----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08b_DiffExp_7_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana Dataset_Label: GSE118757 GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: WTM CONDITION_2_NAME: M2WTM Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: Exon_Regions_Lengths.txt COUNT_DIR: RefSeq_Exon_GTF OUTPUT_PREFIX: DiffExp_v2_GeneBody DiffExp_Index: DiffExp_7a COL_SUFFIX: GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Mar 10 14:01:37 EDT 2020 Running on node : scc-kb2 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08b_DiffExp_7_featureCounts Current job ID : 3784363 Current job name : Step_08b_DiffExp_7a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3784363.1.linga Loading required modules... ------------------------------------------ Sample_DIR: WTM_1 Sample_ID: WTM_1 Description: WTM_1 M_Num: 1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: WTM_1 Sample_DIR: WTM_2 Sample_ID: WTM_2 Description: WTM_2 M_Num: 2 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: WTM_2 Sample_DIR: WTM_3 Sample_ID: WTM_3 Description: WTM_3 M_Num: 3 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: WTM_3 M_Num_Cond1_List: 123 ------------------------------------------ ------------------------------------------ Sample_DIR: M2WTM_1 Sample_ID: M2WTM_1 Description: M2WTM_1 M_Num: 1 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: M2WTM_1 Sample_DIR: M2WTM_2 Sample_ID: M2WTM_2 Description: M2WTM_2 M_Num: 2 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: M2WTM_2 M_Num_Cond2_List: 12 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 3 NUM_REP_CONDITION1: 3 ========================================================== Renaming input count files Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. Counting program: Not HTSeq No lines removed. number of mapped reads 16398557 17132473 17007806 19470602 20827075 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 291522 Mar 10 14:01 /scratch/3784363.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 244439 Mar 10 14:01 /scratch/3784363.1.linga/Input/M2WTM0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:01 /scratch/3784363.1.linga/Input/M2WTM0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244409 Mar 10 14:01 /scratch/3784363.1.linga/Input/M2WTM1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:01 /scratch/3784363.1.linga/Input/M2WTM1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244611 Mar 10 14:01 /scratch/3784363.1.linga/Input/WTM0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:01 /scratch/3784363.1.linga/Input/WTM0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244876 Mar 10 14:01 /scratch/3784363.1.linga/Input/WTM1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:01 /scratch/3784363.1.linga/Input/WTM1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246806 Mar 10 14:01 /scratch/3784363.1.linga/Input/WTM2.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:01 /scratch/3784363.1.linga/Input/WTM2_num_mapped_reads.txt /scratch/3784363.1.linga/Input/M2WTM: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:01 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:01 .. /scratch/3784363.1.linga/Input/WTM: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:01 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:01 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R WTM M2WTM 3 2 RefSeq_GeneBody.gtf /scratch/3784363.1.linga/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "WTM" [1] "M2WTM" [1] 3 [1] 2 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/3784363.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" [1] "sum1:334014.77711272" "sum1:342844.833115938" "sum1:323799.763210109" [4] "sum1:333553.124479589" [1] "sum2:375420.380858273" "sum2:363571.169179333" "sum2:369495.775018803" load GTF file ... parse attributes ... [1] "output file is in: /scratch/3784363.1.linga/Input/DiffExp_v2_GeneBody_WTM_M2WTM.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_WTM_M2WTM.txt M2WTM_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_GeneBody_WTM_M2WTM.txt M2WTM_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== Comparison_Info: M2WTM_GSE118757_12_WTM_GSE118757_123 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R M2WTM_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'M2WTM_GSE118757_12_WTM_GSE118757_123 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2WTM_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 1109 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 1596 7 [1] "Check out Up_Genes_DESeq_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt!" [1] "Check out Down_Genes_DESeq_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt!" Rscript Diff_Genes.R M2WTM_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'M2WTM_GSE118757_12_WTM_GSE118757_123 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "M2WTM_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 1195 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 1969 7 [1] "Check out Up_Genes_EdgeR_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt!" [1] "Check out Down_Genes_EdgeR_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt Down_Genes_EdgeR_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt GeneBody_Counting DiffExp_7a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_7a" [1] "-----------------" [1] "Down.DESeq.GeneBody.HTSeq" [1] "Down.EdgeR.GeneBody.