----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/09c_DiffExp_1_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_3h_Vehicle CONDITION_2_NAME: Male_3h_TCPOBOP Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: ncRNA_genebodies_for_counting_lengths.txt COUNT_DIR: LncRNA_GeneBody_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_GeneBody DiffExp_Index: DiffExp_1e COL_SUFFIX: LncRNA_GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Dec 10 12:03:41 EST 2018 Running on node : scc-ka2 Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/09c_DiffExp_1_lncRNA_featureCounts Current job ID : 56268 Current job name : Step_09c_DiffExp_1e Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/56268.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G123_M1 Sample_ID: G123_M1 Description: Male_3h_Vehicle_1 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: G123_M2 Sample_ID: G123_M2 Description: Male_3h_Vehicle_2 M_Num: M2 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: M1M2 ------------------------------------------ ------------------------------------------ Sample_DIR: G123_M3 Sample_ID: G123_M3 Description: Male_3h_TCPOBOP_1 M_Num: M3 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G123_M4 Sample_ID: G123_M4 Description: Male_3h_TCPOBOP_2 M_Num: M4 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: M3M4 ------------------------------------------ ========================================================== 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_M3_sorted.bam Assigned 14301095 Unassigned_Ambiguity 1051701 Unassigned_MultiMapping 0 Unassigned_NoFeatures 442110 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G123_M4_sorted.bam Assigned 21995231 Unassigned_Ambiguity 1437263 Unassigned_MultiMapping 0 Unassigned_NoFeatures 673313 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G123_M1_sorted.bam Assigned 15418460 Unassigned_Ambiguity 1028979 Unassigned_MultiMapping 0 Unassigned_NoFeatures 473549 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G123_M2_sorted.bam Assigned 13639127 Unassigned_Ambiguity 949880 Unassigned_MultiMapping 0 Unassigned_NoFeatures 449169 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 720260 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 298 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_TCPOBOP0.summary -rw-r--r-- 1 kkarri waxmanlab 723913 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 298 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_TCPOBOP1.summary -rw-r--r-- 1 kkarri waxmanlab 720720 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 298 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_Vehicle0.summary -rw-r--r-- 1 kkarri waxmanlab 719830 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 297 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_Vehicle1.summary -rw-r--r-- 1 kkarri waxmanlab 815529 Dec 10 12:03 /scratch/56268.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/56268.1.linga/Input/Male_3h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 10 12:03 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 10 12:03 .. /scratch/56268.1.linga/Input/Male_3h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 10 12:03 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 10 12:03 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Male_3h_Vehicle Male_3h_TCPOBOP 2 2 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/56268.1.linga/Input DiffExp_v2_LncRNA_GeneBody ncRNA_genebodies_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Male_3h_Vehicle" [1] "Male_3h_TCPOBOP" [1] 2 [1] 2 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/56268.1.linga/Input" [1] "DiffExp_v2_LncRNA_GeneBody" [1] "ncRNA_genebodies_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/56268.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_Male_3h_Vehicle_Male_3h_TCPOBOP.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_GeneBody_Male_3h_Vehicle_Male_3h_TCPOBOP.txt Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload 1 LncRNA_GeneBody ========================================================== Comparison_Info: Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_GeneBody'_'Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 9 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 2 7 [1] "Check out Up_Genes_DESeq_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt!" Rscript Diff_Genes.R Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_GeneBody'_'Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 56 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 25 7 [1] "Check out Up_Genes_EdgeR_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt Down_Genes_EdgeR_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt LncRNA_GeneBody_Counting DiffExp_1e [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1e" [1] "-----------------" [1] "Down.DESeq.GeneBody.HTSeq" [1] "Down.EdgeR.GeneBody.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_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt Up_Genes_EdgeR_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt LncRNA_GeneBody_Counting DiffExp_1e [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1e" [1] "-----------------" [1] "Up.DESeq.GeneBody.HTSeq" [1] "Up.EdgeR.GeneBody.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_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 302 Dec 10 12:04 /scratch/56268.1.linga/Input/DiffExp_1e_Venn_Tables_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 5007986 Dec 10 12:04 /scratch/56268.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Dec 10 12:03 /scratch/56268.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 389 Dec 10 12:04 /scratch/56268.1.linga/Input/Down_Genes_DESeq_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 2793 Dec 10 12:04 /scratch/56268.1.linga/Input/Down_Genes_EdgeR_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 720260 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 298 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_TCPOBOP0.summary -rw-r--r-- 1 kkarri waxmanlab 723913 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 298 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_TCPOBOP1.summary -rw-r--r-- 1 kkarri waxmanlab 1670225 Dec 10 12:04 /scratch/56268.1.linga/Input/Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1716899 Dec 10 12:04 /scratch/56268.1.linga/Input/Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 720720 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 298 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_Vehicle0.summary -rw-r--r-- 1 kkarri waxmanlab 719830 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 297 Dec 10 12:03 /scratch/56268.1.linga/Input/Male_3h_Vehicle1.summary -rw-r--r-- 1 kkarri waxmanlab 894 Dec 10 12:04 /scratch/56268.1.linga/Input/Up_Genes_DESeq_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 4680 Dec 10 12:04 /scratch/56268.1.linga/Input/Up_Genes_EdgeR_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Dec 10 12:03 /scratch/56268.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 35292 Dec 10 12:04 /scratch/56268.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 35246 Dec 10 12:04 /scratch/56268.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 4968 Dec 10 12:03 /scratch/56268.1.linga/Input/formatForSegex_ver3.R -rw-r--r-- 1 kkarri waxmanlab 815529 Dec 10 12:03 /scratch/56268.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/56268.1.linga/Input/Male_3h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 10 12:03 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 10 12:04 .. /scratch/56268.1.linga/Input/Male_3h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 10 12:03 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 10 12:04 .. ========================================================== List files in scratch total 3.5M drwx------ 3 kkarri waxmanlab 4.0K Dec 10 12:04 . drwxrwxrwt. 36 root root 116K Dec 10 12:04 .. -rw-r--r-- 1 kkarri waxmanlab 101 Dec 10 12:03 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 101 Dec 10 12:03 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Dec 10 12:04 Input -rwxr-xr-x 1 kkarri waxmanlab 13K Dec 10 12:03 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Dec 10 12:03 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 6.1M drwxr-sr-x 2 kkarri waxmanlab 32K Dec 10 12:04 . drwxr-sr-x 7 kkarri waxmanlab 32K Dec 10 12:03 .. -rw-r--r-- 1 kkarri waxmanlab 302 Dec 10 12:04 DiffExp_1e_Venn_Tables_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.8M Dec 10 12:04 DiffExp_v2_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 389 Dec 10 12:04 Down_Genes_DESeq_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.8K Dec 10 12:04 Down_Genes_EdgeR_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.6M Dec 10 12:04 Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.7M Dec 10 12:04 Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 894 Dec 10 12:04 Up_Genes_DESeq_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.6K Dec 10 12:04 Up_Genes_EdgeR_LncRNA_GeneBody_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 35K Dec 10 12:04 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 35K Dec 10 12:04 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Dec 10 12:04:38 EST 2018 0 minutes and 57 seconds elapsed. ==========================================================