----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/09a_DiffExp_9_HTSeq Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170 Dataset_Label: G170 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: F_Placebo_TD229 CONDITION_2_NAME: F_140mg/kg_CPA_2cycle_TD229 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_9c COL_SUFFIX: Intronic_Only COUNT_PROGRAM: HTSeq ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri Sep 6 15:02:27 EDT 2019 Running on node : scc-tm2 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/09a_DiffExp_9_HTSeq Current job ID : 9183579 Current job name : Step_09a_DiffExp_9c Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9183579.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G170_M20 Sample_ID: G170_M20 Description: F_Placebo_Pool1_TD229 M_Num: M20 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G170_M20 Sample_DIR: G170_M21 Sample_ID: G170_M21 Description: F_Placebo_Pool2_TD229 M_Num: M21 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: G170_M21 M_Num_Cond1_List: M20M21 ------------------------------------------ ------------------------------------------ Sample_DIR: G170_M30 Sample_ID: G170_M30 Description: F_140mg/kg_CPA_2_cycles_Pool11_TD229 M_Num: M30 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G170_M30 Sample_DIR: G170_M31 Sample_ID: G170_M31 Description: F_140mg/kg_CPA_2_cycles_Pool12_TD229 M_Num: M31 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: G170_M31 M_Num_Cond2_List: M30M31 ------------------------------------------ ========================================================== 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: Not HTSeq No lines removed. number of mapped reads 44524767 45401633 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 239957 Sep 6 15:02 /scratch/9183579.1.linga/Input/F_Placebo_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 15:02 /scratch/9183579.1.linga/Input/F_Placebo_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 241413 Sep 6 15:02 /scratch/9183579.1.linga/Input/F_Placebo_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 15:02 /scratch/9183579.1.linga/Input/F_Placebo_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Sep 6 15:02 /scratch/9183579.1.linga/Input/Intron_Only_Regions_Lengths.txt /scratch/9183579.1.linga/Input/Condition_2: total 492 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 6 15:02 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 6 15:02 .. -rw-r--r-- 1 kkarri waxmanlab 243087 Sep 6 15:02 G170_M30_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 15:02 G170_M30_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238028 Sep 6 15:02 G170_M31_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 15:02 G170_M31_num_mapped_reads.txt /scratch/9183579.1.linga/Input/F_Placebo_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 6 15:02 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 6 15:02 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R F_Placebo_TD229 F_140mg/kg_CPA_2cycle_TD229 2 2 RefSeq_GeneBody.gtf /scratch/9183579.1.linga/Input DiffExp_v2_Intronic_Only Intron_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "F_Placebo_TD229" [1] "F_140mg/kg_CPA_2cycle_TD229" [1] 2 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/9183579.1.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_F_Placebo_TD229_F_140mg/kg_CPA_2cycle_TD229.txt F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_Intronic_Only_F_Placebo_TD229_F_140mg/kg_CPA_2cycle_TD229.txt F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload 1 Intronic_Only ========================================================== Comparison_Info: F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Intronic_Only'_'F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_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_F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21" [1] "-----------------" [1] "DESeq or EdgeR job most likely failed." [1] "Quitting R now." Rscript Diff_Genes.R F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Intronic_Only'_'F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_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_F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21" [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_F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt Down_Genes_EdgeR_Intronic_Only_F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt Intronic_Only_Counting DiffExp_9c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Intronic_Only_F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Intronic_Only_F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_9c" [1] "-----------------" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_Intronic_Only_F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt Up_Genes_EdgeR_Intronic_Only_F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt Intronic_Only_Counting DiffExp_9c [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Intronic_Only_F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Intronic_Only_F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt" [1] "Subtitle:" [1] "Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_9c" [1] "-----------------" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rwxr-xr-x 1 kkarri waxmanlab 7394 Sep 6 15:02 /scratch/9183579.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 239957 Sep 6 15:02 /scratch/9183579.1.linga/Input/F_Placebo_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 15:02 /scratch/9183579.1.linga/Input/F_Placebo_TD2290_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 241413 Sep 6 15:02 /scratch/9183579.1.linga/Input/F_Placebo_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 15:02 /scratch/9183579.1.linga/Input/F_Placebo_TD2291_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 300238 Sep 6 15:02 /scratch/9183579.1.linga/Input/Intron_Only_Regions_Lengths.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Sep 6 15:02 /scratch/9183579.1.linga/Input/Venn_Diff_Genes.R -rwxr-xr-x 1 kkarri waxmanlab 3925 Sep 6 15:02 /scratch/9183579.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Sep 6 15:02 /scratch/9183579.1.linga/Input/formatForSegex_ver4.R /scratch/9183579.1.linga/Input/Condition_2: total 492 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 6 15:02 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 6 15:02 .. -rw-r--r-- 1 kkarri waxmanlab 243087 Sep 6 15:02 G170_M30_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 15:02 G170_M30_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 238028 Sep 6 15:02 G170_M31_HTSeq.out -rw-r--r-- 1 kkarri waxmanlab 9 Sep 6 15:02 G170_M31_num_mapped_reads.txt /scratch/9183579.1.linga/Input/F_Placebo_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 6 15:02 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 6 15:02 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Sep 6 15:02 . drwxrwxrwt. 15 root root 4.0K Sep 6 15:02 .. -rw-r--r-- 1 kkarri waxmanlab 113 Sep 6 15:02 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 143 Sep 6 15:02 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Sep 6 15:02 Input -rw-r--r-- 1 kkarri waxmanlab 72M Sep 6 15:02 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K Sep 6 15:02 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 4.0K drwxr-xr-x 2 kkarri waxmanlab 6 Sep 6 14:56 . drwxr-xr-x 6 kkarri waxmanlab 4.0K Sep 6 14:56 .. ========================================================== ========================================================== Finished on : Fri Sep 6 15:02:48 EDT 2019 0 minutes and 21 seconds elapsed. ==========================================================