----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/09b_DiffExp_3_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples Dataset_Label: G167 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: WT_Con CONDITION_2_NAME: GM_KO_Con Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: Exon_Regions_Lengths.txt COUNT_DIR: RefSeq_Exon_GTF OUTPUT_PREFIX: DiffExp_v2_GeneBody DiffExp_Index: DiffExp_3a COL_SUFFIX: GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Jul 23 13:41:27 EDT 2018 Running on node : scc-tm3 Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/09b_DiffExp_3_featureCounts Current job ID : 7056290 Current job name : Step_09b_DiffExp_3a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/7056290.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G167_M1 Sample_ID: G167_M1 Description: WT_Con1 M_Num: M1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G167_M1 Sample_DIR: G167_M2 Sample_ID: G167_M2 Description: WT_Con2 M_Num: M2 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G167_M2 Sample_DIR: G167_M3 Sample_ID: G167_M3 Description: WT_Con3 M_Num: M3 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G167_M3 M_Num_Cond1_List: M1M2M3 ------------------------------------------ ------------------------------------------ Sample_DIR: G167_M4 Sample_ID: G167_M4 Description: GM_KO_Con1 M_Num: M4 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G167_M4 Sample_DIR: G167_M5 Sample_ID: G167_M5 Description: GM_KO_Con2 M_Num: M5 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G167_M5 Sample_DIR: G167_M6 Sample_ID: G167_M6 Description: GM_KO_Con3 M_Num: M6 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G167_M6 M_Num_Cond2_List: M4M5M6 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 3 NUM_REP_CONDITION1: 3 ========================================================== Renaming input count files Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. number of mapped reads 15011398 15932501 13925414 20905454 17099690 12968997 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291522 Jul 23 13:41 /scratch/7056290.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 241976 Jul 23 13:41 /scratch/7056290.1.linga/Input/GM_KO_Con0.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 23 13:41 /scratch/7056290.1.linga/Input/GM_KO_Con0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 242047 Jul 23 13:41 /scratch/7056290.1.linga/Input/GM_KO_Con1.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 23 13:41 /scratch/7056290.1.linga/Input/GM_KO_Con1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 242944 Jul 23 13:41 /scratch/7056290.1.linga/Input/GM_KO_Con2.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 23 13:41 /scratch/7056290.1.linga/Input/GM_KO_Con2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 243655 Jul 23 13:41 /scratch/7056290.1.linga/Input/WT_Con0.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 23 13:41 /scratch/7056290.1.linga/Input/WT_Con0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 243033 Jul 23 13:41 /scratch/7056290.1.linga/Input/WT_Con1.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 23 13:41 /scratch/7056290.1.linga/Input/WT_Con1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 241860 Jul 23 13:41 /scratch/7056290.1.linga/Input/WT_Con2.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 23 13:41 /scratch/7056290.1.linga/Input/WT_Con2_num_mapped_reads.txt /scratch/7056290.1.linga/Input/GM_KO_Con: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Jul 23 13:41 . drwxr-xr-x 4 kkarri waxmanlab 4096 Jul 23 13:41 .. /scratch/7056290.1.linga/Input/WT_Con: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Jul 23 13:41 . drwxr-xr-x 4 kkarri waxmanlab 4096 Jul 23 13:41 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WT_Con GM_KO_Con 3 3 RefSeq_GeneBody.gtf /scratch/7056290.1.linga/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WT_Con" [1] "GM_KO_Con" [1] 3 [1] 3 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/7056290.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" load GTF file ... parse attributes ... [1] "output file is in: /scratch/7056290.1.linga/Input/DiffExp_v2_GeneBody_WT_Con_GM_KO_Con.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_WT_Con_GM_KO_Con.txt GM_KO_Con_G167_M4M5M6_vs_WT_Con_G167_M1M2M3_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== Comparison_Info: GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R GM_KO_Con_G167_M4M5M6_vs_WT_Con_G167_M1M2M3_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "GM_KO_Con_G167_M4M5M6_vs_WT_Con_G167_M1M2M3_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 6 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 0 7 [1] "Check out Up_Genes_DESeq_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt!" [1] "Check out Down_Genes_DESeq_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt!" Rscript Diff_Genes.R GM_KO_Con_G167_M4M5M6_vs_WT_Con_G167_M1M2M3_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "GM_KO_Con_G167_M4M5M6_vs_WT_Con_G167_M1M2M3_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 14 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 1 7 [1] "Check out Up_Genes_EdgeR_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt!" [1] "Check out Down_Genes_EdgeR_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt Down_Genes_EdgeR_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt GeneBody_Counting DiffExp_3a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3a" [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_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt Up_Genes_EdgeR_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt GeneBody_Counting DiffExp_3a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3a" [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: GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 285 Jul 23 13:43 /scratch/7056290.1.linga/Input/DiffExp_3a_Venn_Tables_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt -rw-r--r-- 1 kkarri waxmanlab 7309144 Jul 23 13:42 /scratch/7056290.1.linga/Input/DiffExp_v2_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Jul 23 13:41 /scratch/7056290.