----------------------- 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_1_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: WTF CONDITION_2_NAME: Ezh12F 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_1c COL_SUFFIX: Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Mar 9 19:34:07 EDT 2020 Running on node : scc-kb8 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08b_DiffExp_1_featureCounts Current job ID : 3778542 Current job name : Step_08b_DiffExp_1c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3778542.1.linga Loading required modules... ------------------------------------------ Sample_DIR: WTF_1 Sample_ID: WTF_1 Description: WTF_1 M_Num: 1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: WTF_1 Sample_DIR: WTF_2 Sample_ID: WTF_2 Description: WTF_2 M_Num: 2 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: WTF_2 M_Num_Cond1_List: 12 ------------------------------------------ ------------------------------------------ Sample_DIR: Ezh12F_1 Sample_ID: Ezh12F_1 Description: Ezh12F_1 M_Num: 1 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: Ezh12F_1 Sample_DIR: Ezh12F_2 Sample_ID: Ezh12F_2 Description: Ezh12F_2 M_Num: 2 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: Ezh12F_2 Sample_DIR: Ezh12F_3 Sample_ID: Ezh12F_3 Description: Ezh12F_3 M_Num: 3 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: Ezh12F_3 Sample_DIR: Ezh12F_4 Sample_ID: Ezh12F_4 Description: Ezh12F_4 M_Num: 4 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: Ezh12F_4 Sample_DIR: Ezh12F_5 Sample_ID: Ezh12F_5 Description: Ezh12F_5 M_Num: 5 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: Ezh12F_5 M_Num_Cond2_List: 12345 ------------------------------------------ ========================================================== 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. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. number of mapped reads 17458557 19999815 19216346 20730440 18248587 23876814 22256053 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 241718 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 241150 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238866 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F2.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238566 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F3.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F3_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 239603 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F4.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F4_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Mar 9 19:34 /scratch/3778542.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 240235 Mar 9 19:34 /scratch/3778542.1.linga/Input/WTF0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:34 /scratch/3778542.1.linga/Input/WTF0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 239905 Mar 9 19:34 /scratch/3778542.1.linga/Input/WTF1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:34 /scratch/3778542.1.linga/Input/WTF1_num_mapped_reads.txt /scratch/3778542.1.linga/Input/Ezh12F: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 9 19:34 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 9 19:34 .. /scratch/3778542.1.linga/Input/WTF: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 9 19:34 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 9 19:34 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WTF Ezh12F 2 5 RefSeq_GeneBody.gtf /scratch/3778542.1.linga/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WTF" [1] "Ezh12F" [1] 2 [1] 5 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/3778542.1.linga/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" "sum2:NaN" "sum2:NaN" load GTF file ... parse attributes ... [1] "output file is in: /scratch/3778542.1.linga/Input/DiffExp_v2_Intronic_Only_WTF_Ezh12F.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_WTF_Ezh12F.txt Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_Intronic_Only_WTF_Ezh12F.txt Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== Comparison_Info: Ezh12F_GSE118757_12345_WTF_GSE118757_12 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'Ezh12F_GSE118757_12345_WTF_GSE118757_12 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Ezh12F_GSE118757_12345_vs_WTF_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_Ezh12F_GSE118757_12345_WTF_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 254 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 114 7 [1] "Check out Up_Genes_DESeq_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt!" [1] "Check out Down_Genes_DESeq_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt!" Rscript Diff_Genes.R Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'Ezh12F_GSE118757_12345_WTF_GSE118757_12 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Ezh12F_GSE118757_12345_vs_WTF_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_Ezh12F_GSE118757_12345_WTF_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 218 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 150 7 [1] "Check out Up_Genes_EdgeR_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt!" [1] "Check out Down_Genes_EdgeR_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt Down_Genes_EdgeR_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt Intronic_Only_Counting DiffExp_1c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1c" [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_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt Up_Genes_EdgeR_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt Intronic_Only_Counting DiffExp_1c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1c" [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 325 Mar 9 19:35 /scratch/3778542.1.linga/Input/DiffExp_1c_Venn_Tables_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 9486928 Mar 9 19:35 /scratch/3778542.1.linga/Input/DiffExp_v2_Intronic_Only_WTF_Ezh12F.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Mar 9 19:34 /scratch/3778542.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 11459 Mar 9 19:35 /scratch/3778542.1.linga/Input/Down_Genes_DESeq_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 15960 Mar 9 19:35 /scratch/3778542.1.linga/Input/Down_Genes_EdgeR_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 241718 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 241150 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238866 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F2.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238566 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F3.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F3_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 239603 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F4.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:34 /scratch/3778542.1.linga/Input/Ezh12F4_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2983310 Mar 9 19:35 /scratch/3778542.1.linga/Input/Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 3297871 Mar 9 19:35 /scratch/3778542.1.linga/Input/Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 2281595 Mar 9 19:35 /scratch/3778542.1.linga/Input/Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2596156 Mar 9 19:35 /scratch/3778542.1.linga/Input/Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Mar 9 19:34 /scratch/3778542.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 24197 Mar 9 19:35 /scratch/3778542.1.linga/Input/Up_Genes_DESeq_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 23863 Mar 9 19:35 /scratch/3778542.1.linga/Input/Up_Genes_EdgeR_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Mar 9 19:34 /scratch/3778542.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 42434 Mar 9 19:35 /scratch/3778542.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 42007 Mar 9 19:35 /scratch/3778542.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 240235 Mar 9 19:34 /scratch/3778542.1.linga/Input/WTF0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:34 /scratch/3778542.1.linga/Input/WTF0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 239905 Mar 9 19:34 /scratch/3778542.1.linga/Input/WTF1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 9 19:34 /scratch/3778542.1.linga/Input/WTF1_num_mapped_reads.txt -rwxr-xr-x 1 kkarri waxmanlab 3925 Mar 9 19:34 /scratch/3778542.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Mar 9 19:34 /scratch/3778542.1.linga/Input/formatForSegex_ver4.R /scratch/3778542.1.linga/Input/Ezh12F: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 9 19:34 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 9 19:35 .. /scratch/3778542.1.linga/Input/WTF: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 9 19:34 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 9 19:35 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Mar 9 19:35 . drwxrwxrwt. 23 root root 4.0K Mar 9 19:36 .. -rw-r--r-- 1 kkarri waxmanlab 69 Mar 9 19:34 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 168 Mar 9 19:34 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 9 19:35 Input -rw-r--r-- 1 kkarri waxmanlab 72M Mar 9 19:34 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K Mar 9 19:34 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 30M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 9 19:28 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 9 19:26 .. -rw-r--r-- 1 kkarri waxmanlab 325 Mar 9 19:28 DiffExp_1c_Venn_Tables_Ezh12F_GSE118757_12345_WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 9.1M Mar 9 19:28 DiffExp_v2_Intronic_Only_WTF_Ezh12F_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 12K Mar 9 19:28 Down_Genes_DESeq_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 16K Mar 9 19:28 Down_Genes_EdgeR_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.9M Mar 9 19:28 Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 9 19:28 Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.2M Mar 9 19:28 Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.5M Mar 9 19:28 Ezh12F_GSE118757_12345_vs_WTF_GSE118757_12_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 24K Mar 9 19:28 Up_Genes_DESeq_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 24K Mar 9 19:28 Up_Genes_EdgeR_Intronic_Only_Ezh12F_GSE118757_12345_WTF_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 42K Mar 9 19:28 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 42K Mar 9 19:28 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Mar 9 19:36:04 EDT 2020 1 minutes and 57 seconds elapsed. ==========================================================