----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/09c_DiffExp_1_lncRNA_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G123_Env Dataset_Label: G123 ANNOTATION_FILE_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt CONDITION_1_NAME: Male_3h_Vehicle CONDITION_2_NAME: Male_3h_TCPOBOP Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: exonic_only_gene_models_ncRNA_for_counting_lengths.txt COUNT_DIR: LncRNA_Exonic_Only_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_Exonic_Only DiffExp_Index: DiffExp_1f COL_SUFFIX: LncRNA_Exonic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed Dec 19 13:50:02 EST 2018 Running on node : scc-tm3 Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/09c_DiffExp_1_lncRNA_featureCounts Current job ID : 386633 Current job name : Step_09c_DiffExp_1f Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/386633.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G123_M1 Sample_ID: G123_M1 Description: Male_3h_Vehicle_1 M_Num: M1 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G123_M2 Sample_ID: G123_M2 Description: Male_3h_Vehicle_2 M_Num: M2 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder M_Num_Cond1_List: M1M2 ------------------------------------------ ------------------------------------------ Sample_DIR: G123_M3 Sample_ID: G123_M3 Description: Male_3h_TCPOBOP_1 M_Num: M3 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G123_M4 Sample_ID: G123_M4 Description: Male_3h_TCPOBOP_2 M_Num: M4 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder M_Num_Cond2_List: M3M4 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 2 NUM_REP_CONDITION1: 2 ========================================================== Renaming input count files number of mapped reads (feature count summary) Status Assigned Unassigned_Ambiguity Unassigned_MultiMapping Unassigned_NoFeatures Unassigned_Unmapped Unassigned_MappingQuality Unassigned_FragmentLength Unassigned_Chimera Unassigned_Secondary Unassigned_Nonjunction Unassigned_Duplicate Status Assigned Unassigned_Ambiguity Unassigned_MultiMapping Unassigned_NoFeatures Unassigned_Unmapped Unassigned_MappingQuality Unassigned_FragmentLength Unassigned_Chimera Unassigned_Secondary Unassigned_Nonjunction Unassigned_Duplicate Status Assigned Unassigned_Ambiguity Unassigned_MultiMapping Unassigned_NoFeatures Unassigned_Unmapped Unassigned_MappingQuality Unassigned_FragmentLength Unassigned_Chimera Unassigned_Secondary Unassigned_Nonjunction Unassigned_Duplicate Status Assigned Unassigned_Ambiguity Unassigned_MultiMapping Unassigned_NoFeatures Unassigned_Unmapped Unassigned_MappingQuality Unassigned_FragmentLength Unassigned_Chimera Unassigned_Secondary Unassigned_Nonjunction Unassigned_Duplicate ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 794718 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 239 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_TCPOBOP0.summary -rw-r--r-- 1 kkarri waxmanlab 794718 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 239 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_TCPOBOP1.summary -rw-r--r-- 1 kkarri waxmanlab 794718 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 239 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_Vehicle0.summary -rw-r--r-- 1 kkarri waxmanlab 794718 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 239 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_Vehicle1.summary -rw-r--r-- 1 kkarri waxmanlab 794757 Dec 19 13:50 /scratch/386633.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/386633.1.linga/Input/Male_3h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 19 13:50 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 19 13:50 .. /scratch/386633.1.linga/Input/Male_3h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 19 13:50 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 19 13:50 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Male_3h_Vehicle Male_3h_TCPOBOP 2 2 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/386633.1.linga/Input DiffExp_v2_LncRNA_Exonic_Only exonic_only_gene_models_ncRNA_for_counting_lengths.txt WARNING: ignoring environment value of R_HOME ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Exonic_Only_Male_3h_Vehicle_Male_3h_TCPOBOP.txt Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload 1 LncRNA_Exonic_Only WARNING: ignoring environment value of R_HOME ========================================================== Comparison_Info: Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Exonic_Only'_'Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "LncRNA_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2" [1] "-----------------" [1] "DESeq or EdgeR job most likely failed." [1] "Quitting R now." Rscript Diff_Genes.R Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Exonic_Only'_'Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "LncRNA_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2" [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_LncRNA_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt Down_Genes_EdgeR_LncRNA_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt LncRNA_Exonic_Only_Counting DiffExp_1f WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1f" [1] "-----------------" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_LncRNA_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt Up_Genes_EdgeR_LncRNA_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt LncRNA_Exonic_Only_Counting DiffExp_1f WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Exonic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_1f" [1] "-----------------" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- Comparison_Info: Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 0 Dec 19 13:50 /scratch/386633.1.linga/Input/DiffExp_1f_Venn_Tables_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Dec 19 13:50 /scratch/386633.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 794718 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_TCPOBOP0.out -rw-r--r-- 1 kkarri waxmanlab 239 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_TCPOBOP0.summary -rw-r--r-- 1 kkarri waxmanlab 794718 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_TCPOBOP1.out -rw-r--r-- 1 kkarri waxmanlab 239 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_TCPOBOP1.summary -rw-r--r-- 1 kkarri waxmanlab 794718 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_Vehicle0.out -rw-r--r-- 1 kkarri waxmanlab 239 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_Vehicle0.summary -rw-r--r-- 1 kkarri waxmanlab 794718 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_Vehicle1.out -rw-r--r-- 1 kkarri waxmanlab 239 Dec 19 13:50 /scratch/386633.1.linga/Input/Male_3h_Vehicle1.summary -rwxr-xr-x 1 kkarri waxmanlab 9993 Dec 19 13:50 /scratch/386633.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 794757 Dec 19 13:50 /scratch/386633.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt -rwxr-xr-x 1 kkarri waxmanlab 4968 Dec 19 13:50 /scratch/386633.1.linga/Input/formatForSegex_ver3.R /scratch/386633.1.linga/Input/Male_3h_TCPOBOP: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 19 13:50 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 19 13:50 .. /scratch/386633.1.linga/Input/Male_3h_Vehicle: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Dec 19 13:50 . drwxr-xr-x 4 kkarri waxmanlab 4096 Dec 19 13:50 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Dec 19 13:50 . drwxrwxrwt. 7 root root 36K Dec 19 13:50 .. -rw-r--r-- 1 kkarri waxmanlab 101 Dec 19 13:50 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 101 Dec 19 13:50 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Dec 19 13:50 Input -rwxr-xr-x 1 kkarri waxmanlab 13K Dec 19 13:50 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Dec 19 13:50 ncRNA_output_filtered_final_gene.txt ========================================================== 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 Dec 19 13:50 . drwxr-sr-x 7 kkarri waxmanlab 32K Dec 19 13:50 .. -rw-r--r-- 1 kkarri waxmanlab 0 Dec 19 13:50 DiffExp_1f_Venn_Tables_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2_featureCounts.txt ========================================================== ========================================================== Finished on : Wed Dec 19 13:50:07 EST 2018 0 minutes and 5 seconds elapsed. ==========================================================