----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/09c_DiffExp_2_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_Nuclear CONDITION_2_NAME: F_Cytoplasmic 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_2f COL_SUFFIX: LncRNA_Exonic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed Aug 30 08:02:28 EDT 2017 Running on node : scc-kb6 Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/09c_DiffExp_2_lncRNA_featureCounts Current job ID : 462240 Current job name : Step_09c_DiffExp_2f Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/462240.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G160_M3 Sample_ID: G160_M3 Description: Female_Nuclear M_Num: M3 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G160_M33 Sample_ID: G160_M33 Description: Female_Nuclear_RNA_II M_Num: M33 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: M3M33 ------------------------------------------ ------------------------------------------ Sample_DIR: G160_M4 Sample_ID: G160_M4 Description: Female M_Num: M4 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G160_M44 Sample_ID: G160_M44 Description: Female_Cytoplasmic_RNA_II M_Num: M44 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: M4M44 ------------------------------------------ ========================================================== 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_M44_sorted.bam Assigned 1725561 Unassigned_Ambiguity 68148 Unassigned_MultiMapping 0 Unassigned_NoFeatures 8749834 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G160_M4_sorted.bam Assigned 2003492 Unassigned_Ambiguity 4314 Unassigned_MultiMapping 0 Unassigned_NoFeatures 8535737 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G160_M33_sorted.bam Assigned 4689904 Unassigned_Ambiguity 19371 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3964598 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G160_M3_sorted.bam Assigned 4689904 Unassigned_Ambiguity 19371 Unassigned_MultiMapping 0 Unassigned_NoFeatures 3964598 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 698795 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Cytoplasmic0.out -rw-r--r-- 1 kkarri pulmseq 297 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Cytoplasmic0.summary -rw-r--r-- 1 kkarri pulmseq 699356 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Cytoplasmic1.out -rw-r--r-- 1 kkarri pulmseq 295 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Cytoplasmic1.summary -rw-r--r-- 1 kkarri pulmseq 712657 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Nuclear0.out -rw-r--r-- 1 kkarri pulmseq 297 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Nuclear0.summary -rw-r--r-- 1 kkarri pulmseq 712657 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Nuclear1.out -rw-r--r-- 1 kkarri pulmseq 296 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Nuclear1.summary -rw-r--r-- 1 kkarri pulmseq 794757 Aug 30 08:02 /scratch/462240.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/462240.1.linga/Input/F_Cytoplasmic: total 8 drwxr-xr-x 2 kkarri pulmseq 4096 Aug 30 08:02 . drwxr-xr-x 4 kkarri pulmseq 4096 Aug 30 08:02 .. /scratch/462240.1.linga/Input/F_Nuclear: total 8 drwxr-xr-x 2 kkarri pulmseq 4096 Aug 30 08:02 . drwxr-xr-x 4 kkarri pulmseq 4096 Aug 30 08:02 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R F_Nuclear F_Cytoplasmic 2 2 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/462240.1.linga/Input DiffExp_v2_LncRNA_Exonic_Only exonic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "F_Nuclear" [1] "F_Cytoplasmic" [1] 2 [1] 2 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/462240.1.linga/Input" [1] "DiffExp_v2_LncRNA_Exonic_Only" [1] "exonic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] 15558 23 [1] 15558 48 [1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" "chr9" [1] "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" [10] "chr19" [1] "chrX" "chrY" [1] "output file is in: /scratch/462240.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_F_Nuclear_F_Cytoplasmic.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Exonic_Only_F_Nuclear_F_Cytoplasmic.txt F_Cytoplasmic_G160_M4M44_vs_F_Nuclear_G160_M3M33_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload 1 LncRNA_Exonic_Only ========================================================== Comparison_Info: F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R F_Cytoplasmic_G160_M4M44_vs_F_Nuclear_G160_M3M33_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Exonic_Only'_'F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_Cytoplasmic_G160_M4M44_vs_F_Nuclear_G160_M3M33_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_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 2 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 0 7 [1] "Check out Up_Genes_DESeq_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt!" Rscript Diff_Genes.R F_Cytoplasmic_G160_M4M44_vs_F_Nuclear_G160_M3M33_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Exonic_Only'_'F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_Cytoplasmic_G160_M4M44_vs_F_Nuclear_G160_M3M33_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_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 199 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 1021 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt Down_Genes_EdgeR_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt LncRNA_Exonic_Only_Counting DiffExp_2f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2f" [1] "-----------------" [1] "Down.DESeq.Exonic_Only.HTSeq" [1] "Down.EdgeR.Exonic_Only.