----------------------- 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_9_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_2cycle_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_9a COL_SUFFIX: GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Sep 16 10:31:41 EDT 2019 Running on node : scc-kb5 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/09b_DiffExp_9_featureCounts Current job ID : 9373669 Current job name : Step_09b_DiffExp_9a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9373669.1.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_M30 Sample_ID: G170_M30 Description: F_CPA_2_cycle11_TD229 M_Num: M30 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G170_M30 Sample_DIR: G170_M31 Sample_ID: G170_M31 Description: F_CPA_2_cycle12_TD229 M_Num: M31 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G170_M31 M_Num_Cond2_List: M30M31 ------------------------------------------ ========================================================== 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 35703972 18726093 44524767 45401633 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291522 Sep 16 10:31 /scratch/9373669.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 253108 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_CPA_2cycle_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_CPA_2cycle_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249010 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_CPA_2cycle_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_CPA_2cycle_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 252909 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_Placebo_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_Placebo_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 253556 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_Placebo_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_Placebo_TD2291_num_mapped_reads.txt /scratch/9373669.1.linga/Input/F_CPA_2cycle_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:31 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:31 .. /scratch/9373669.1.linga/Input/F_Placebo_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:31 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:31 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R F_Placebo_TD229 F_CPA_2cycle_TD229 2 2 RefSeq_GeneBody.gtf /scratch/9373669.1.linga/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "F_Placebo_TD229" [1] "F_CPA_2cycle_TD229" [1] 2 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/9373669.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" [1] "sum1:287182.057180504" "sum1:252675.815460196" "sum1:269928.93632035" [1] "sum2:270174.900929823" "sum2:291386.294132435" "sum2:280780.597531129" load GTF file ... parse attributes ... [1] "output file is in: /scratch/9373669.1.linga/Input/DiffExp_v2_GeneBody_F_Placebo_TD229_F_CPA_2cycle_TD229.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_F_Placebo_TD229_F_CPA_2cycle_TD229.txt F_CPA_2cycle_TD229_G170_M30M31_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_2cycle_TD229.txt F_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== Comparison_Info: F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R F_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_CPA_2cycle_TD229_G170_M30M31_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_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 2622 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 782 7 [1] "Check out Up_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt!" [1] "Check out Down_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt!" Rscript Diff_Genes.R F_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_CPA_2cycle_TD229_G170_M30M31_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_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 3064 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 749 7 [1] "Check out Up_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt!" [1] "Check out Down_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_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_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt Down_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt GeneBody_Counting DiffExp_9a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_9a" [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_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt Up_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt GeneBody_Counting DiffExp_9a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_9a" [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_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 299 Sep 16 10:33 /scratch/9373669.1.linga/Input/DiffExp_9a_Venn_Tables_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 9858003 Sep 16 10:33 /scratch/9373669.1.linga/Input/DiffExp_v2_GeneBody_F_Placebo_TD229_F_CPA_2cycle_TD229.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Sep 16 10:31 /scratch/9373669.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 82659 Sep 16 10:33 /scratch/9373669.1.linga/Input/Down_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 71724 Sep 16 10:33 /scratch/9373669.1.linga/Input/Down_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 291522 Sep 16 10:31 /scratch/9373669.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 253108 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_CPA_2cycle_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_CPA_2cycle_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 249010 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_CPA_2cycle_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_CPA_2cycle_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 5136832 Sep 16 10:33 /scratch/9373669.1.linga/Input/F_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 3878588 Sep 16 10:33 /scratch/9373669.1.linga/Input/F_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 5161027 Sep 16 10:33 /scratch/9373669.1.linga/Input/F_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 3902783 Sep 16 10:33 /scratch/9373669.1.linga/Input/F_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 252909 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_Placebo_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_Placebo_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 253556 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_Placebo_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 16 10:31 /scratch/9373669.1.linga/Input/F_Placebo_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 497132 Sep 16 10:33 /scratch/9373669.1.linga/Input/Up_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 415791 Sep 16 10:33 /scratch/9373669.1.linga/Input/Up_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Sep 16 10:31 /scratch/9373669.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 43569 Sep 16 10:33 /scratch/9373669.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 40548 Sep 16 10:33 /scratch/9373669.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 Sep 16 10:31 /scratch/9373669.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Sep 16 10:31 /scratch/9373669.1.linga/Input/formatForSegex_ver4.R /scratch/9373669.1.linga/Input/F_CPA_2cycle_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:31 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:33 .. /scratch/9373669.1.linga/Input/F_Placebo_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 10:31 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 10:33 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Sep 16 10:33 . drwxrwxrwt. 39 root root 4.0K Sep 16 10:31 .. -rw-r--r-- 1 kkarri waxmanlab 103 Sep 16 10:31 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 113 Sep 16 10:31 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Sep 16 10:33 Input -rw-r--r-- 1 kkarri waxmanlab 72M Sep 16 10:31 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K Sep 16 10:31 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 49M drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 10:27 . drwxr-xr-x 6 kkarri waxmanlab 4.0K Sep 16 10:26 .. -rw-r--r-- 1 kkarri waxmanlab 299 Sep 16 10:27 DiffExp_9a_Venn_Tables_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 9.5M Sep 16 10:27 DiffExp_v2_GeneBody_F_Placebo_TD229_F_CPA_2cycle_TD229_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 81K Sep 16 10:27 Down_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 71K Sep 16 10:27 Down_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.9M Sep 16 10:27 F_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.7M Sep 16 10:27 F_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.0M Sep 16 10:27 F_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.8M Sep 16 10:27 F_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 486K Sep 16 10:27 Up_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 407K Sep 16 10:27 Up_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 43K Sep 16 10:27 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 40K Sep 16 10:27 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Sep 16 10:33:15 EDT 2019 1 minutes and 34 seconds elapsed. ==========================================================