----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/09c_DiffExp_1_lncRNA_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G160_Samples Dataset_Label: G160 ANNOTATION_FILE_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt CONDITION_1_NAME: F_Soluble_Nuclear CONDITION_2_NAME: F_Chromatin_Pellet Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: exonic_only_gene_models_ncRNA_for_counting_lengths.txt COUNT_DIR: LncRNA_Exonic_Only_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_Exonic_Only DiffExp_Index: DiffExp_1f COL_SUFFIX: LncRNA_Exonic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Thu Aug 31 08:11:29 EDT 2017 Running on node : scc-kb2 Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/09c_DiffExp_1_lncRNA_featureCounts Current job ID : 477045 Current job name : Step_09c_DiffExp_1f Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/477045.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G160_M1 Sample_ID: G160_M1 Description: Female_Soluble_Nuclear_Extract M_Num: M1 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G160_M11 Sample_ID: G160_M11 Description: Duplicate M_Num: M11 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: M1M11 ------------------------------------------ ------------------------------------------ Sample_DIR: G160_M2 Sample_ID: G160_M2 Description: Female_Chromatin_Pellet_Extract 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: G160_M22 Sample_ID: G160_M22 Description: DuplicateM22 M_Num: M22 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: M2M22 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 2 NUM_REP_CONDITION1: 2 ========================================================== Renaming input count files number of mapped reads (feature count summary) Status G160_M22_sorted.bam Assigned 5977777 Unassigned_Ambiguity 32754 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3337030 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G160_M2_sorted.bam Assigned 5977777 Unassigned_Ambiguity 32754 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3337030 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G160_M11_sorted.bam Assigned 3923893 Unassigned_Ambiguity 12692 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3856071 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G160_M1_sorted.bam Assigned 3923893 Unassigned_Ambiguity 12692 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3856071 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 ========================================================== List files in Input -rw-r--r-- 1 kkarri pulmseq 713303 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Chromatin_Pellet0.out -rw-r--r-- 1 kkarri pulmseq 297 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Chromatin_Pellet0.summary -rw-r--r-- 1 kkarri pulmseq 713303 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Chromatin_Pellet1.out -rw-r--r-- 1 kkarri pulmseq 296 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Chromatin_Pellet1.summary -rw-r--r-- 1 kkarri pulmseq 710869 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Soluble_Nuclear0.out -rw-r--r-- 1 kkarri pulmseq 297 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Soluble_Nuclear0.summary -rw-r--r-- 1 kkarri pulmseq 710869 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Soluble_Nuclear1.out -rw-r--r-- 1 kkarri pulmseq 296 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Soluble_Nuclear1.summary -rw-r--r-- 1 kkarri pulmseq 794757 Aug 31 08:11 /scratch/477045.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/477045.1.linga/Input/F_Chromatin_Pellet: total 8 drwxr-xr-x 2 kkarri pulmseq 4096 Aug 31 08:11 . drwxr-xr-x 4 kkarri pulmseq 4096 Aug 31 08:11 .. /scratch/477045.1.linga/Input/F_Soluble_Nuclear: total 8 drwxr-xr-x 2 kkarri pulmseq 4096 Aug 31 08:11 . drwxr-xr-x 4 kkarri pulmseq 4096 Aug 31 08:11 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R F_Soluble_Nuclear F_Chromatin_Pellet 2 2 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/477045.1.linga/Input DiffExp_v2_LncRNA_Exonic_Only exonic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "F_Soluble_Nuclear" [1] "F_Chromatin_Pellet" [1] 2 [1] 2 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/477045.1.linga/Input" [1] "DiffExp_v2_LncRNA_Exonic_Only" [1] "exonic_only_gene_models_ncRNA_for_counting_lengths.