----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/09b_DiffExp_7_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170 Dataset_Label: G170 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: F_Placebo_TD229 CONDITION_2_NAME: F_CPA_3D_TD229 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_7a COL_SUFFIX: GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Sep 16 10:23:34 EDT 2019 Running on node : scc-kb4 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/09b_DiffExp_7_featureCounts Current job ID : 9373630 Current job name : Step_09b_DiffExp_7a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9373630.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G170_M20 Sample_ID: G170_M20 Description: F_Placebo1_TD229 M_Num: M20 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G170_M20 Sample_DIR: G170_M21 Sample_ID: G170_M21 Description: F_Placebo2_TD229 M_Num: M21 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G170_M21 M_Num_Cond1_List: M20M21 ------------------------------------------ ------------------------------------------ Sample_DIR: G170_M26 Sample_ID: G170_M26 Description: F_CPA_3D7_TD229 M_Num: M26 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G170_M26 Sample_DIR: G170_M27 Sample_ID: G170_M27 Description: F_CPA_3D8_TD229 M_Num: M27 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G170_M27 M_Num_Cond2_List: M26M27 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 2 NUM_REP_CONDITION1: 2 ========================================================== 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. number of mapped reads 42566996 43136047 44524767 45401633 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291522 Sep 16 10:23 /scratch/9373630.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 253166 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_CPA_3D_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_CPA_3D_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 253451 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_CPA_3D_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_CPA_3D_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 252909 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_Placebo_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_Placebo_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 253556 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_Placebo_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_Placebo_TD2291_num_mapped_reads.txt /scratch/9373630.1.linga/Input/F_CPA_3D_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:23 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:23 .. /scratch/9373630.1.linga/Input/F_Placebo_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:23 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:23 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R F_Placebo_TD229 F_CPA_3D_TD229 2 2 RefSeq_GeneBody.gtf /scratch/9373630.1.linga/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "F_Placebo_TD229" [1] "F_CPA_3D_TD229" [1] 2 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/9373630.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" [1] "sum1:287182.057180504" "sum1:252675.815460196" "sum1:269928.93632035" [1] "sum2:269988.009481969" "sum2:269697.621352937" "sum2:269842.815417453" load GTF file ... parse attributes ... [1] "output file is in: /scratch/9373630.1.linga/Input/DiffExp_v2_GeneBody_F_Placebo_TD229_F_CPA_3D_TD229.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_F_Placebo_TD229_F_CPA_3D_TD229.txt F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_GeneBody_F_Placebo_TD229_F_CPA_3D_TD229.txt F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== Comparison_Info: F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_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_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 114 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 39 7 [1] "Check out Up_Genes_DESeq_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt!" [1] "Check out Down_Genes_DESeq_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt!" Rscript Diff_Genes.R F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_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_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 189 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 65 7 [1] "Check out Up_Genes_EdgeR_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt!" [1] "Check out Down_Genes_EdgeR_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt Down_Genes_EdgeR_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt GeneBody_Counting DiffExp_7a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_7a" [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_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt Up_Genes_EdgeR_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt GeneBody_Counting DiffExp_7a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_7a" [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: F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 292 Sep 16 10:24 /scratch/9373630.1.linga/Input/DiffExp_7a_Venn_Tables_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 9492313 Sep 16 10:24 /scratch/9373630.1.linga/Input/DiffExp_v2_GeneBody_F_Placebo_TD229_F_CPA_3D_TD229.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Sep 16 10:23 /scratch/9373630.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 4925 Sep 16 10:24 /scratch/9373630.1.linga/Input/Down_Genes_DESeq_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 10384 Sep 16 10:24 /scratch/9373630.1.linga/Input/Down_Genes_EdgeR_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 291522 Sep 16 10:23 /scratch/9373630.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 253166 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_CPA_3D_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_CPA_3D_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 253451 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_CPA_3D_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_CPA_3D_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 3660811 Sep 16 10:24 /scratch/9373630.1.linga/Input/F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 4483509 Sep 16 10:24 /scratch/9373630.1.linga/Input/F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 3660809 Sep 16 10:24 /scratch/9373630.1.linga/Input/F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 4483507 Sep 16 10:24 /scratch/9373630.1.linga/Input/F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 252909 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_Placebo_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_Placebo_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 253556 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_Placebo_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:23 /scratch/9373630.1.linga/Input/F_Placebo_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 12643 Sep 16 10:24 /scratch/9373630.1.linga/Input/Up_Genes_DESeq_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 21083 Sep 16 10:24 /scratch/9373630.1.linga/Input/Up_Genes_EdgeR_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Sep 16 10:23 /scratch/9373630.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 41468 Sep 16 10:24 /scratch/9373630.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 39325 Sep 16 10:24 /scratch/9373630.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 Sep 16 10:23 /scratch/9373630.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Sep 16 10:23 /scratch/9373630.1.linga/Input/formatForSegex_ver4.R /scratch/9373630.1.linga/Input/F_CPA_3D_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:23 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:24 .. /scratch/9373630.1.linga/Input/F_Placebo_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:23 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:24 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Sep 16 10:24 . drwxrwxrwt. 41 root root 4.0K Sep 16 10:23 .. -rw-r--r-- 1 kkarri waxmanlab 103 Sep 16 10:23 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 101 Sep 16 10:23 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Sep 16 10:24 Input -rw-r--r-- 1 kkarri waxmanlab 72M Sep 16 10:23 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K Sep 16 10:23 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 47M drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 10:19 . drwxr-xr-x 6 kkarri waxmanlab 4.0K Sep 16 10:18 .. -rw-r--r-- 1 kkarri waxmanlab 292 Sep 16 10:19 DiffExp_7a_Venn_Tables_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 9.1M Sep 16 10:19 DiffExp_v2_GeneBody_F_Placebo_TD229_F_CPA_3D_TD229_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.9K Sep 16 10:19 Down_Genes_DESeq_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 11K Sep 16 10:19 Down_Genes_EdgeR_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.5M Sep 16 10:19 F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.3M Sep 16 10:19 F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.5M Sep 16 10:19 F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.3M Sep 16 10:19 F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 13K Sep 16 10:19 Up_Genes_DESeq_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 21K Sep 16 10:19 Up_Genes_EdgeR_GeneBody_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 41K Sep 16 10:19 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 39K Sep 16 10:19 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Sep 16 10:24:59 EDT 2019 1 minutes and 25 seconds elapsed. ==========================================================