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_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt Up_Genes_EdgeR_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt LncRNA_Exonic_Only_Counting DiffExp_2f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2f" [1] "-----------------" [1] "Up.DESeq.Exonic_Only.HTSeq" [1] "Up.EdgeR.Exonic_Only.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: F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri pulmseq 326 Aug 30 08:03 /scratch/462240.1.linga/Input/DiffExp_2f_Venn_Tables_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt -rw-r--r-- 1 kkarri pulmseq 4396422 Aug 30 08:03 /scratch/462240.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt -rwxr-xr-x 1 kkarri pulmseq 7706 Aug 30 08:02 /scratch/462240.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri pulmseq 217 Aug 30 08:03 /scratch/462240.1.linga/Input/Down_Genes_DESeq_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt -rw-r--r-- 1 kkarri pulmseq 122053 Aug 30 08:03 /scratch/462240.1.linga/Input/Down_Genes_EdgeR_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt -rw-r--r-- 1 kkarri pulmseq 698795 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Cytoplasmic0.out -rw-r--r-- 1 kkarri pulmseq 297 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Cytoplasmic0.summary -rw-r--r-- 1 kkarri pulmseq 699356 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Cytoplasmic1.out -rw-r--r-- 1 kkarri pulmseq 295 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Cytoplasmic1.summary -rw-r--r-- 1 kkarri pulmseq 1654680 Aug 30 08:03 /scratch/462240.1.linga/Input/F_Cytoplasmic_G160_M4M44_vs_F_Nuclear_G160_M3M33_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri pulmseq 2354790 Aug 30 08:03 /scratch/462240.1.linga/Input/F_Cytoplasmic_G160_M4M44_vs_F_Nuclear_G160_M3M33_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri pulmseq 712657 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Nuclear0.out -rw-r--r-- 1 kkarri pulmseq 297 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Nuclear0.summary -rw-r--r-- 1 kkarri pulmseq 712657 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Nuclear1.out -rw-r--r-- 1 kkarri pulmseq 296 Aug 30 08:02 /scratch/462240.1.linga/Input/F_Nuclear1.summary -rw-r--r-- 1 kkarri pulmseq 351 Aug 30 08:03 /scratch/462240.1.linga/Input/Up_Genes_DESeq_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt -rw-r--r-- 1 kkarri pulmseq 22213 Aug 30 08:03 /scratch/462240.1.linga/Input/Up_Genes_EdgeR_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33.txt -rwxr-xr-x 1 kkarri pulmseq 9993 Aug 30 08:02 /scratch/462240.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri pulmseq 32639 Aug 30 08:03 /scratch/462240.1.linga/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri pulmseq 30192 Aug 30 08:03 /scratch/462240.1.linga/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri pulmseq 794757 Aug 30 08:02 /scratch/462240.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt -rwxr-xr-x 1 kkarri pulmseq 4968 Aug 30 08:02 /scratch/462240.1.linga/Input/formatForSegex_ver3.R /scratch/462240.1.linga/Input/F_Cytoplasmic: total 8 drwxr-xr-x 2 kkarri pulmseq 4096 Aug 30 08:02 . drwxr-xr-x 4 kkarri pulmseq 4096 Aug 30 08:03 .. /scratch/462240.1.linga/Input/F_Nuclear: total 8 drwxr-xr-x 2 kkarri pulmseq 4096 Aug 30 08:02 . drwxr-xr-x 4 kkarri pulmseq 4096 Aug 30 08:03 .. ========================================================== List files in scratch total 3.4M drwxr-xr-x 3 kkarri pulmseq 4.0K Aug 30 08:03 . drwxrwxrwt. 62 root root 12K Aug 30 08:03 .. -rw-r--r-- 1 kkarri pulmseq 104 Aug 30 08:02 Condition_1.txt -rw-r--r-- 1 kkarri pulmseq 100 Aug 30 08:02 Condition_2.txt drwxr-xr-x 4 kkarri pulmseq 4.0K Aug 30 08:03 Input -rwxr-xr-x 1 kkarri pulmseq 13K Aug 30 08:02 differentialAnalysis.R -rw-r--r-- 1 kkarri pulmseq 3.3M Aug 30 08:02 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 7.1M drwxr-sr-x 2 kkarri waxmanlab 32K Aug 30 08:03 . drwxr-sr-x 7 kkarri waxmanlab 32K Aug 30 08:03 .. -rw-r--r-- 1 kkarri waxmanlab 326 Aug 30 08:03 DiffExp_2f_Venn_Tables_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.2M Aug 30 08:03 DiffExp_v2_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 217 Aug 30 08:03 Down_Genes_DESeq_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 120K Aug 30 08:03 Down_Genes_EdgeR_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.6M Aug 30 08:03 F_Cytoplasmic_G160_M4M44_vs_F_Nuclear_G160_M3M33_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Aug 30 08:03 F_Cytoplasmic_G160_M4M44_vs_F_Nuclear_G160_M3M33_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 351 Aug 30 08:03 Up_Genes_DESeq_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 22K Aug 30 08:03 Up_Genes_EdgeR_LncRNA_Exonic_Only_F_Cytoplasmic_G160_M4M44_F_Nuclear_G160_M3M33_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 32K Aug 30 08:03 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 30K Aug 30 08:03 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Wed Aug 30 08:03:59 EDT 2017 1 minutes and 31 seconds elapsed. ==========================================================