----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08b_DiffExp_2_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana Dataset_Label: GSE118757 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: Exon_Only_Regions.gtf CONDITION_1_NAME: WTM CONDITION_2_NAME: Ezh12M Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: Exon_Only_Regions_Lengths.txt COUNT_DIR: RefSeq_Exon_Only_GTF OUTPUT_PREFIX: DiffExp_v2_Exonic_Only DiffExp_Index: DiffExp_2b COL_SUFFIX: Exonic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Mar 9 19:35:04 EDT 2020 Running on node : scc-tm4 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08b_DiffExp_2_featureCounts Current job ID : 3778606 Current job name : Step_08b_DiffExp_2b Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3778606.1.linga Loading required modules... ------------------------------------------ Sample_DIR: WTM_1 Sample_ID: WTM_1 Description: WTM_1 M_Num: 1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: WTM_1 Sample_DIR: WTM_2 Sample_ID: WTM_2 Description: WTM_2 M_Num: 2 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: WTM_2 Sample_DIR: WTM_3 Sample_ID: WTM_3 Description: WTM_3 M_Num: 3 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: WTM_3 M_Num_Cond1_List: 123 ------------------------------------------ ------------------------------------------ Sample_DIR: Ezh12M_1 Sample_ID: Ezh12M_1 Description: Ezh12M_1 M_Num: 1 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: Ezh12M_1 Sample_DIR: Ezh12M_2 Sample_ID: Ezh12M_2 Description: Ezh12M_2 M_Num: 2 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: Ezh12M_2 M_Num_Cond2_List: 12 ------------------------------------------ ========================================================== 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. number of mapped reads 18376843 18963942 17007806 19470602 20827075 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291285 Mar 9 19:35 /scratch/3778606.1.linga/Input/Exon_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 241500 Mar 9 19:35 /scratch/3778606.1.linga/Input/Ezh12M0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:35 /scratch/3778606.1.linga/Input/Ezh12M0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 243994 Mar 9 19:35 /scratch/3778606.1.linga/Input/Ezh12M1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:35 /scratch/3778606.1.linga/Input/Ezh12M1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 241978 Mar 9 19:35 /scratch/3778606.1.linga/Input/WTM0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:35 /scratch/3778606.1.linga/Input/WTM0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 242323 Mar 9 19:35 /scratch/3778606.1.linga/Input/WTM1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:35 /scratch/3778606.1.linga/Input/WTM1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244020 Mar 9 19:35 /scratch/3778606.1.linga/Input/WTM2.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:35 /scratch/3778606.1.linga/Input/WTM2_num_mapped_reads.txt /scratch/3778606.1.linga/Input/Ezh12M: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 9 19:35 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 9 19:35 .. /scratch/3778606.1.linga/Input/WTM: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 9 19:35 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 9 19:35 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WTM Ezh12M 3 2 Exon_Only_Regions.gtf /scratch/3778606.1.linga/Input DiffExp_v2_Exonic_Only Exon_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WTM" [1] "Ezh12M" [1] 3 [1] 2 [1] "Exon_Only_Regions.gtf" [1] "/scratch/3778606.1.linga/Input" [1] "DiffExp_v2_Exonic_Only" [1] "Exon_Only_Regions_Lengths.txt" [1] "sum1:223343.992988109" "sum1:230134.207110999" "sum1:216655.067468369" [4] "sum1:223377.755855826" [1] "sum2:194097.095819407" "sum2:244503.937572205" "sum2:219300.516695806" load GTF file ... parse attributes ... [1] "output file is in: /scratch/3778606.1.linga/Input/DiffExp_v2_Exonic_Only_WTM_Ezh12M.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Exonic_Only_WTM_Ezh12M.txt Ezh12M_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_Exonic_Only_forSEGEXUpload 1 Exonic_Only Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_Exonic_Only_WTM_Ezh12M.txt Ezh12M_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_Exonic_Only_forSEGEXUpload 1 Exonic_Only ========================================================== Comparison_Info: Ezh12M_GSE118757_12_WTM_GSE118757_123 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Ezh12M_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Exonic_Only'_'Ezh12M_GSE118757_12_WTM_GSE118757_123 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Ezh12M_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 391 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 159 7 [1] "Check out Up_Genes_DESeq_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt!" [1] "Check out Down_Genes_DESeq_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt!" Rscript Diff_Genes.R Ezh12M_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Exonic_Only'_'Ezh12M_GSE118757_12_WTM_GSE118757_123 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Ezh12M_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 633 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 190 7 [1] "Check out Up_Genes_EdgeR_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt!" [1] "Check out Down_Genes_EdgeR_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt Down_Genes_EdgeR_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt Exonic_Only_Counting DiffExp_2b [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt" [1] "Subtitle:" [1] "Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2b" [1] "-----------------" [1] "Down.DESeq.Exonic_Only.HTSeq" [1] "Down.EdgeR.Exonic_Only.