----------------------- 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_5_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: RefSeq_GeneBody.gtf CONDITION_1_NAME: M2WTM CONDITION_2_NAME: M2Ezh12M Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: Intron_Only_Regions_Lengths.txt COUNT_DIR: RefSeq_Intron_GTF OUTPUT_PREFIX: DiffExp_v2_Intronic_Only DiffExp_Index: DiffExp_5c COL_SUFFIX: Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Mar 9 19:37:09 EDT 2020 Running on node : scc-wb1 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08b_DiffExp_5_featureCounts Current job ID : 3778621 Current job name : Step_08b_DiffExp_5c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3778621.1.w-long Loading required modules... ------------------------------------------ Sample_DIR: M2WTM_1 Sample_ID: M2WTM_1 Description: M2WTM_1 M_Num: 1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: M2WTM_1 Sample_DIR: M2WTM_2 Sample_ID: M2WTM_2 Description: M2WTM_2 M_Num: 2 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: M2WTM_2 M_Num_Cond1_List: 12 ------------------------------------------ ------------------------------------------ Sample_DIR: M2Ezh12M_1 Sample_ID: M2Ezh12M_1 Description: M2Ezh12M_1 M_Num: 1 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: M2Ezh12M_1 Sample_DIR: M2Ezh12M_2 Sample_ID: M2Ezh12M_2 Description: M2Ezh12M_2 M_Num: 2 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: M2Ezh12M_2 Sample_DIR: M2Ezh12M_3 Sample_ID: M2Ezh12M_3 Description: M2Ezh12M_3 M_Num: 3 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: M2Ezh12M_3 M_Num_Cond2_List: 123 ------------------------------------------ ========================================================== 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. Counting program: Not HTSeq No lines removed. number of mapped reads 17521399 17379424 9182533 16398557 17132473 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 300238 Mar 9 19:37 /scratch/3778621.1.w-long/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 242107 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2Ezh12M0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2Ezh12M0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 240403 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2Ezh12M1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2Ezh12M1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235314 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2Ezh12M2.out -rw-r--r-- 1 kkarri waxmanlab 8 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2Ezh12M2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 234877 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2WTM0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2WTM0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 234818 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2WTM1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2WTM1_num_mapped_reads.txt /scratch/3778621.1.w-long/Input/M2Ezh12M: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 9 19:37 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 9 19:37 .. /scratch/3778621.1.w-long/Input/M2WTM: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 9 19:37 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 9 19:37 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R M2WTM M2Ezh12M 2 3 RefSeq_GeneBody.gtf /scratch/3778621.1.w-long/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "M2WTM" [1] "M2Ezh12M" [1] 2 [1] 3 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/3778621.1.w-long/Input" [1] "DiffExp_v2_Intronic_Only" [1] "Intron_Only_Regions_Lengths.txt" [1] "sum1:NaN" "sum1:NaN" "sum1:NaN" [1] "sum2:NaN" "sum2:NaN" "sum2:NaN" "sum2:NaN" load GTF file ... parse attributes ... [1] "output file is in: /scratch/3778621.1.w-long/Input/DiffExp_v2_Intronic_Only_M2WTM_M2Ezh12M.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_M2WTM_M2Ezh12M.txt M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_Intronic_Only_M2WTM_M2Ezh12M.txt M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== Comparison_Info: M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 397 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 534 7 [1] "Check out Up_Genes_DESeq_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt!" [1] "Check out Down_Genes_DESeq_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt!" Rscript Diff_Genes.R M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 622 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 645 7 [1] "Check out Up_Genes_EdgeR_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt!" [1] "Check out Down_Genes_EdgeR_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt Down_Genes_EdgeR_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt Intronic_Only_Counting DiffExp_5c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_5c" [1] "-----------------" [1] "Down.DESeq.Intronic_Only.HTSeq" [1] "Down.EdgeR.Intronic_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_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt Up_Genes_EdgeR_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt Intronic_Only_Counting DiffExp_5c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_5c" [1] "-----------------" [1] "Up.DESeq.Intronic_Only.HTSeq" [1] "Up.EdgeR.Intronic_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 327 Mar 9 19:38 /scratch/3778621.1.w-long/Input/DiffExp_5c_Venn_Tables_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 7942251 Mar 9 19:38 /scratch/3778621.1.w-long/Input/DiffExp_v2_Intronic_Only_M2WTM_M2Ezh12M.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Mar 9 19:37 /scratch/3778621.1.w-long/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 120960 Mar 9 19:38 /scratch/3778621.1.w-long/Input/Down_Genes_DESeq_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 129317 Mar 9 19:38 /scratch/3778621.1.w-long/Input/Down_Genes_EdgeR_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Mar 9 19:37 /scratch/3778621.1.w-long/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 242107 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2Ezh12M0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2Ezh12M0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 240403 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2Ezh12M1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2Ezh12M1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 235314 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2Ezh12M2.out -rw-r--r-- 1 kkarri waxmanlab 8 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2Ezh12M2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 6128924 Mar 9 19:38 /scratch/3778621.1.w-long/Input/M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 5475605 Mar 9 19:38 /scratch/3778621.1.w-long/Input/M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 5451406 Mar 9 19:38 /scratch/3778621.1.w-long/Input/M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 4798087 Mar 9 19:38 /scratch/3778621.1.w-long/Input/M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 234877 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2WTM0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2WTM0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 234818 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2WTM1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:37 /scratch/3778621.1.w-long/Input/M2WTM1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 38088 Mar 9 19:38 /scratch/3778621.1.w-long/Input/Up_Genes_DESeq_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 69007 Mar 9 19:38 /scratch/3778621.1.w-long/Input/Up_Genes_EdgeR_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Mar 9 19:37 /scratch/3778621.1.w-long/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 43534 Mar 9 19:38 /scratch/3778621.1.w-long/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 40853 Mar 9 19:38 /scratch/3778621.1.w-long/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 Mar 9 19:37 /scratch/3778621.1.w-long/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Mar 9 19:37 /scratch/3778621.1.w-long/Input/formatForSegex_ver4.R /scratch/3778621.1.w-long/Input/M2Ezh12M: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 9 19:37 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 9 19:38 .. /scratch/3778621.1.w-long/Input/M2WTM: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 9 19:37 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 9 19:38 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Mar 9 19:38 . drwxrwxrwt. 19 root root 4.0K Mar 9 19:38 .. -rw-r--r-- 1 kkarri waxmanlab 81 Mar 9 19:37 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 132 Mar 9 19:37 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 9 19:38 Input -rw-r--r-- 1 kkarri waxmanlab 72M Mar 9 19:37 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K Mar 9 19:37 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 66M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 9 19:30 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 9 19:29 .. -rw-r--r-- 1 kkarri waxmanlab 327 Mar 9 19:30 DiffExp_5c_Venn_Tables_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 7.6M Mar 9 19:30 DiffExp_v2_Intronic_Only_M2WTM_M2Ezh12M_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 119K Mar 9 19:30 Down_Genes_DESeq_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 127K Mar 9 19:30 Down_Genes_EdgeR_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.9M Mar 9 19:30 M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.3M Mar 9 19:30 M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.2M Mar 9 19:30 M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.6M Mar 9 19:30 M2Ezh12M_GSE118757_123_vs_M2WTM_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 38K Mar 9 19:30 Up_Genes_DESeq_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 68K Mar 9 19:30 Up_Genes_EdgeR_Intronic_Only_M2Ezh12M_GSE118757_123_M2WTM_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 43K Mar 9 19:30 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 40K Mar 9 19:30 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Mar 9 19:38:19 EDT 2020 1 minutes and 10 seconds elapsed. 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