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 140 Jul 23 13:42 /scratch/7056290.1.linga/Input/Down_Genes_DESeq_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt -rw-r--r-- 1 kkarri waxmanlab 195 Jul 23 13:42 /scratch/7056290.1.linga/Input/Down_Genes_EdgeR_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt -rw-r--r-- 1 kkarri waxmanlab 291522 Jul 23 13:41 /scratch/7056290.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 241976 Jul 23 13:41 /scratch/7056290.1.linga/Input/GM_KO_Con0.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 23 13:41 /scratch/7056290.1.linga/Input/GM_KO_Con0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 242047 Jul 23 13:41 /scratch/7056290.1.linga/Input/GM_KO_Con1.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 23 13:41 /scratch/7056290.1.linga/Input/GM_KO_Con1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 242944 Jul 23 13:41 /scratch/7056290.1.linga/Input/GM_KO_Con2.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 23 13:41 /scratch/7056290.1.linga/Input/GM_KO_Con2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 4314116 Jul 23 13:42 /scratch/7056290.1.linga/Input/GM_KO_Con_G167_M4M5M6_vs_WT_Con_G167_M1M2M3_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 4628677 Jul 23 13:42 /scratch/7056290.1.linga/Input/GM_KO_Con_G167_M4M5M6_vs_WT_Con_G167_M1M2M3_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 1033 Jul 23 13:42 /scratch/7056290.1.linga/Input/Up_Genes_DESeq_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt -rw-r--r-- 1 kkarri waxmanlab 2402 Jul 23 13:42 /scratch/7056290.1.linga/Input/Up_Genes_EdgeR_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Jul 23 13:41 /scratch/7056290.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 30857 Jul 23 13:43 /scratch/7056290.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 36983 Jul 23 13:43 /scratch/7056290.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 243655 Jul 23 13:41 /scratch/7056290.1.linga/Input/WT_Con0.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 23 13:41 /scratch/7056290.1.linga/Input/WT_Con0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 243033 Jul 23 13:41 /scratch/7056290.1.linga/Input/WT_Con1.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 23 13:41 /scratch/7056290.1.linga/Input/WT_Con1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 241860 Jul 23 13:41 /scratch/7056290.1.linga/Input/WT_Con2.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 23 13:41 /scratch/7056290.1.linga/Input/WT_Con2_num_mapped_reads.txt -rwxr-xr-x 1 kkarri waxmanlab 3925 Jul 23 13:41 /scratch/7056290.1.linga/Input/formatForSegex_ver3.R /scratch/7056290.1.linga/Input/GM_KO_Con: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Jul 23 13:41 . drwxr-xr-x 4 kkarri waxmanlab 4096 Jul 23 13:43 .. /scratch/7056290.1.linga/Input/WT_Con: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Jul 23 13:41 . drwxr-xr-x 4 kkarri waxmanlab 4096 Jul 23 13:43 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Jul 23 13:43 . drwxrwxrwt. 48 root root 36K Jul 23 13:41 .. -rw-r--r-- 1 kkarri waxmanlab 105 Jul 23 13:41 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 114 Jul 23 13:41 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Jul 23 13:43 Input -rw-r--r-- 1 kkarri waxmanlab 72M Jul 23 13:41 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 16K Jul 23 13:41 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 13M drwxr-sr-x 2 kkarri waxmanlab 32K Jul 23 13:43 . drwxr-sr-x 6 kkarri waxmanlab 32K Jul 23 13:42 .. -rw-r--r-- 1 kkarri waxmanlab 285 Jul 23 13:43 DiffExp_3a_Venn_Tables_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 7.0M Jul 23 13:43 DiffExp_v2_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 140 Jul 23 13:43 Down_Genes_DESeq_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 195 Jul 23 13:43 Down_Genes_EdgeR_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.2M Jul 23 13:43 GM_KO_Con_G167_M4M5M6_vs_WT_Con_G167_M1M2M3_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.5M Jul 23 13:43 GM_KO_Con_G167_M4M5M6_vs_WT_Con_G167_M1M2M3_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.1K Jul 23 13:43 Up_Genes_DESeq_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.4K Jul 23 13:43 Up_Genes_EdgeR_GeneBody_GM_KO_Con_G167_M4M5M6_WT_Con_G167_M1M2M3_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 31K Jul 23 13:43 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 37K Jul 23 13:43 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Jul 23 13:43:00 EDT 2018 1 minutes and 33 seconds elapsed. ==========================================================