----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/09b_DiffExp_2_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline Dataset_Label: Water_Saline GTF_Files_DIR: /restricted/projectnb/waxmanlab/kkarri/GTF_Files1 ANNOTATION_FILE: RefSeq_GeneBody.gtf CONDITION_1_NAME: Control CONDITION_2_NAME: AFLATOXINB1 Lengths_DIR: /restricted/projectnb/waxmanlab/kkarri/GTF_Files1/lengths GENE_LENGTHS_FILE: Exon_Regions_Lengths.txt COUNT_DIR: RefSeq_Exon_GTF OUTPUT_PREFIX: DiffExp_v2_GeneBody DiffExp_Index: DiffExp_2a COL_SUFFIX: GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri Jun 23 15:56:39 EDT 2017 Running on node : scc-ka8 Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/09b_DiffExp_2_featureCounts Current job ID : 9535013 Current job name : Step_09b_DiffExp_2a Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9535013.1.linga Loading required modules... ------------------------------------------ Sample_DIR: C_M1 Sample_ID: C_M1 Description: C_M1 M_Num: M1 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: C_M1 M_Num_Cond1_List: M1 ------------------------------------------ ------------------------------------------ Sample_DIR: MM_M1 Sample_ID: MM_M1 Description: MM_M1 M_Num: M1 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: MM_M1 Sample_DIR: MM_M2 Sample_ID: MM_M2 Description: MM_M2 M_Num: M2 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: MM_M2 Sample_DIR: MM_M3 Sample_ID: MM_M3 Description: MM_M3 M_Num: M3 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: MM_M3 M_Num_Cond2_List: M1M2M3 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 1 NUM_REP_CONDITION1: 1 WARNING: Either your Condition_1 or Condition_2 has only 1 sample (no replicates) The differential expression analysis is designed for cases where there are at least 2 replicates/biological condition. The resulting differential expression analysis will be converted to a stringent version due to absence of replicate samples. Samples from this comparison will be treated as "replicates" to estimate the gene level variance in edgeR and, separately in, DESeq2. Expect very few to zero DE genes from DESeq2, EdgeR should yield a DE gene count. Interpreting the results: use the edgeR fold change or DESeq ratio (not DESeq fold change) Note regarding the SEGEX upload file(s): Since DESeq2 fold changes are not the same as the ratio of the normalized counts between the conditions, so the output of the segex upload file will be different between "DESeq ratio" and "DESeq foldChange". The former is truly the ratio between the normalized counts between the two conditions (plus pseudocounts) whereas the latter is the fold change estimated by DESeq. ========================================================== 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. number of mapped reads 33314720 36664202 36275484 103979138 ========================================================== List files in Input -rw-r--r-- 1 kkarri montilab-p 0 Jun 23 15:56 /scratch/9535013.1.linga/Input/AFLATOXINB10.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 23 15:56 /scratch/9535013.1.linga/Input/AFLATOXINB10_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 0 Jun 23 15:56 /scratch/9535013.1.linga/Input/AFLATOXINB11.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 23 15:56 /scratch/9535013.1.linga/Input/AFLATOXINB11_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 0 Jun 23 15:56 /scratch/9535013.1.linga/Input/AFLATOXINB12.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 23 15:56 /scratch/9535013.1.linga/Input/AFLATOXINB12_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 0 Jun 23 15:56 /scratch/9535013.1.linga/Input/Control0.out -rw-r--r-- 1 kkarri montilab-p 10 Jun 23 15:56 /scratch/9535013.1.linga/Input/Control0_num_mapped_reads.txt -rwx------ 1 kkarri montilab-p 197610 Jun 23 15:56 /scratch/9535013.1.linga/Input/Exon_Regions_Lengths.txt /scratch/9535013.1.linga/Input/AFLATOXINB1: total 8 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 23 15:56 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 23 15:56 .. /scratch/9535013.1.linga/Input/Control: total 8 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 23 15:56 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 23 15:56 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Control AFLATOXINB1 1 3 RefSeq_GeneBody.gtf /scratch/9535013.1.linga/Input DiffExp_v2_GeneBody Exon_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Control" [1] "AFLATOXINB1" [1] 1 [1] 3 [1] "RefSeq_GeneBody.gtf" [1] "/scratch/9535013.1.linga/Input" [1] "DiffExp_v2_GeneBody" [1] "Exon_Regions_Lengths.