----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/09b_DiffExp_3_featureCounts Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq Dataset_Label: SRR GTF_Files_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/GTF_Files ANNOTATION_FILE: Exon_Only_Regions.gtf CONDITION_1_NAME: B_cell CONDITION_2_NAME: Endothelial Lengths_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/GTF_Files/lengths GENE_LENGTHS_FILE: Exon_Only_Regions_Lengths.txt COUNT_DIR: RefSeq_Exon_Only_GTF OUTPUT_PREFIX: DiffExp_v2_Exonic_Only DiffExp_Index: DiffExp_3b COL_SUFFIX: Exonic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Fri Oct 19 00:31:44 EDT 2018 Running on node : scc-kb4 Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/09b_DiffExp_3_featureCounts Current job ID : 9022725 Current job name : Step_09b_DiffExp_3b Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9022725.1.linga Loading required modules... ------------------------------------------ Sample_DIR: SRR6575881 Sample_ID: A21-MAA000907-3_11_M-1-1 Description: B_cell M_Num: 11 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: A21-MAA000907-3_11_M-1-1 Sample_DIR: SRR6575459 Sample_ID: A2-MAA000907-3_11_M-1-1 Description: B_cell M_Num: 11 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: A2-MAA000907-3_11_M-1-1 Sample_DIR: SRR6575504 Sample_ID: A4-MAA000907-3_11_M-1-1 Description: B_cell M_Num: 11 Copy Condition_1 sample count files to Condition_1 folder calculate mapped reads: A4-MAA000907-3_11_M-1-1 M_Num_Cond1_List: 111111 ------------------------------------------ ------------------------------------------ Sample_DIR: SRR6575637 Sample_ID: A10-MAA000907-3_11_M-1-1 Description: endothelial_cell_of_hepatic_sinusoid M_Num: 11 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: A10-MAA000907-3_11_M-1-1 Sample_DIR: SRR6575659 Sample_ID: A11-MAA000907-3_11_M-1-1 Description: endothelial_cell_of_hepatic_sinusoid M_Num: 11 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: A11-MAA000907-3_11_M-1-1 Sample_DIR: SRR6575837 Sample_ID: A19-MAA000907-3_11_M-1-1 Description: endothelial_cell_of_hepatic_sinusoid M_Num: 11 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: A19-MAA000907-3_11_M-1-1 Sample_DIR: SRR6575859 Sample_ID: A20-MAA000907-3_11_M-1-1 Description: endothelial_cell_of_hepatic_sinusoid M_Num: 11 Copy Condition_2 sample count files to Condition_2 folder calculate mapped reads: A20-MAA000907-3_11_M-1-1 M_Num_Cond2_List: 11111111 ------------------------------------------ ========================================================== 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. number of mapped reads 334378 489733 394754 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 226962 Oct 19 00:31 /scratch/9022725.1.linga/Input/B_cell0.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 00:31 /scratch/9022725.1.linga/Input/B_cell0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 227355 Oct 19 00:31 /scratch/9022725.1.linga/Input/B_cell1.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 00:31 /scratch/9022725.1.linga/Input/B_cell1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 227205 Oct 19 00:31 /scratch/9022725.1.linga/Input/B_cell2.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 00:31 /scratch/9022725.1.linga/Input/B_cell2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 292699 Oct 19 00:31 /scratch/9022725.1.linga/Input/Exon_Only_Regions_Lengths.txt /scratch/9022725.1.linga/Input/B_cell: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Oct 19 00:31 . drwxr-xr-x 4 kkarri waxmanlab 4096 Oct 19 00:31 .. /scratch/9022725.1.linga/Input/Endothelial: total 24 drwxr-xr-x 2 kkarri waxmanlab 4096 Oct 19 00:31 . drwxr-xr-x 4 kkarri waxmanlab 4096 Oct 19 00:31 .. -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 00:31 A10-MAA000907-3_11_M-1-1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 00:31 A11-MAA000907-3_11_M-1-1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 00:31 A19-MAA000907-3_11_M-1-1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 00:31 A20-MAA000907-3_11_M-1-1_num_mapped_reads.txt ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R B_cell Endothelial 3 0 Exon_Only_Regions.gtf /scratch/9022725.1.linga/Input DiffExp_v2_Exonic_Only Exon_Only_Regions_Lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "B_cell" [1] "Endothelial" [1] 3 [1] 0 [1] "Exon_Only_Regions.gtf" [1] "/scratch/9022725.1.linga/Input" [1] "DiffExp_v2_Exonic_Only" [1] "Exon_Only_Regions_Lengths.