----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/09a_DiffExp_4_HTSeq Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_Env Dataset_Label: G123 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: Female_27h_Vehicle_G123_M13M14 CONDITION_2_NAME: Female_27h_TCPOBOP_G123_M15M16 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_4c COL_SUFFIX: Intronic_Only COUNT_PROGRAM: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri Feb 22 12:33:46 EST 2019 Running on node : scc-kb3 Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/09a_DiffExp_4_HTSeq Current job ID : 2972972 Current job name : Step_09a_DiffExp_4c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/2972972.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G123_M13 Sample_ID: G123_M13 Description: Female_27h_Vehicle_1 M_Num: M13 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G123_M13 Sample_DIR: G123_M14 Sample_ID: G123_M14 Description: Female_27h_Vehicle_2 M_Num: M14 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G123_M14 M_Num_Cond1_List: M13M14 ------------------------------------------ ------------------------------------------ Sample_DIR: G123_M15 Sample_ID: G123_M15 Description: Female_27h_TCPOBOP_1 M_Num: M15 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G123_M15 Sample_DIR: G123_M16 Sample_ID: G123_M16 Description: Female_27h_TCPOBOP_2 M_Num: M16 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G123_M16 M_Num_Cond2_List: M15M16 ------------------------------------------ ========================================================== 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 29753199 41817533 35844349 26909636 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 245918 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_TCPOBOP_G123_M15M160.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_TCPOBOP_G123_M15M160_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247479 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_TCPOBOP_G123_M15M161.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_TCPOBOP_G123_M15M161_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 245915 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_Vehicle_G123_M13M140.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_Vehicle_G123_M13M140_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244160 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_Vehicle_G123_M13M141.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_Vehicle_G123_M13M141_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Feb 22 12:33 /scratch/2972972.1.linga/Input/Intron_Only_Regions_Lengths.txt /scratch/2972972.1.linga/Input/Female_27h_TCPOBOP_G123_M15M16: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Feb 22 12:33 . drwxr-xr-x 4 kkarri waxmanlab 4096 Feb 22 12:33 .. /scratch/2972972.1.linga/Input/Female_27h_Vehicle_G123_M13M14: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Feb 22 12:33 . drwxr-xr-x 4 kkarri waxmanlab 4096 Feb 22 12:33 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Female_27h_Vehicle_G123_M13M14 Female_27h_TCPOBOP_G123_M15M16 2 2 RefSeq_GeneBody.gtf /scratch/2972972.1.linga/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Female_27h_Vehicle_G123_M13M14" [1] "Female_27h_TCPOBOP_G123_M15M16" [1] 2 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/2972972.1.linga/Input" [1] "DiffExp_v2_Intronic_Only" [1] "Intron_Only_Regions_Lengths.txt" load GTF file ... parse attributes ... [1] "output file is in: /scratch/2972972.1.linga/Input/DiffExp_v2_Intronic_Only_Female_27h_Vehicle_G123_M13M14_Female_27h_TCPOBOP_G123_M15M16.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_Female_27h_Vehicle_G123_M13M14_Female_27h_TCPOBOP_G123_M15M16.txt Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_G123_M13M14_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== Comparison_Info: Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_G123_M13M14_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_G123_M13M14_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_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 376 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 235 7 [1] "Check out Up_Genes_DESeq_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt!" [1] "Check out Down_Genes_DESeq_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt!" Rscript Diff_Genes.R Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_G123_M13M14_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_G123_M13M14_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_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 528 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 287 7 [1] "Check out Up_Genes_EdgeR_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt!" [1] "Check out Down_Genes_EdgeR_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt Down_Genes_EdgeR_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt Intronic_Only_Counting DiffExp_4c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_4c" [1] "-----------------" [1] "Down.DESeq.Intronic_Only.HTSeq" [1] "Down.EdgeR.Intronic_Only.HTSeq" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt Up_Genes_EdgeR_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt Intronic_Only_Counting DiffExp_4c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_4c" [1] "-----------------" [1] "Up.DESeq.Intronic_Only.HTSeq" [1] "Up.EdgeR.Intronic_Only.