----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/09b_DiffExp_1_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV Dataset_Label: G166_Env GTF_Files_DIR: /restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: M_control CONDITION_2_NAME: M_TCPO_1d Lengths_DIR: /restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/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 : Wed Apr 24 20:22:00 EDT 2019 Running on node : scc-tl4 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/09b_DiffExp_1_featureCounts Current job ID : 5561626 Current job name : Step_09b_DiffExp_1c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5561626.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G166_M1 Sample_ID: G166_M1 Description: M1_control M_Num: M1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G166_M1 Sample_DIR: G166_M2 Sample_ID: G166_M2 Description: M2_control M_Num: M2 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G166_M2 M_Num_Cond1_List: M1M2 ------------------------------------------ ------------------------------------------ Sample_DIR: G166_M4 Sample_ID: G166_M4 Description: Male_TCPOBOP_1d M_Num: M4 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G166_M4 Sample_DIR: G166_M5 Sample_ID: G166_M5 Description: Male_TCPOBOP_1d M_Num: M5 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G166_M5 Sample_DIR: G166_M6 Sample_ID: G166_M6 Description: Male_TCPOBOP_1d M_Num: M6 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G166_M6 M_Num_Cond2_List: M4M5M6 ------------------------------------------ ========================================================== 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 19234636 37112559 3293793 9260240 51593070 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 300238 Apr 24 20:22 /scratch/5561626.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 244315 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_TCPO_1d0.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_TCPO_1d0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247537 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_TCPO_1d1.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_TCPO_1d1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 232476 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_TCPO_1d2.out -rw-r--r-- 1 kkarri waxmanlab 8 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_TCPO_1d2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 240356 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_control0.out -rw-r--r-- 1 kkarri waxmanlab 8 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_control0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 250012 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_control1.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_control1_num_mapped_reads.txt /scratch/5561626.1.linga/Input/M_TCPO_1d: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 24 20:22 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 24 20:22 .. /scratch/5561626.1.linga/Input/M_control: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 24 20:22 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 24 20:22 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R M_control M_TCPO_1d 2 3 RefSeq_GeneBody.gtf /scratch/5561626.1.linga/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "M_control" [1] "M_TCPO_1d" [1] 2 [1] 3 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/5561626.1.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" load GTF file ... parse attributes ... [1] "output file is in: /scratch/5561626.1.linga/Input/DiffExp_v2_Intronic_Only_M_control_M_TCPO_1d.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_M_control_M_TCPO_1d.txt M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_Intronic_Only_M_control_M_TCPO_1d.txt M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== Comparison_Info: M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_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_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 23 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 0 7 [1] "Check out Up_Genes_DESeq_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt!" [1] "Check out Down_Genes_DESeq_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt!" Rscript Diff_Genes.R M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_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_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 7 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 0 7 [1] "Check out Up_Genes_EdgeR_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt!" [1] "Check out Down_Genes_EdgeR_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt Down_Genes_EdgeR_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt Intronic_Only_Counting DiffExp_1c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.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" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt Up_Genes_EdgeR_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt Intronic_Only_Counting DiffExp_1c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.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 #---------------------------------------------------------------------------------- Comparison_Info: M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 157 Apr 24 20:23 /scratch/5561626.1.linga/Input/DiffExp_1c_Venn_Tables_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 8371272 Apr 24 20:23 /scratch/5561626.1.linga/Input/DiffExp_v2_Intronic_Only_M_control_M_TCPO_1d.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Apr 24 20:22 /scratch/5561626.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 178 Apr 24 20:23 /scratch/5561626.1.linga/Input/Down_Genes_DESeq_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 178 Apr 24 20:23 /scratch/5561626.1.linga/Input/Down_Genes_EdgeR_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Apr 24 20:22 /scratch/5561626.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 244315 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_TCPO_1d0.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_TCPO_1d0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247537 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_TCPO_1d1.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_TCPO_1d1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 232476 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_TCPO_1d2.out -rw-r--r-- 1 kkarri waxmanlab 8 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_TCPO_1d2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 3249486 Apr 24 20:23 /scratch/5561626.1.linga/Input/M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2692955 Apr 24 20:23 /scratch/5561626.1.linga/Input/M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 2571968 Apr 24 20:23 /scratch/5561626.1.linga/Input/M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2015437 Apr 24 20:23 /scratch/5561626.1.linga/Input/M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 240356 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_control0.out -rw-r--r-- 1 kkarri waxmanlab 8 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_control0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 250012 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_control1.out -rw-r--r-- 1 kkarri waxmanlab 9 Apr 24 20:22 /scratch/5561626.1.linga/Input/M_control1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2642 Apr 24 20:23 /scratch/5561626.1.linga/Input/Up_Genes_DESeq_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt -rw-r--r-- 1 kkarri waxmanlab 715 Apr 24 20:23 /scratch/5561626.1.linga/Input/Up_Genes_EdgeR_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Apr 24 20:22 /scratch/5561626.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 35282 Apr 24 20:23 /scratch/5561626.1.linga/Input/Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 3925 Apr 24 20:22 /scratch/5561626.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Apr 24 20:22 /scratch/5561626.1.linga/Input/formatForSegex_ver4.R /scratch/5561626.1.linga/Input/M_TCPO_1d: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 24 20:22 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 24 20:23 .. /scratch/5561626.1.linga/Input/M_control: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 24 20:22 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 24 20:23 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Apr 24 20:23 . drwxrwxrwt. 18 root root 40K Apr 24 20:22 .. -rw-r--r-- 1 kkarri waxmanlab 87 Apr 24 20:22 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 129 Apr 24 20:22 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Apr 24 20:23 Input -rw-r--r-- 1 kkarri waxmanlab 72M Apr 24 20:22 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K Apr 24 20:22 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 Apr 24 20:18 . drwxr-xr-x 6 kkarri waxmanlab 4.0K Apr 24 20:16 .. -rw-r--r-- 1 kkarri waxmanlab 157 Apr 24 20:18 DiffExp_1c_Venn_Tables_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 8.0M Apr 24 20:18 DiffExp_v2_Intronic_Only_M_control_M_TCPO_1d_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 178 Apr 24 20:18 Down_Genes_DESeq_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 178 Apr 24 20:18 Down_Genes_EdgeR_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.1M Apr 24 20:18 M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.6M Apr 24 20:18 M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.5M Apr 24 20:18 M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.0M Apr 24 20:18 M_TCPO_1d_G166_Env_M4M5M6_vs_M_control_G166_Env_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.6K Apr 24 20:18 Up_Genes_DESeq_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 715 Apr 24 20:18 Up_Genes_EdgeR_Intronic_Only_M_TCPO_1d_G166_Env_M4M5M6_M_control_G166_Env_M1M2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 35K Apr 24 20:18 Venn_Up.DESeq.Intronic_Only.HTSeq.Up.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Wed Apr 24 20:23:46 EDT 2019 1 minutes and 46 seconds elapsed. ==========================================================