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_Exonic_Only_B_cell_Endothelial.txt Endothelial_SRR_11111111_vs_B_cell_SRR_111111_DiffExp_v2_Exonic_Only_forSEGEXUpload 1 Exonic_Only ========================================================== Comparison_Info: Endothelial_SRR_11111111_B_cell_SRR_111111 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Endothelial_SRR_11111111_vs_B_cell_SRR_111111_DiffExp_v2_Exonic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq Exonic_Only'_'Endothelial_SRR_11111111_B_cell_SRR_111111 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Endothelial_SRR_11111111_vs_B_cell_SRR_111111_DiffExp_v2_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] "Exonic_Only_Endothelial_SRR_11111111_B_cell_SRR_111111" [1] "-----------------" [1] "DESeq or EdgeR job most likely failed." [1] "Quitting R now." Rscript Diff_Genes.R Endothelial_SRR_11111111_vs_B_cell_SRR_111111_DiffExp_v2_Exonic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR Exonic_Only'_'Endothelial_SRR_11111111_B_cell_SRR_111111 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Endothelial_SRR_11111111_vs_B_cell_SRR_111111_DiffExp_v2_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] "Exonic_Only_Endothelial_SRR_11111111_B_cell_SRR_111111" [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_Exonic_Only_Endothelial_SRR_11111111_B_cell_SRR_111111.txt Down_Genes_EdgeR_Exonic_Only_Endothelial_SRR_11111111_B_cell_SRR_111111.txt Exonic_Only_Counting DiffExp_3b [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_Exonic_Only_Endothelial_SRR_11111111_B_cell_SRR_111111.txt" [1] "File2:" [1] "Down_Genes_EdgeR_Exonic_Only_Endothelial_SRR_11111111_B_cell_SRR_111111.txt" [1] "Subtitle:" [1] "Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3b" [1] "-----------------" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_Exonic_Only_Endothelial_SRR_11111111_B_cell_SRR_111111.txt Up_Genes_EdgeR_Exonic_Only_Endothelial_SRR_11111111_B_cell_SRR_111111.txt Exonic_Only_Counting DiffExp_3b [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_Exonic_Only_Endothelial_SRR_11111111_B_cell_SRR_111111.txt" [1] "File2:" [1] "Up_Genes_EdgeR_Exonic_Only_Endothelial_SRR_11111111_B_cell_SRR_111111.txt" [1] "Subtitle:" [1] "Exonic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_3b" [1] "-----------------" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- Comparison_Info: Endothelial_SRR_11111111_B_cell_SRR_111111 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 226962 Oct 19 00:31 /scratch/9022725.1.linga/Input/B_cell0.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 00:31 /scratch/9022725.1.linga/Input/B_cell0_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 227355 Oct 19 00:31 /scratch/9022725.1.linga/Input/B_cell1.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 00:31 /scratch/9022725.1.linga/Input/B_cell1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 227205 Oct 19 00:31 /scratch/9022725.1.linga/Input/B_cell2.out -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 00:31 /scratch/9022725.1.linga/Input/B_cell2_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 0 Oct 19 00:32 /scratch/9022725.1.linga/Input/DiffExp_3b_Venn_Tables_Endothelial_SRR_11111111_B_cell_SRR_111111.txt -rwxr-xr-x 1 kkarri waxmanlab 7394 Oct 19 00:31 /scratch/9022725.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 292699 Oct 19 00:31 /scratch/9022725.1.linga/Input/Exon_Only_Regions_Lengths.txt -rwxr-xr-x 1 kkarri waxmanlab 9553 Oct 19 00:31 /scratch/9022725.1.linga/Input/Venn_Diff_Genes.R -rwxr-xr-x 1 kkarri waxmanlab 3925 Oct 19 00:31 /scratch/9022725.1.linga/Input/formatForSegex_ver3.R /scratch/9022725.1.linga/Input/B_cell: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Oct 19 00:31 . drwxr-xr-x 4 kkarri waxmanlab 4096 Oct 19 00:32 .. /scratch/9022725.1.linga/Input/Endothelial: total 24 drwxr-xr-x 2 kkarri waxmanlab 4096 Oct 19 00:31 . drwxr-xr-x 4 kkarri waxmanlab 4096 Oct 19 00:32 .. -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 00:31 A10-MAA000907-3_11_M-1-1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 00:31 A11-MAA000907-3_11_M-1-1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 00:31 A19-MAA000907-3_11_M-1-1_num_mapped_reads.txt -rw-r--r-- 1 kkarri waxmanlab 7 Oct 19 00:31 A20-MAA000907-3_11_M-1-1_num_mapped_reads.txt ========================================================== List files in scratch total 200K drwx------ 3 kkarri waxmanlab 4.0K Oct 19 00:32 . drwxrwxrwt. 106 root root 164K Oct 19 00:31 .. -rw-r--r-- 1 kkarri waxmanlab 160 Oct 19 00:31 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 325 Oct 19 00:31 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Oct 19 00:32 Input -rwxr-xr-x 1 kkarri waxmanlab 16K Oct 19 00:31 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 Oct 19 00:32 . drwxr-sr-x 6 kkarri waxmanlab 32K Oct 19 00:31 .. -rw-r--r-- 1 kkarri waxmanlab 0 Oct 19 00:32 DiffExp_3b_Venn_Tables_Endothelial_SRR_11111111_B_cell_SRR_111111_featureCounts.txt ========================================================== ========================================================== Finished on : Fri Oct 19 00:32:01 EDT 2018 0 minutes and 17 seconds elapsed. ==========================================================