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 Feb 22 12:36 /scratch/2972972.1.linga/Input/DiffExp_4c_Venn_Tables_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt -rw-r--r-- 1 kkarri waxmanlab 7080313 Feb 22 12:36 /scratch/2972972.1.linga/Input/DiffExp_v2_Intronic_Only_Female_27h_Vehicle_G123_M13M14_Female_27h_TCPOBOP_G123_M15M16.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Feb 22 12:33 /scratch/2972972.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 26946 Feb 22 12:36 /scratch/2972972.1.linga/Input/Down_Genes_DESeq_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt -rw-r--r-- 1 kkarri waxmanlab 33746 Feb 22 12:36 /scratch/2972972.1.linga/Input/Down_Genes_EdgeR_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt -rw-r--r-- 1 kkarri waxmanlab 245918 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_TCPOBOP_G123_M15M160.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_TCPOBOP_G123_M15M160_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 247479 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_TCPOBOP_G123_M15M161.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_TCPOBOP_G123_M15M161_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2378436 Feb 22 12:36 /scratch/2972972.1.linga/Input/Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_G123_M13M14_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2402633 Feb 22 12:36 /scratch/2972972.1.linga/Input/Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_G123_M13M14_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 245915 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_Vehicle_G123_M13M140.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_Vehicle_G123_M13M140_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244160 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_Vehicle_G123_M13M141.out -rw-r--r-- 1 kkarri waxmanlab 9 Feb 22 12:33 /scratch/2972972.1.linga/Input/Female_27h_Vehicle_G123_M13M141_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Feb 22 12:33 /scratch/2972972.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 27661 Feb 22 12:36 /scratch/2972972.1.linga/Input/Up_Genes_DESeq_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt -rw-r--r-- 1 kkarri waxmanlab 40840 Feb 22 12:36 /scratch/2972972.1.linga/Input/Up_Genes_EdgeR_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14.txt -rwxr-xr-x 1 kkarri waxmanlab 9554 Feb 22 12:33 /scratch/2972972.1.linga/Input/Venn_Diff_Genes.R -rwxr-xr-x 1 kkarri waxmanlab 3925 Feb 22 12:33 /scratch/2972972.1.linga/Input/formatForSegex_ver3.R /scratch/2972972.1.linga/Input/Female_27h_TCPOBOP_G123_M15M16: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Feb 22 12:33 . drwxr-xr-x 4 kkarri waxmanlab 4096 Feb 22 12:36 .. /scratch/2972972.1.linga/Input/Female_27h_Vehicle_G123_M13M14: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Feb 22 12:33 . drwxr-xr-x 4 kkarri waxmanlab 4096 Feb 22 12:36 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Feb 22 12:36 . drwxrwxrwt. 15 root root 112K Feb 22 12:35 .. -rw-r--r-- 1 kkarri waxmanlab 111 Feb 22 12:33 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 111 Feb 22 12:33 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Feb 22 12:36 Input -rw-r--r-- 1 kkarri waxmanlab 72M Feb 22 12:33 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 16K Feb 22 12:33 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 11M drwxr-sr-x 2 kkarri waxmanlab 32K Feb 22 12:36 . drwxr-sr-x 6 kkarri waxmanlab 32K Feb 22 12:33 .. -rw-r--r-- 1 kkarri waxmanlab 0 Feb 22 12:36 DiffExp_4c_Venn_Tables_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 6.8M Feb 22 12:36 DiffExp_v2_Intronic_Only_Female_27h_Vehicle_G123_M13M14_Female_27h_TCPOBOP_G123_M15M16_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 27K Feb 22 12:36 Down_Genes_DESeq_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 33K Feb 22 12:36 Down_Genes_EdgeR_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Feb 22 12:36 Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_G123_M13M14_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Feb 22 12:36 Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_vs_Female_27h_Vehicle_G123_M13M14_G123_M13M14_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 28K Feb 22 12:36 Up_Genes_DESeq_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14_HTSeq.txt -rw-r--r-- 1 kkarri waxmanlab 40K Feb 22 12:36 Up_Genes_EdgeR_Intronic_Only_Female_27h_TCPOBOP_G123_M15M16_G123_M15M16_Female_27h_Vehicle_G123_M13M14_G123_M13M14_HTSeq.txt ========================================================== ========================================================== Finished on : Fri Feb 22 12:36:08 EST 2019 2 minutes and 22 seconds elapsed. ==========================================================