----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/09a_DiffExp_1_HTSeq Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples Dataset_Label: G167 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: WT_Con CONDITION_2_NAME: WT_24h_WY 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: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed Jul 18 12:04:49 EDT 2018 Running on node : scc-ka7 Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/09a_DiffExp_1_HTSeq Current job ID : 6965110 Current job name : Step_09a_DiffExp_1c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/6965110.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G167_M1 Sample_ID: G167_M1 Description: WT_Con1 M_Num: M1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G167_M1 Sample_DIR: G167_M2 Sample_ID: G167_M2 Description: WT_Con2 M_Num: M2 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G167_M2 Sample_DIR: G167_M3 Sample_ID: G167_M3 Description: WT_Con3 M_Num: M3 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G167_M3 M_Num_Cond1_List: M1M2M3 ------------------------------------------ ------------------------------------------ Sample_DIR: G167_M7 Sample_ID: G167_M7 Description: WT_24h_WY1 M_Num: M7 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G167_M7 Sample_DIR: G167_M8 Sample_ID: G167_M8 Description: WT_24h_WY2 M_Num: M8 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G167_M8 Sample_DIR: G167_M9 Sample_ID: G167_M9 Description: WT_24h_WY3 M_Num: M9 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G167_M9 M_Num_Cond2_List: M7M8M9 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 3 NUM_REP_CONDITION1: 3 ========================================================== 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) Counting program: HTSeq Removing last 5 lines (remove special counters) Counting program: HTSeq Removing last 5 lines (remove special counters) number of mapped reads 19181043 16953572 18883194 20905454 17099690 12968997 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 300238 Jul 18 12:04 /scratch/6965110.1.linga/Input/Intron_Only_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 37854 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_24h_WY0.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_24h_WY0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 37854 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_24h_WY1.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_24h_WY1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 37854 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_24h_WY2.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_24h_WY2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 37854 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_Con0.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_Con0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 37854 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_Con1.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_Con1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 37854 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_Con2.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_Con2_num_mapped_reads.txt /scratch/6965110.1.linga/Input/WT_24h_WY: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Jul 18 12:04 . drwxr-xr-x 4 kkarri waxmanlab 4096 Jul 18 12:04 .. /scratch/6965110.1.linga/Input/WT_Con: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Jul 18 12:04 . drwxr-xr-x 4 kkarri waxmanlab 4096 Jul 18 12:04 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WT_Con WT_24h_WY 3 3 RefSeq_GeneBody.gtf /scratch/6965110.1.linga/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WT_Con" [1] "WT_24h_WY" [1] 3 [1] 3 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/6965110.1.linga/Input" [1] "DiffExp_v2_Intronic_Only" [1] "Intron_Only_Regions_Lengths.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Intronic_Only_WT_Con_WT_24h_WY.txt WT_24h_WY_G167_M7M8M9_vs_WT_Con_G167_M1M2M3_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== Comparison_Info: WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R WT_24h_WY_G167_M7M8M9_vs_WT_Con_G167_M1M2M3_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "WT_24h_WY_G167_M7M8M9_vs_WT_Con_G167_M1M2M3_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_WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3" [1] "-----------------" [1] "DESeq or EdgeR job most likely failed." [1] "Quitting R now." Rscript Diff_Genes.R WT_24h_WY_G167_M7M8M9_vs_WT_Con_G167_M1M2M3_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "WT_24h_WY_G167_M7M8M9_vs_WT_Con_G167_M1M2M3_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_WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3" [1] "-----------------" [1] "DESeq or EdgeR job most likely failed." [1] "Quitting R now." #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_Intronic_Only_WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3.txt Down_Genes_EdgeR_Intronic_Only_WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3.txt Intronic_Only_Counting DiffExp_1c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1c" [1] "-----------------" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_Intronic_Only_WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3.txt Up_Genes_EdgeR_Intronic_Only_WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3.txt Intronic_Only_Counting DiffExp_1c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1c" [1] "-----------------" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 0 Jul 18 12:05 /scratch/6965110.1.linga/Input/DiffExp_1c_Venn_Tables_WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Jul 18 12:04 /scratch/6965110.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 300238 Jul 18 12:04 /scratch/6965110.1.linga/Input/Intron_Only_Regions_Lengths.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Jul 18 12:04 /scratch/6965110.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 37854 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_24h_WY0.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_24h_WY0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 37854 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_24h_WY1.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_24h_WY1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 37854 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_24h_WY2.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_24h_WY2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 37854 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_Con0.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_Con0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 37854 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_Con1.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_Con1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 37854 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_Con2.out -rw-r--r-- 1 kkarri waxmanlab 9 Jul 18 12:04 /scratch/6965110.1.linga/Input/WT_Con2_num_mapped_reads.txt -rwxr-xr-x 1 kkarri waxmanlab 3925 Jul 18 12:04 /scratch/6965110.1.linga/Input/formatForSegex_ver3.R /scratch/6965110.1.linga/Input/WT_24h_WY: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Jul 18 12:04 . drwxr-xr-x 4 kkarri waxmanlab 4096 Jul 18 12:05 .. /scratch/6965110.1.linga/Input/WT_Con: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Jul 18 12:04 . drwxr-xr-x 4 kkarri waxmanlab 4096 Jul 18 12:05 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Jul 18 12:05 . drwxrwxrwt. 107 root root 340K Jul 18 12:04 .. -rw-r--r-- 1 kkarri waxmanlab 105 Jul 18 12:04 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 114 Jul 18 12:04 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Jul 18 12:05 Input -rw-r--r-- 1 kkarri waxmanlab 72M Jul 18 12:04 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 16K Jul 18 12:04 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 32K drwxr-sr-x 2 kkarri waxmanlab 512 Jul 18 12:05 . drwxr-sr-x 7 kkarri waxmanlab 32K Jul 18 12:04 .. -rw-r--r-- 1 kkarri waxmanlab 0 Jul 18 12:05 DiffExp_1c_Venn_Tables_WT_24h_WY_G167_M7M8M9_WT_Con_G167_M1M2M3_HTSeq.txt ========================================================== ========================================================== Finished on : Wed Jul 18 12:05:23 EDT 2018 0 minutes and 34 seconds elapsed. ==========================================================