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Exonic_Only_F_Soluble_Nuclear_F_Chromatin_Pellet.txt F_Chromatin_Pellet_G160_M2M22_vs_F_Soluble_Nuclear_G160_M1M11_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload 1 LncRNA_Exonic_Only ========================================================== Comparison_Info: F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R F_Chromatin_Pellet_G160_M2M22_vs_F_Soluble_Nuclear_G160_M1M11_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Exonic_Only'_'F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_Chromatin_Pellet_G160_M2M22_vs_F_Soluble_Nuclear_G160_M1M11_DiffExp_v2_LncRNA_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] "LncRNA_Exonic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11" [1] "-----------------" [1] "DESeq or EdgeR job most likely failed." [1] "Quitting R now." Rscript Diff_Genes.R F_Chromatin_Pellet_G160_M2M22_vs_F_Soluble_Nuclear_G160_M1M11_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Exonic_Only'_'F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_Chromatin_Pellet_G160_M2M22_vs_F_Soluble_Nuclear_G160_M1M11_DiffExp_v2_LncRNA_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] "LncRNA_Exonic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11" [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_Exonic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt Down_Genes_EdgeR_LncRNA_Exonic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt LncRNA_Exonic_Only_Counting DiffExp_1f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Exonic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Exonic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1f" [1] "-----------------" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_LncRNA_Exonic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt Up_Genes_EdgeR_LncRNA_Exonic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt LncRNA_Exonic_Only_Counting DiffExp_1f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Exonic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Exonic_Only_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1f" [1] "-----------------" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- Comparison_Info: F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri pulmseq 0 Aug 31 08:12 /scratch/477045.1.linga/Input/DiffExp_1f_Venn_Tables_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11.txt -rwxr-xr-x 1 kkarri pulmseq 7706 Aug 31 08:11 /scratch/477045.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri pulmseq 713303 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Chromatin_Pellet0.out -rw-r--r-- 1 kkarri pulmseq 297 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Chromatin_Pellet0.summary -rw-r--r-- 1 kkarri pulmseq 713303 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Chromatin_Pellet1.out -rw-r--r-- 1 kkarri pulmseq 296 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Chromatin_Pellet1.summary -rw-r--r-- 1 kkarri pulmseq 710869 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Soluble_Nuclear0.out -rw-r--r-- 1 kkarri pulmseq 297 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Soluble_Nuclear0.summary -rw-r--r-- 1 kkarri pulmseq 710869 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Soluble_Nuclear1.out -rw-r--r-- 1 kkarri pulmseq 296 Aug 31 08:11 /scratch/477045.1.linga/Input/F_Soluble_Nuclear1.summary -rwxr-xr-x 1 kkarri pulmseq 9993 Aug 31 08:11 /scratch/477045.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri pulmseq 794757 Aug 31 08:11 /scratch/477045.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt -rwxr-xr-x 1 kkarri pulmseq 4968 Aug 31 08:11 /scratch/477045.1.linga/Input/formatForSegex_ver3.R /scratch/477045.1.linga/Input/F_Chromatin_Pellet: total 8 drwxr-xr-x 2 kkarri pulmseq 4096 Aug 31 08:11 . drwxr-xr-x 4 kkarri pulmseq 4096 Aug 31 08:12 .. /scratch/477045.1.linga/Input/F_Soluble_Nuclear: total 8 drwxr-xr-x 2 kkarri pulmseq 4096 Aug 31 08:11 . drwxr-xr-x 4 kkarri pulmseq 4096 Aug 31 08:12 .. ========================================================== List files in scratch total 3.4M drwxr-xr-x 3 kkarri pulmseq 4.0K Aug 31 08:12 . drwxrwxrwt. 68 root root 92K Aug 31 08:11 .. -rw-r--r-- 1 kkarri pulmseq 108 Aug 31 08:11 Condition_1.txt -rw-r--r-- 1 kkarri pulmseq 112 Aug 31 08:11 Condition_2.txt drwxr-xr-x 4 kkarri pulmseq 4.0K Aug 31 08:12 Input -rwxr-xr-x 1 kkarri pulmseq 13K Aug 31 08:11 differentialAnalysis.R -rw-r--r-- 1 kkarri pulmseq 3.3M Aug 31 08:11 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 Aug 31 08:12 . drwxr-sr-x 7 kkarri waxmanlab 32K Aug 31 08:11 .. -rw-r--r-- 1 kkarri waxmanlab 0 Aug 31 08:12 DiffExp_1f_Venn_Tables_F_Chromatin_Pellet_G160_M2M22_F_Soluble_Nuclear_G160_M1M11_featureCounts.txt ========================================================== ========================================================== Finished on : Thu Aug 31 08:12:04 EDT 2017 0 minutes and 35 seconds elapsed. ==========================================================