----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/09c_DiffExp_9_lncRNA_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP Dataset_Label: G168_TCPO_Env 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: MetEGFKO_F_Liv CONDITION_2_NAME: MetEGFKO_TCPO_D2 Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: ncRNA_genebodies_for_counting_lengths.txt COUNT_DIR: LncRNA_GeneBody_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_GeneBody DiffExp_Index: DiffExp_9e COL_SUFFIX: LncRNA_GeneBody COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Apr 22 19:57:57 EDT 2019 Running on node : scc-ka1 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/09c_DiffExp_9_lncRNA_featureCounts Current job ID : 5524893 Current job name : Step_09c_DiffExp_9e Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5524893.1.linga Loading required modules... ------------------------------------------ Sample_DIR: G168_G169_M4 Sample_ID: G168_G169_M4 Description: Met_EGFKO1_F_Liv M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G168_G169_M5 Sample_ID: G168_G169_M5 Description: Met_EGFKO2_F_Liv M_Num: G169 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: G168_G169_M6 Sample_ID: G168_G169_M6 Description: Met_EGFKO3_F_Liv M_Num: G169 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: G169G169G169 ------------------------------------------ ------------------------------------------ Sample_DIR: G168_G169_M15 Sample_ID: G168_G169_M15 Description: Met_EGFKO1_TCPO_D2 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G168_G169_M16 Sample_ID: G168_G169_M16 Description: Met_EGFKO2_TCPO_D2 M_Num: G169 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: G168_G169_M17 Sample_ID: G168_G169_M17 Description: Met_EGFKO3_TCPO_D2 M_Num: G169 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: G169G169G169 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 3 NUM_REP_CONDITION1: 3 ========================================================== Renaming input count files number of mapped reads (feature count summary) Status G168_G169_M4_sorted.bam Assigned 20389169 Unassigned_Ambiguity 1280177 Unassigned_MultiMapping 0 Unassigned_NoFeatures 978583 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M5_sorted.bam Assigned 18352648 Unassigned_Ambiguity 1166191 Unassigned_MultiMapping 0 Unassigned_NoFeatures 824057 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M6_sorted.bam Assigned 18538169 Unassigned_Ambiguity 1211689 Unassigned_MultiMapping 0 Unassigned_NoFeatures 872300 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M15_sorted.bam Assigned 20658965 Unassigned_Ambiguity 1327612 Unassigned_MultiMapping 0 Unassigned_NoFeatures 1089963 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M16_sorted.bam Assigned 20343449 Unassigned_Ambiguity 1363232 Unassigned_MultiMapping 0 Unassigned_NoFeatures 1164625 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status G168_G169_M17_sorted.bam Assigned 16351735 Unassigned_Ambiguity 1088617 Unassigned_MultiMapping 0 Unassigned_NoFeatures 686594 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 718372 Apr 22 19:57 /scratch/5524893.1.linga/Input/MetEGFKO_F_Liv0.out -rw-r--r-- 1 kkarri waxmanlab 303 Apr 22 19:57 /scratch/5524893.1.linga/Input/MetEGFKO_F_Liv0.summary -rw-r--r-- 1 kkarri waxmanlab 717190 Apr 22 19:57 /scratch/5524893.1.linga/Input/MetEGFKO_F_Liv1.out -rw-r--r-- 1 kkarri waxmanlab 303 Apr 22 19:57 /scratch/5524893.1.linga/Input/MetEGFKO_F_Liv1.summary -rw-r--r-- 1 kkarri waxmanlab 716689 Apr 22 19:57 /scratch/5524893.1.linga/Input/MetEGFKO_F_Liv2.out -rw-r--r-- 1 kkarri waxmanlab 303 Apr 22 19:58 /scratch/5524893.1.linga/Input/MetEGFKO_F_Liv2.summary -rw-r--r-- 1 kkarri waxmanlab 718365 Apr 22 19:58 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D20.out -rw-r--r-- 1 kkarri waxmanlab 305 Apr 22 19:58 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D20.summary -rw-r--r-- 1 kkarri waxmanlab 718426 Apr 22 19:58 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D21.out -rw-r--r-- 1 kkarri waxmanlab 305 Apr 22 19:58 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D21.summary -rw-r--r-- 1 kkarri waxmanlab 717909 Apr 22 19:58 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D22.out -rw-r--r-- 1 kkarri waxmanlab 304 Apr 22 19:58 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D22.summary -rw-r--r-- 1 kkarri waxmanlab 815529 Apr 22 19:58 /scratch/5524893.