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_GeneBody_Control_AFLATOXINB1.txt AFLATOXINB1_Water_Saline_M1M2M3_vs_Control_Water_Saline_M1_DiffExp_v2_GeneBody_forSEGEXUpload 1 GeneBody ========================================================== Comparison_Info: AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R AFLATOXINB1_Water_Saline_M1M2M3_vs_Control_Water_Saline_M1_DiffExp_v2_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq GeneBody'_'AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "AFLATOXINB1_Water_Saline_M1M2M3_vs_Control_Water_Saline_M1_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_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1" [1] "-----------------" [1] "DESeq or EdgeR job most likely failed." [1] "Quitting R now." Rscript Diff_Genes.R AFLATOXINB1_Water_Saline_M1M2M3_vs_Control_Water_Saline_M1_DiffExp_v2_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR GeneBody'_'AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "AFLATOXINB1_Water_Saline_M1M2M3_vs_Control_Water_Saline_M1_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_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1" [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_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt Down_Genes_EdgeR_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt GeneBody_Counting DiffExp_2a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt" [1] "File2:" [1] "Down_Genes_EdgeR_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2a" [1] "-----------------" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt Up_Genes_EdgeR_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt GeneBody_Counting DiffExp_2a [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt" [1] "File2:" [1] "Up_Genes_EdgeR_GeneBody_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt" [1] "Subtitle:" [1] "GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_2a" [1] "-----------------" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- Comparison_Info: AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri montilab-p 0 Jun 23 15:56 /scratch/9535013.1.linga/Input/AFLATOXINB10.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 23 15:56 /scratch/9535013.1.linga/Input/AFLATOXINB10_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 0 Jun 23 15:56 /scratch/9535013.1.linga/Input/AFLATOXINB11.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 23 15:56 /scratch/9535013.1.linga/Input/AFLATOXINB11_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 0 Jun 23 15:56 /scratch/9535013.1.linga/Input/AFLATOXINB12.out -rw-r--r-- 1 kkarri montilab-p 9 Jun 23 15:56 /scratch/9535013.1.linga/Input/AFLATOXINB12_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 0 Jun 23 15:56 /scratch/9535013.1.linga/Input/Control0.out -rw-r--r-- 1 kkarri montilab-p 10 Jun 23 15:56 /scratch/9535013.1.linga/Input/Control0_num_mapped_reads.txt -rw-r--r-- 1 kkarri montilab-p 0 Jun 23 15:57 /scratch/9535013.1.linga/Input/DiffExp_2a_Venn_Tables_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1.txt -rwxr-xr-x 1 kkarri montilab-p 7394 Jun 23 15:56 /scratch/9535013.1.linga/Input/Diff_Genes.R -rwx------ 1 kkarri montilab-p 197610 Jun 23 15:56 /scratch/9535013.1.linga/Input/Exon_Regions_Lengths.txt -rwxr-xr-x 1 kkarri montilab-p 9553 Jun 23 15:56 /scratch/9535013.1.linga/Input/Venn_Diff_Genes.R -rwxr-xr-x 1 kkarri montilab-p 3925 Jun 23 15:56 /scratch/9535013.1.linga/Input/formatForSegex_ver3.R /scratch/9535013.1.linga/Input/AFLATOXINB1: total 8 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 23 15:56 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 23 15:57 .. /scratch/9535013.1.linga/Input/Control: total 8 drwxr-xr-x 2 kkarri montilab-p 4096 Jun 23 15:56 . drwxr-xr-x 4 kkarri montilab-p 4096 Jun 23 15:57 .. ========================================================== List files in scratch total 41M drwxr-xr-x 3 kkarri montilab-p 4.0K Jun 23 15:57 . drwxrwxrwt. 168 root root 72K Jun 23 15:56 .. -rw-r--r-- 1 kkarri montilab-p 48 Jun 23 15:56 Condition_1.txt -rw-r--r-- 1 kkarri montilab-p 87 Jun 23 15:56 Condition_2.txt drwxr-xr-x 4 kkarri montilab-p 4.0K Jun 23 15:57 Input -rwx------ 1 kkarri montilab-p 41M Jun 23 15:56 RefSeq_GeneBody.gtf -rwxr-xr-x 1 kkarri montilab-p 16K Jun 23 15:56 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 Jun 23 15:57 . drwxr-sr-x 6 kkarri waxmanlab 32K Jun 23 15:56 .. -rw-r--r-- 1 kkarri waxmanlab 0 Jun 23 15:57 DiffExp_2a_Venn_Tables_AFLATOXINB1_Water_Saline_M1M2M3_Control_Water_Saline_M1_featureCounts.txt ========================================================== ========================================================== Finished on : Fri Jun 23 15:57:14 EDT 2017 0 minutes and 35 seconds elapsed. ==========================================================