----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/09c_DiffExp_2_lncRNA_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New Dataset_Label: G123 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: Male_27h_Vehicle CONDITION_2_NAME: Male_27h_TCPOBOP Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: intronic_only_gene_models_ncRNA_for_counting_lengths.txt COUNT_DIR: LncRNA_Intronic_Only_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_Intronic_Only DiffExp_Index: DiffExp_2g COL_SUFFIX: LncRNA_Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Sat Dec 8 01:15:58 EST 2018 Running on node : scc-ka3 Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/09c_DiffExp_2_lncRNA_featureCounts Current job ID : 29161 Current job name : Step_09c_DiffExp_2g Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/29161.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G123_M5 Sample_ID: G123_M5 Description: Male_27h_Vehicle_1 M_Num: M5 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G123_M6 Sample_ID: G123_M6 Description: Male_27h_Vehicle_2 M_Num: M6 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: M5M6 ------------------------------------------ ------------------------------------------ Sample_DIR: G123_M7 Sample_ID: G123_M7 Description: Male_27h_TCPOBOP_1 M_Num: M7 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G123_M8 Sample_ID: G123_M8 Description: Male_27h_TCPOBOP_2 M_Num: M8 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: M7M8 ------------------------------------------ ========================================================== 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 G123_M7_sorted.bam Assigned 5365579 Unassigned_Ambiguity 419182 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11429049 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G123_M8_sorted.bam Assigned 4897069 Unassigned_Ambiguity 394219 Unassigned_MultiMapping 0 Unassigned_NoFeatures 10801107 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G123_M5_sorted.bam Assigned 4254662 Unassigned_Ambiguity 284627 Unassigned_MultiMapping 0 Unassigned_NoFeatures 10182919 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G123_M6_sorted.bam Assigned 5964889 Unassigned_Ambiguity 375232 Unassigned_MultiMapping 0 Unassigned_NoFeatures 14129332 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 waxmanlab 355689 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 298 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_TCPOBOP0.summary -rw-r--r-- 1 kkarri waxmanlab 355101 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 298 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_TCPOBOP1.summary -rw-r--r-- 1 kkarri waxmanlab 353958 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 298 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_Vehicle0.summary -rw-r--r-- 1 kkarri waxmanlab 356223 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 298 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_Vehicle1.summary -rw-r--r-- 1 kkarri waxmanlab 414633 Dec 8 01:15 /scratch/29161.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/29161.1.linga/Input/Male_27h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 01:15 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 01:15 .. /scratch/29161.1.linga/Input/Male_27h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 01:15 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 01:15 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Male_27h_Vehicle Male_27h_TCPOBOP 2 2 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/29161.1.linga/Input DiffExp_v2_LncRNA_Intronic_Only intronic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Male_27h_Vehicle" [1] "Male_27h_TCPOBOP" [1] 2 [1] 2 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/29161.1.linga/Input" [1] "DiffExp_v2_LncRNA_Intronic_Only" [1] "intronic_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/29161.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_Male_27h_Vehicle_Male_27h_TCPOBOP.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Intronic_Only_Male_27h_Vehicle_Male_27h_TCPOBOP.txt Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload 1 LncRNA_Intronic_Only ========================================================== Comparison_Info: Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Intronic_Only'_'Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_LncRNA_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] "LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 39 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 10 7 [1] "Check out Up_Genes_DESeq_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt!" Rscript Diff_Genes.R Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Intronic_Only'_'Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_LncRNA_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] "LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 87 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 41 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt Down_Genes_EdgeR_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt LncRNA_Intronic_Only_Counting DiffExp_2g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2g" [1] "-----------------" [1] "Down.DESeq.Intronic_Only.HTSeq" [1] "Down.EdgeR.Intronic_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_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt Up_Genes_EdgeR_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt LncRNA_Intronic_Only_Counting DiffExp_2g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2g" [1] "-----------------" [1] "Up.DESeq.Intronic_Only.HTSeq" [1] "Up.EdgeR.Intronic_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: Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 334 Dec 8 01:16 /scratch/29161.1.linga/Input/DiffExp_2g_Venn_Tables_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 3331756 Dec 8 01:16 /scratch/29161.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Dec 8 01:15 /scratch/29161.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 1113 Dec 8 01:16 /scratch/29161.1.linga/Input/Down_Genes_DESeq_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 4585 Dec 8 01:16 /scratch/29161.1.linga/Input/Down_Genes_EdgeR_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 355689 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 298 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_TCPOBOP0.summary -rw-r--r-- 1 kkarri waxmanlab 355101 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 298 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_TCPOBOP1.summary -rw-r--r-- 1 kkarri waxmanlab 3755034 Dec 8 01:16 /scratch/29161.1.linga/Input/Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 4190658 Dec 8 01:16 /scratch/29161.1.linga/Input/Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 353958 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 298 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_Vehicle0.summary -rw-r--r-- 1 kkarri waxmanlab 356223 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 298 Dec 8 01:15 /scratch/29161.1.linga/Input/Male_27h_Vehicle1.summary -rw-r--r-- 1 kkarri waxmanlab 8595 Dec 8 01:16 /scratch/29161.1.linga/Input/Up_Genes_DESeq_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rw-r--r-- 1 kkarri waxmanlab 21275 Dec 8 01:16 /scratch/29161.1.linga/Input/Up_Genes_EdgeR_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Dec 8 01:15 /scratch/29161.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 38246 Dec 8 01:16 /scratch/29161.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 38571 Dec 8 01:16 /scratch/29161.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 4968 Dec 8 01:15 /scratch/29161.1.linga/Input/formatForSegex_ver3.R -rw-r--r-- 1 kkarri waxmanlab 414633 Dec 8 01:15 /scratch/29161.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/29161.1.linga/Input/Male_27h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 01:15 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 01:16 .. /scratch/29161.1.linga/Input/Male_27h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 8 01:15 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 8 01:16 .. ========================================================== List files in scratch total 3.5M drwx------ 3 kkarri waxmanlab 4.0K Dec 8 01:16 . drwxrwxrwt. 32 root root 108K Dec 8 01:15 .. -rw-r--r-- 1 kkarri waxmanlab 103 Dec 8 01:15 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 103 Dec 8 01:15 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Dec 8 01:16 Input -rwxr-xr-x 1 kkarri waxmanlab 13K Dec 8 01:15 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Dec 8 01:15 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 9.1M drwxr-sr-x 2 kkarri waxmanlab 32K Dec 8 01:16 . drwxr-sr-x 7 kkarri waxmanlab 32K Dec 8 01:15 .. -rw-r--r-- 1 kkarri waxmanlab 334 Dec 8 01:16 DiffExp_2g_Venn_Tables_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.2M Dec 8 01:16 DiffExp_v2_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.1K Dec 8 01:16 Down_Genes_DESeq_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.5K Dec 8 01:16 Down_Genes_EdgeR_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.6M Dec 8 01:16 Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.0M Dec 8 01:16 Male_27h_TCPOBOP_G123_M7M8_vs_Male_27h_Vehicle_G123_M5M6_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 8.4K Dec 8 01:16 Up_Genes_DESeq_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 21K Dec 8 01:16 Up_Genes_EdgeR_LncRNA_Intronic_Only_Male_27h_TCPOBOP_G123_M7M8_Male_27h_Vehicle_G123_M5M6_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 38K Dec 8 01:16 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 38K Dec 8 01:16 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Sat Dec 8 01:16:49 EST 2018 0 minutes and 51 seconds elapsed. ==========================================================