules... ------------------------------------------ Sample_DIR: C_IP1 Sample_ID: C_IP1 Description: C_IP1 M_Num: IP1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: C_IP1 Sample_DIR: C_IP2 Sample_ID: C_IP2 Description: C_IP2 M_Num: IP2 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: C_IP2 Sample_DIR: C_IP3 Sample_ID: C_IP3 Description: C_IP3 M_Num: IP3 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: C_IP3 Sample_DIR: C_IP4 Sample_ID: C_IP4 Description: C_IP4 M_Num: IP4 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: C_IP4 Sample_DIR: C_IP5 Sample_ID: C_IP5 Description: C_IP5 M_Num: IP5 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: C_IP5 Sample_DIR: C_IP6 Sample_ID: C_IP6 Description: C_IP6 M_Num: IP6 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: C_IP6 M_Num_Cond1_List: IP1IP2IP3IP4IP5IP6 ------------------------------------------ ------------------------------------------ Sample_DIR: NSM_IP1 Sample_ID: NSM_IP1 Description: NSM_IP1 M_Num: IP1 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: NSM_IP1 Sample_DIR: NSM_IP2 Sample_ID: NSM_IP2 Description: NSM_IP2 M_Num: IP2 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: NSM_IP2 Sample_DIR: NSM_IP3 Sample_ID: NSM_IP3 Description: NSM_IP3 M_Num: IP3 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: NSM_IP3 M_Num_Cond2_List: IP1IP2IP3 ------------------------------------------ ========================================================== 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/9501415.1.linga/Input/Control: total 32 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 22 17:01 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 22 17:01 .. -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 C_IP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 C_IP2_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 C_IP3_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 C_IP4_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 C_IP5_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 C_IP6_num_mapped_reads.txt /scratch/9501415.1.linga/Input/N-NITROSODIMETHYLAMINE: total 20 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 22 17:01 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 22 17:01 .. -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 NSM_IP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 NSM_IP2_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 NSM_IP3_num_mapped_reads.txt ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Control N-NITROSODIMETHYLAMINE 0 0 Exon_Only_Regions.gtf /scratch/9501415.1.linga/Input DiffExp_v2_Exonic_Only Exon_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Control" [1] "N-NITROSODIMETHYLAMINE" [1] 0 [1] 0 [1] "Exon_Only_Regions.gtf" [1] "/scratch/9501415.1.linga/Input" [1] "DiffExp_v2_Exonic_Only" [1] "Exon_Only_Regions_Lengths.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Exonic_Only_Control_N-NITROSODIMETHYLAMINE.txt N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_vs_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_DiffExp_v2_Exonic_Only_forSEGEXUpload 1 Exonic_Only ========================================================== Comparison_Info: N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_vs_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Exonic_Only'_'N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_vs_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "Exonic_Only_N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6" [1] "-----------------" [1] "DESeq or EdgeR job most likely failed." [1] "Quitting R now." Rscript Diff_Genes.R N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_vs_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Exonic_Only'_'N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_vs_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "Exonic_Only_N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6" [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_Exonic_Only_N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt Down_Genes_EdgeR_Exonic_Only_N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt Exonic_Only_Counting DiffExp_2b [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Exonic_Only_N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Exonic_Only_N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt" [1] "Subtitle:" [1] "Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2b" [1] "-----------------" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_Exonic_Only_N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt Up_Genes_EdgeR_Exonic_Only_N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt Exonic_Only_Counting DiffExp_2b [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Exonic_Only_N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Exonic_Only_N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt" [1] "Subtitle:" [1] "Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2b" [1] "-----------------" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri montilab-p 0 Jun 22 17:01 /scratch/9501415.1.linga/Input/DiffExp_2b_Venn_Tables_N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6.txt -rwxr-xr-x 1 kkarri montilab-p 7394 Jun 22 17:01 /scratch/9501415.1.linga/Input/Diff_Genes.R -rwxr-xr-x 1 kkarri montilab-p 9553 Jun 22 17:01 /scratch/9501415.1.linga/Input/Venn_Diff_Genes.R -rwxr-xr-x 1 kkarri montilab-p 3925 Jun 22 17:01 /scratch/9501415.1.linga/Input/formatForSegex_ver3.R /scratch/9501415.1.linga/Input/Control: total 32 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 22 17:01 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 22 17:01 .. -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 C_IP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 C_IP2_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 C_IP3_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 C_IP4_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 C_IP5_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 C_IP6_num_mapped_reads.txt /scratch/9501415.1.linga/Input/N-NITROSODIMETHYLAMINE: total 20 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 22 17:01 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 22 17:01 .. -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 NSM_IP1_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 NSM_IP2_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 9 Jun 22 17:01 NSM_IP3_num_mapped_reads.txt ========================================================== List files in scratch total 128K drwxr-xr-x 3 kkarri montilab-p 4.0K Jun 22 17:01 . drwxrwxrwt. 100 root root 92K Jun 22 17:01 .. -rw-r--r-- 1 kkarri montilab-p 141 Jun 22 17:01 Condition_1.txt -rw-r--r-- 1 kkarri montilab-p 105 Jun 22 17:01 Condition_2.txt drwxr-xr-x 4 kkarri montilab-p 4.0K Jun 22 17:01 Input -rwxr-xr-x 1 kkarri montilab-p 16K Jun 22 17:01 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 22 17:01 . drwxr-sr-x 6 kkarri waxmanlab 32K Jun 22 17:01 .. -rw-r--r-- 1 kkarri waxmanlab 0 Jun 22 17:01 DiffExp_2b_Venn_Tables_N-NITROSODIMETHYLAMINE_IP_Saline_IP1IP2IP3_Control_IP_Saline_IP1IP2IP3IP4IP5IP6_HTSeq.txt ========================================================== ========================================================== Finished on : Thu Jun 22 17:01:20 EDT 2017 0 minutes and 16 seconds elapsed. ==========================================================