----------------------- 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/09a_DiffExp_9_HTSeq 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: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri Sep 6 17:20:00 EDT 2019 Running on node : scc-tm1 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/09a_DiffExp_9_HTSeq Current job ID : 9186277 Current job name : Step_09a_DiffExp_9a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9186277.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G170_M20 Sample_ID: G170_M20 Description: F_Placebo_Pool1_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_Placebo_Pool2_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_M20 Sample_ID: G170_M20 Description: F_Placebo_Pool1_TD229 M_Num: M20 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G170_M20 Sample_DIR: G170_M21 Sample_ID: G170_M21 Description: F_Placebo_Pool2_TD229 M_Num: M21 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G170_M21 M_Num_Cond2_List: M20M21 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 2 NUM_REP_CONDITION1: 2 ========================================================== Renaming input count files Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) number of mapped reads 44524767 45401633 44524767 45401633 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291522 Sep 6 17:20 /scratch/9186277.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 252482 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_CPA_2cycle_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_CPA_2cycle_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 253108 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_CPA_2cycle_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_CPA_2cycle_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 252482 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_Placebo_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_Placebo_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 253108 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_Placebo_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_Placebo_TD2291_num_mapped_reads.txt /scratch/9186277.1.linga/Input/F_CPA_2cycle_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 6 17:20 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 6 17:20 .. /scratch/9186277.1.linga/Input/F_Placebo_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 6 17:20 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 6 17:20 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R F_Placebo_TD229 F_CPA_2cycle_TD229 2 2 RefSeq_GeneBody.gtf /scratch/9186277.1.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/9186277.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" [1] "sum1:261362.801146407" "sum1:230375.801736605" "sum1:245869.301441506" [1] "sum2:261362.801146407" "sum2:230375.801736605" "sum2:245869.301441506" load GTF file ... parse attributes ... [1] "output file is in: /scratch/9186277.1.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_M20M21_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_GeneBody_F_Placebo_TD229_F_CPA_2cycle_TD229.txt F_CPA_2cycle_TD229_G170_M20M21_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== Comparison_Info: F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R F_CPA_2cycle_TD229_G170_M20M21_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_CPA_2cycle_TD229_G170_M20M21_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_M20M21_F_Placebo_TD229_G170_M20M21" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 0 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 0 7 [1] "Check out Up_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21.txt!" [1] "Check out Down_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21.txt!" Rscript Diff_Genes.R F_CPA_2cycle_TD229_G170_M20M21_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_CPA_2cycle_TD229_G170_M20M21_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_M20M21_F_Placebo_TD229_G170_M20M21" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 0 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 0 7 [1] "Check out Up_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21.txt!" [1] "Check out Down_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_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_M20M21_F_Placebo_TD229_G170_M20M21.txt Down_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_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_M20M21_F_Placebo_TD229_G170_M20M21.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_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" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21.txt Up_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_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_M20M21_F_Placebo_TD229_G170_M20M21.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_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" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 0 Sep 6 17:21 /scratch/9186277.1.linga/Input/DiffExp_9a_Venn_Tables_F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 8047352 Sep 6 17:21 /scratch/9186277.1.linga/Input/DiffExp_v2_GeneBody_F_Placebo_TD229_F_CPA_2cycle_TD229.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Sep 6 17:20 /scratch/9186277.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 158 Sep 6 17:21 /scratch/9186277.1.linga/Input/Down_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 158 Sep 6 17:21 /scratch/9186277.1.linga/Input/Down_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 291522 Sep 6 17:20 /scratch/9186277.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 252482 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_CPA_2cycle_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_CPA_2cycle_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 253108 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_CPA_2cycle_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_CPA_2cycle_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 1628267 Sep 6 17:21 /scratch/9186277.1.linga/Input/F_CPA_2cycle_TD229_G170_M20M21_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1192721 Sep 6 17:21 /scratch/9186277.1.linga/Input/F_CPA_2cycle_TD229_G170_M20M21_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 1628265 Sep 6 17:21 /scratch/9186277.1.linga/Input/F_CPA_2cycle_TD229_G170_M20M21_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1192719 Sep 6 17:21 /scratch/9186277.1.linga/Input/F_CPA_2cycle_TD229_G170_M20M21_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 252482 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_Placebo_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_Placebo_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 253108 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_Placebo_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 17:20 /scratch/9186277.1.linga/Input/F_Placebo_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 158 Sep 6 17:21 /scratch/9186277.1.linga/Input/Up_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 158 Sep 6 17:21 /scratch/9186277.1.linga/Input/Up_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 2204 Sep 6 17:21 /scratch/9186277.1.linga/Input/VennDiagram2019-09-06_17-21-47.log -rw-r--r-- 1 kkarri waxmanlab 2204 Sep 6 17:21 /scratch/9186277.1.linga/Input/VennDiagram2019-09-06_17-21-49.log -rwxr-xr-x 1 kkarri waxmanlab 9553 Sep 6 17:20 /scratch/9186277.1.linga/Input/Venn_Diff_Genes.R -rwxr-xr-x 1 kkarri waxmanlab 3925 Sep 6 17:20 /scratch/9186277.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Sep 6 17:20 /scratch/9186277.1.linga/Input/formatForSegex_ver4.R /scratch/9186277.1.linga/Input/F_CPA_2cycle_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 6 17:20 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 6 17:21 .. /scratch/9186277.1.linga/Input/F_Placebo_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 6 17:20 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 6 17:21 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Sep 6 17:21 . drwxrwxrwt. 20 root root 4.0K Sep 6 17:19 .. -rw-r--r-- 1 kkarri waxmanlab 113 Sep 6 17:20 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 113 Sep 6 17:20 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Sep 6 17:21 Input -rw-r--r-- 1 kkarri waxmanlab 72M Sep 6 17:20 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K Sep 6 17:20 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 28M drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 6 17:16 . drwxr-xr-x 6 kkarri waxmanlab 4.0K Sep 6 17:14 .. -rw-r--r-- 1 kkarri waxmanlab 0 Sep 6 17:16 DiffExp_9a_Venn_Tables_F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 7.7M Sep 6 17:16 DiffExp_v2_GeneBody_F_Placebo_TD229_F_CPA_2cycle_TD229_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 158 Sep 6 17:16 Down_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 158 Sep 6 17:16 Down_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 1.6M Sep 6 17:16 F_CPA_2cycle_TD229_G170_M20M21_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 1.2M Sep 6 17:16 F_CPA_2cycle_TD229_G170_M20M21_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 1.6M Sep 6 17:16 F_CPA_2cycle_TD229_G170_M20M21_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 1.2M Sep 6 17:16 F_CPA_2cycle_TD229_G170_M20M21_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 158 Sep 6 17:16 Up_Genes_DESeq_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 158 Sep 6 17:16 Up_Genes_EdgeR_GeneBody_F_CPA_2cycle_TD229_G170_M20M21_F_Placebo_TD229_G170_M20M21_HTSeq.txt ========================================================== ========================================================== Finished on : Fri Sep 6 17:21:52 EDT 2019 1 minutes and 52 seconds elapsed. ==========================================================