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_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt Up_Genes_EdgeR_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt GeneBody_Counting DiffExp_7a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_7a" [1] "-----------------" [1] "Up.DESeq.GeneBody.HTSeq" [1] "Up.EdgeR.GeneBody.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 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 14:03 /scratch/3784363.1.linga/Input/DiffExp_7a_Venn_Tables_M2WTM_GSE118757_12_WTM_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 10169008 Mar 10 14:03 /scratch/3784363.1.linga/Input/DiffExp_v2_GeneBody_WTM_M2WTM.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Mar 10 14:01 /scratch/3784363.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 128653 Mar 10 14:03 /scratch/3784363.1.linga/Input/Down_Genes_DESeq_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 158875 Mar 10 14:03 /scratch/3784363.1.linga/Input/Down_Genes_EdgeR_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 291522 Mar 10 14:01 /scratch/3784363.1.linga/Input/Exon_Regions_Lengths.txt -rw-r--r-- 1 kkarri waxmanlab 244439 Mar 10 14:01 /scratch/3784363.1.linga/Input/M2WTM0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:01 /scratch/3784363.1.linga/Input/M2WTM0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244409 Mar 10 14:01 /scratch/3784363.1.linga/Input/M2WTM1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:01 /scratch/3784363.1.linga/Input/M2WTM1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 2547728 Mar 10 14:03 /scratch/3784363.1.linga/Input/M2WTM_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2571925 Mar 10 14:03 /scratch/3784363.1.linga/Input/M2WTM_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 2596120 Mar 10 14:03 /scratch/3784363.1.linga/Input/M2WTM_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2620317 Mar 10 14:03 /scratch/3784363.1.linga/Input/M2WTM_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 88627 Mar 10 14:03 /scratch/3784363.1.linga/Input/Up_Genes_DESeq_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt -rw-r--r-- 1 kkarri waxmanlab 96716 Mar 10 14:03 /scratch/3784363.1.linga/Input/Up_Genes_EdgeR_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Mar 10 14:01 /scratch/3784363.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 42045 Mar 10 14:03 /scratch/3784363.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 39562 Mar 10 14:03 /scratch/3784363.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 244611 Mar 10 14:01 /scratch/3784363.1.linga/Input/WTM0.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:01 /scratch/3784363.1.linga/Input/WTM0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 244876 Mar 10 14:01 /scratch/3784363.1.linga/Input/WTM1.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:01 /scratch/3784363.1.linga/Input/WTM1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 246806 Mar 10 14:01 /scratch/3784363.1.linga/Input/WTM2.out -rw-r--r-- 1 kkarri waxmanlab 9 Mar 10 14:01 /scratch/3784363.1.linga/Input/WTM2_num_mapped_reads.txt -rwxr-xr-x 1 kkarri waxmanlab 3925 Mar 10 14:01 /scratch/3784363.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 3929 Mar 10 14:01 /scratch/3784363.1.linga/Input/formatForSegex_ver4.R /scratch/3784363.1.linga/Input/M2WTM: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:01 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:03 .. /scratch/3784363.1.linga/Input/WTM: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 10 14:01 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 10 14:03 .. ========================================================== List files in scratch total 72M drwx------ 3 kkarri waxmanlab 4.0K Mar 10 14:03 . drwxrwxrwt. 65 root root 12K Mar 10 14:01 .. -rw-r--r-- 1 kkarri waxmanlab 87 Mar 10 14:01 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 81 Mar 10 14:01 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 10 14:03 Input -rw-r--r-- 1 kkarri waxmanlab 72M Mar 10 14:01 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri waxmanlab 17K Mar 10 14:01 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 30M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 10 13:55 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 10 13:55 .. -rw-r--r-- 1 kkarri waxmanlab 300 Mar 10 13:55 DiffExp_7a_Venn_Tables_M2WTM_GSE118757_12_WTM_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 9.7M Mar 10 13:55 DiffExp_v2_GeneBody_WTM_M2WTM_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 126K Mar 10 13:55 Down_Genes_DESeq_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 156K Mar 10 13:55 Down_Genes_EdgeR_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.5M Mar 10 13:55 M2WTM_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.5M Mar 10 13:55 M2WTM_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.5M Mar 10 13:55 M2WTM_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.5M Mar 10 13:55 M2WTM_GSE118757_12_vs_WTM_GSE118757_123_DiffExp_v2_GeneBody_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 87K Mar 10 13:55 Up_Genes_DESeq_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 95K Mar 10 13:55 Up_Genes_EdgeR_GeneBody_M2WTM_GSE118757_12_WTM_GSE118757_123_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 42K Mar 10 13:55 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 39K Mar 10 13:55 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Tue Mar 10 14:03:28 EDT 2020 1 minutes and 51 seconds elapsed. ==========================================================