----------------------- 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/09c_DiffExp_7_lncRNA_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170 Dataset_Label: G170 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: F_Placebo_TD229 CONDITION_2_NAME: F_CPA_3D_TD229 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_7f COL_SUFFIX: LncRNA_Exonic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Sep 16 11:03:39 EDT 2019 Running on node : scc-tk1 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/09c_DiffExp_7_lncRNA_featureCounts Current job ID : 9374022 Current job name : Step_09c_DiffExp_7f Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9374022.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G170_M20 Sample_ID: G170_M20 Description: F_Placebo1_TD229 M_Num: M20 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G170_M21 Sample_ID: G170_M21 Description: F_Placebo2_TD229 M_Num: M21 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: M20M21 ------------------------------------------ ------------------------------------------ Sample_DIR: G170_M26 Sample_ID: G170_M26 Description: F_CPA_3D7_TD229 M_Num: M26 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G170_M27 Sample_ID: G170_M27 Description: F_CPA_3D8_TD229 M_Num: M27 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: M26M27 ------------------------------------------ ========================================================== 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 G170_M26_sorted.bam Assigned 10815158 Unassigned_Ambiguity 4054 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2599890 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G170_M27_sorted.bam Assigned 11103631 Unassigned_Ambiguity 4319 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2558351 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G170_M20_sorted.bam Assigned 10987636 Unassigned_Ambiguity 3900 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2422628 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G170_M21_sorted.bam Assigned 10898050 Unassigned_Ambiguity 3794 Unassigned_MultiMapping 0 Unassigned_NoFeatures 2909948 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 714676 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_CPA_3D_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_CPA_3D_TD2290.summary -rw-r--r-- 1 kkarri waxmanlab 714949 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_CPA_3D_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_CPA_3D_TD2291.summary -rw-r--r-- 1 kkarri waxmanlab 714197 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_Placebo_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_Placebo_TD2290.summary -rw-r--r-- 1 kkarri waxmanlab 714768 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_Placebo_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_Placebo_TD2291.summary -rw-r--r-- 1 kkarri waxmanlab 794757 Sep 16 11:03 /scratch/9374022.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/9374022.1.linga/Input/F_CPA_3D_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 11:03 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 11:03 .. /scratch/9374022.1.linga/Input/F_Placebo_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 11:03 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 11:03 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R F_Placebo_TD229 F_CPA_3D_TD229 2 2 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/9374022.1.linga/Input DiffExp_v2_LncRNA_Exonic_Only exonic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "F_Placebo_TD229" [1] "F_CPA_3D_TD229" [1] 2 [1] 2 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/9374022.1.linga/Input" [1] "DiffExp_v2_LncRNA_Exonic_Only" [1] "exonic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] 15558 23 [1] 15558 48 [1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" "chr9" [1] "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" [10] "chr19" [1] "chrX" "chrY" [1] "output file is in: /scratch/9374022.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_F_Placebo_TD229_F_CPA_3D_TD229.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Exonic_Only_F_Placebo_TD229_F_CPA_3D_TD229.txt F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload 1 LncRNA_Exonic_Only ========================================================== Comparison_Info: F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Exonic_Only'_'F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_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_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 4 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 0 7 [1] "Check out Up_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt!" Rscript Diff_Genes.R F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Exonic_Only'_'F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_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_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 15 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 5 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt Down_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt LncRNA_Exonic_Only_Counting DiffExp_7f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_7f" [1] "-----------------" [1] "Down.DESeq.Exonic_Only.HTSeq" [1] "Down.EdgeR.Exonic_Only.HTSeq" null device 1 [1] "Removing VennDiagram*.log files" [1] "Check out Venn diagram and Count.Table!" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt Up_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt LncRNA_Exonic_Only_Counting DiffExp_7f [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt" [1] "Subtitle:" [1] "LncRNA_Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_7f" [1] "-----------------" [1] "Up.DESeq.Exonic_Only.HTSeq" [1] "Up.EdgeR.Exonic_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: F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 318 Sep 16 11:04 /scratch/9374022.1.linga/Input/DiffExp_7f_Venn_Tables_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 3722386 Sep 16 11:04 /scratch/9374022.1.linga/Input/DiffExp_v2_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Sep 16 11:03 /scratch/9374022.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 224 Sep 16 11:04 /scratch/9374022.1.linga/Input/Down_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 596 Sep 16 11:04 /scratch/9374022.1.linga/Input/Down_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 714676 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_CPA_3D_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_CPA_3D_TD2290.summary -rw-r--r-- 1 kkarri waxmanlab 714949 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_CPA_3D_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_CPA_3D_TD2291.summary -rw-r--r-- 1 kkarri waxmanlab 1592455 Sep 16 11:04 /scratch/9374022.1.linga/Input/F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1685803 Sep 16 11:04 /scratch/9374022.1.linga/Input/F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 714197 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_Placebo_TD2290.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_Placebo_TD2290.summary -rw-r--r-- 1 kkarri waxmanlab 714768 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_Placebo_TD2291.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 16 11:03 /scratch/9374022.1.linga/Input/F_Placebo_TD2291.summary -rw-r--r-- 1 kkarri waxmanlab 479 Sep 16 11:04 /scratch/9374022.1.linga/Input/Up_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt -rw-r--r-- 1 kkarri waxmanlab 1412 Sep 16 11:04 /scratch/9374022.1.linga/Input/Up_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Sep 16 11:03 /scratch/9374022.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 32572 Sep 16 11:04 /scratch/9374022.1.linga/Input/Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 36851 Sep 16 11:04 /scratch/9374022.1.linga/Input/Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 794757 Sep 16 11:03 /scratch/9374022.1.linga/Input/exonic_only_gene_models_ncRNA_for_counting_lengths.txt -rwxr-xr-x 1 kkarri waxmanlab 4968 Sep 16 11:03 /scratch/9374022.1.linga/Input/formatForSegex_ver3.R /scratch/9374022.1.linga/Input/F_CPA_3D_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 11:03 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 11:04 .. /scratch/9374022.1.linga/Input/F_Placebo_TD229: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Sep 16 11:03 . drwxr-xr-x 4 kkarri waxmanlab 4096 Sep 16 11:04 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Sep 16 11:04 . drwxrwxrwt. 14 root root 4.0K Sep 16 11:03 .. -rw-r--r-- 1 kkarri waxmanlab 103 Sep 16 11:03 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 101 Sep 16 11:03 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Sep 16 11:04 Input -rwxr-xr-x 1 kkarri waxmanlab 13K Sep 16 11:03 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Sep 16 11:03 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 12M drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 10:58 . drwxr-xr-x 8 kkarri waxmanlab 4.0K Sep 16 10:58 .. -rw-r--r-- 1 kkarri waxmanlab 318 Sep 16 10:58 DiffExp_7f_Venn_Tables_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 3.6M Sep 16 10:58 DiffExp_v2_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 224 Sep 16 10:58 Down_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 596 Sep 16 10:58 Down_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.6M Sep 16 10:58 F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.7M Sep 16 10:58 F_CPA_3D_TD229_G170_M26M27_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_LncRNA_Exonic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 479 Sep 16 10:58 Up_Genes_DESeq_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.4K Sep 16 10:58 Up_Genes_EdgeR_LncRNA_Exonic_Only_F_CPA_3D_TD229_G170_M26M27_F_Placebo_TD229_G170_M20M21_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 32K Sep 16 10:58 Venn_Down.DESeq.Exonic_Only.HTSeq.Down.EdgeR.Exonic_Only.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 36K Sep 16 10:58 Venn_Up.DESeq.Exonic_Only.HTSeq.Up.EdgeR.Exonic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Sep 16 11:04:10 EDT 2019 0 minutes and 31 seconds elapsed. ==========================================================