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_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt Up_Genes_EdgeR_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt Exonic_Only_Counting DiffExp_2b [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt" [1] "Subtitle:" [1] "Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2b" [1] "-----------------" [1] "Up.DESeq.Exonic_Only.HTSeq" [1] "Up.EdgeR.Exonic_Only.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 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 314 Mar 9 19:35 /scratch/3778606.1.linga/Input/DiffExp_2b_Venn_Tables_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 9043369 Mar 9 19:35 /scratch/3778606.1.linga/Input/DiffExp_v2_Exonic_Only_WTM_Ezh12M.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Mar 9 19:35 /scratch/3778606.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 21435 Mar 9 19:35 /scratch/3778606.1.linga/Input/Down_Genes_DESeq_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 22171 Mar 9 19:35 /scratch/3778606.1.linga/Input/Down_Genes_EdgeR_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 291285 Mar 9 19:35 /scratch/3778606.1.linga/Input/Exon_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 241500 Mar 9 19:35 /scratch/3778606.1.linga/Input/Ezh12M0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:35 /scratch/3778606.1.linga/Input/Ezh12M0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 243994 Mar 9 19:35 /scratch/3778606.1.linga/Input/Ezh12M1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:35 /scratch/3778606.1.linga/Input/Ezh12M1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 4749677 Mar 9 19:35 /scratch/3778606.1.linga/Input/Ezh12M_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 6661240 Mar 9 19:35 /scratch/3778606.1.linga/Input/Ezh12M_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 4798069 Mar 9 19:35 /scratch/3778606.1.linga/Input/Ezh12M_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_Exonic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 6709632 Mar 9 19:35 /scratch/3778606.1.linga/Input/Ezh12M_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_Exonic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 66015 Mar 9 19:35 /scratch/3778606.1.linga/Input/Up_Genes_DESeq_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 156783 Mar 9 19:35 /scratch/3778606.1.linga/Input/Up_Genes_EdgeR_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Mar 9 19:35 /scratch/3778606.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 43895 Mar 9 19:35 /scratch/3778606.1.linga/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 41011 Mar 9 19:35 /scratch/3778606.1.linga/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 241978 Mar 9 19:35 /scratch/3778606.1.linga/Input/WTM0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:35 /scratch/3778606.1.linga/Input/WTM0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 242323 Mar 9 19:35 /scratch/3778606.1.linga/Input/WTM1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:35 /scratch/3778606.1.linga/Input/WTM1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244020 Mar 9 19:35 /scratch/3778606.1.linga/Input/WTM2.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:35 /scratch/3778606.1.linga/Input/WTM2_num_mapped_reads.txt -rwxr-xr-x 1 kkarri waxmanlab 3925 Mar 9 19:35 /scratch/3778606.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Mar 9 19:35 /scratch/3778606.1.linga/Input/formatForSegex_ver4.R /scratch/3778606.1.linga/Input/Ezh12M: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 9 19:35 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 9 19:35 .. /scratch/3778606.1.linga/Input/WTM: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 9 19:35 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 9 19:35 .. ========================================================== List files in scratch total 19M drwx------ 3 kkarri waxmanlab 4.0K Mar 9 19:35 . drwxrwxrwt. 18 root root 4.0K Mar 9 19:35 .. -rw-r--r-- 1 kkarri waxmanlab 87 Mar 9 19:35 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 87 Mar 9 19:35 Condition_2.txt -rw-r--r-- 1 kkarri waxmanlab 19M Mar 9 19:35 Exon_Only_Regions.gtf drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 9 19:35 Input -rwxr-xr-x 1 kkarri waxmanlab 17K Mar 9 19:35 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 65M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 9 19:28 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 9 19:27 .. -rw-r--r-- 1 kkarri waxmanlab 314 Mar 9 19:28 DiffExp_2b_Venn_Tables_Ezh12M_GSE118757_12_WTM_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 8.7M Mar 9 19:28 DiffExp_v2_Exonic_Only_WTM_Ezh12M_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 21K Mar 9 19:28 Down_Genes_DESeq_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 22K Mar 9 19:28 Down_Genes_EdgeR_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.6M Mar 9 19:28 Ezh12M_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 6.4M Mar 9 19:28 Ezh12M_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.6M Mar 9 19:28 Ezh12M_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_Exonic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 6.4M Mar 9 19:28 Ezh12M_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_Exonic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 65K Mar 9 19:28 Up_Genes_DESeq_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 154K Mar 9 19:28 Up_Genes_EdgeR_Exonic_Only_Ezh12M_GSE118757_12_WTM_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 43K Mar 9 19:28 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 41K Mar 9 19:28 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Mar 9 19:35:58 EDT 2020 0 minutes and 54 seconds elapsed. ==========================================================