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/5524893.1.linga/Input/MetEGFKO_F_Liv: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 19:58 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 19:58 .. /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D2: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 19:58 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 19:58 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R MetEGFKO_F_Liv MetEGFKO_TCPO_D2 3 3 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/5524893.1.linga/Input DiffExp_v2_LncRNA_GeneBody ncRNA_genebodies_for_counting_lengths.txt WARNING: ignoring environment value of R_HOME [1] "Arguments for differentialAnalysisDESeq.R:" [1] "MetEGFKO_F_Liv" [1] "MetEGFKO_TCPO_D2" [1] 3 [1] 3 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/5524893.1.linga/Input" [1] "DiffExp_v2_LncRNA_GeneBody" [1] "ncRNA_genebodies_for_counting_lengths.txt" [1] "sum1:65747.358709891" "sum1:68919.9819946216" "sum1:72562.1258244104" [4] "sum1:69076.4888429743" [1] "sum2:65272.2454035604" "sum2:65005.092217459" "sum2:67464.8809651427" [4] "sum2:65914.072862054" [1] 15558 23 [1] 15558 63 [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/5524893.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_MetEGFKO_F_Liv_MetEGFKO_TCPO_D2.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_GeneBody_MetEGFKO_F_Liv_MetEGFKO_TCPO_D2.txt MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload 1 LncRNA_GeneBody WARNING: ignoring environment value of R_HOME Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_LncRNA_GeneBody_MetEGFKO_F_Liv_MetEGFKO_TCPO_D2.txt MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload 1 LncRNA_GeneBody WARNING: ignoring environment value of R_HOME ========================================================== Comparison_Info: MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_GeneBody'_'MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 97 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 58 7 [1] "Check out Up_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt!" Rscript Diff_Genes.R MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_GeneBody'_'MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169 WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 125 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 87 7 [1] "Check out Up_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt Down_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt LncRNA_GeneBody_Counting DiffExp_9e WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_9e" [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_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt Up_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt LncRNA_GeneBody_Counting DiffExp_9e WARNING: ignoring environment value of R_HOME [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt" [1] "Subtitle:" [1] "LncRNA_GeneBody_Counting" [1] "DiffExp_Index:" [1] "DiffExp_9e" [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 #---------------------------------------------------------------------------------- Comparison_Info: MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 305 Apr 22 20:02 /scratch/5524893.1.linga/Input/DiffExp_9e_Venn_Tables_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 5929932 Apr 22 20:00 /scratch/5524893.1.linga/Input/DiffExp_v2_LncRNA_GeneBody_MetEGFKO_F_Liv_MetEGFKO_TCPO_D2.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Apr 22 19:57 /scratch/5524893.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 5769 Apr 22 20:00 /scratch/5524893.1.linga/Input/Down_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 9500 Apr 22 20:00 /scratch/5524893.1.linga/Input/Down_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 718372 Apr 22 19:57 /scratch/5524893.1.linga/Input/MetEGFKO_F_Liv0.out -rw-r--r-- 1 kkarri waxmanlab 303 Apr 22 19:57 /scratch/5524893.1.linga/Input/MetEGFKO_F_Liv0.summary -rw-r--r-- 1 kkarri waxmanlab 717190 Apr 22 19:57 /scratch/5524893.1.linga/Input/MetEGFKO_F_Liv1.out -rw-r--r-- 1 kkarri waxmanlab 303 Apr 22 19:57 /scratch/5524893.1.linga/Input/MetEGFKO_F_Liv1.summary -rw-r--r-- 1 kkarri waxmanlab 716689 Apr 22 19:57 /scratch/5524893.1.linga/Input/MetEGFKO_F_Liv2.out -rw-r--r-- 1 kkarri waxmanlab 303 Apr 22 19:58 /scratch/5524893.1.linga/Input/MetEGFKO_F_Liv2.summary -rw-r--r-- 1 kkarri waxmanlab 718365 Apr 22 19:58 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D20.out -rw-r--r-- 1 kkarri waxmanlab 305 Apr 22 19:58 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D20.summary -rw-r--r-- 1 kkarri waxmanlab 718426 Apr 22 19:58 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D21.out -rw-r--r-- 1 kkarri waxmanlab 305 Apr 22 19:58 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D21.summary -rw-r--r-- 1 kkarri waxmanlab 717909 Apr 22 19:58 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D22.out -rw-r--r-- 1 kkarri waxmanlab 304 Apr 22 19:58 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D22.summary -rw-r--r-- 1 kkarri waxmanlab 2432567 Apr 22 20:00 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 2308103 Apr 22 20:00 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 1263379 Apr 22 20:00 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1654763 Apr 22 20:00 /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 12143 Apr 22 20:00 /scratch/5524893.1.linga/Input/Up_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rw-r--r-- 1 kkarri waxmanlab 14841 Apr 22 20:00 /scratch/5524893.1.linga/Input/Up_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169.txt -rwxr-xr-x 1 kkarri waxmanlab 9993 Apr 22 19:57 /scratch/5524893.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 44323 Apr 22 20:02 /scratch/5524893.1.linga/Input/Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq.png -rw-r--r-- 1 kkarri waxmanlab 42627 Apr 22 20:02 /scratch/5524893.1.linga/Input/Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 4968 Apr 22 19:57 /scratch/5524893.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Apr 22 19:57 /scratch/5524893.1.linga/Input/formatForSegex_ver4.R -rw-r--r-- 1 kkarri waxmanlab 815529 Apr 22 19:58 /scratch/5524893.1.linga/Input/ncRNA_genebodies_for_counting_lengths.txt /scratch/5524893.1.linga/Input/MetEGFKO_F_Liv: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 19:58 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 20:02 .. /scratch/5524893.1.linga/Input/MetEGFKO_TCPO_D2: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Apr 22 19:58 . drwxr-xr-x 4 kkarri waxmanlab 4096 Apr 22 20:02 .. ========================================================== List files in scratch total 3.5M drwx------ 3 kkarri waxmanlab 4.0K Apr 22 20:02 . drwxrwxrwt. 69 root root 124K Apr 22 20:01 .. -rw-r--r-- 1 kkarri waxmanlab 162 Apr 22 19:57 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 174 Apr 22 19:57 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Apr 22 20:02 Input -rwxr-xr-x 1 kkarri waxmanlab 15K Apr 22 19:57 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Apr 22 19:57 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 29M drwxr-sr-x 2 kkarri waxmanlab 4.0K Apr 22 19:57 . drwxr-sr-x 7 kkarri waxmanlab 4.0K Apr 22 19:52 .. -rw-r--r-- 1 kkarri waxmanlab 305 Apr 22 19:57 DiffExp_9e_Venn_Tables_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.7M Apr 22 19:57 DiffExp_v2_LncRNA_GeneBody_MetEGFKO_F_Liv_MetEGFKO_TCPO_D2_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 5.7K Apr 22 19:57 Down_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 9.3K Apr 22 19:57 Down_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.4M Apr 22 19:57 MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 2.3M Apr 22 19:57 MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.3M Apr 22 19:57 MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.6M Apr 22 19:57 MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_vs_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_DiffExp_v2_LncRNA_GeneBody_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 12K Apr 22 19:57 Up_Genes_DESeq_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 15K Apr 22 19:57 Up_Genes_EdgeR_LncRNA_GeneBody_MetEGFKO_TCPO_D2_G168_TCPO_Env_G169G169G169_MetEGFKO_F_Liv_G168_TCPO_Env_G169G169G169_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 44K Apr 22 19:57 Venn_Down.DESeq.GeneBody.HTSeq.Down.EdgeR.GeneBody.HTSeq_featureCounts.png -rw-r--r-- 1 kkarri waxmanlab 42K Apr 22 19:57 Venn_Up.DESeq.GeneBody.HTSeq.Up.EdgeR.GeneBody.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Mon Apr 22 20:02:45 EDT 2019 4 minutes and 48 seconds elapsed. 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