----------------------- Start of variable list: ----------------------- Sample_ID: WT11 Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo Sample_Labels_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/00_Setup_Pipeline GTF_Files_DIR: /restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files STRANDEDNESS_featureCount: 2 FEATURE_ID: gene_id SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08b_Extract_Counts_featureCounts ANNOTATION_FILE: RefSeq_GeneBody.gtf FEATURE_TYPE: exon ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed May 1 03:21:58 EDT 2019 Running on node : scc-ka1 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08b_Extract_Counts_featureCounts Current job ID : 5790333 Current job name : Step_08b_WT11 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5790333.1.linga Loading required modules... List files in scratch directory: total 335M drwx------ 2 kkarri waxmanlab 4.0K May 1 03:22 . drwxrwxrwt. 67 root root 124K May 1 03:21 .. -rw-r--r-- 1 kkarri waxmanlab 72M May 1 03:22 RefSeq_GeneBody.gtf -rw-r--r-- 1 kkarri waxmanlab 0 May 1 03:22 WT11_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 264M May 1 03:22 WT11_primary_unique.bam Starting to run my commands Starting featureCounts GTF file name: RefSeq_GeneBody Rscript Parse_GTF.R RefSeq_GeneBody.gtf GeneSym_List.txt [1] "Print arguments:" [1] "-----------------" [1] "GTF_File:" [1] "RefSeq_GeneBody.gtf" [1] "Subset_List:" [1] "GeneSym_List.txt" [1] "-----------------" [1] "Loading RefSeq_GeneBody.gtf" [1] "Loading GeneSym_List.txt" [1] "Number of gene symbols in common:" [1] "1713" [1] "Percentage overlap:" [1] "98%" [1] "How many GeneSym in the GTF list and not in Subset list:" [1] "(Expect high number)" [1] 22484 [1] "How many GeneSym in the Subset list and not in GTF list:" [1] "(Due to updated RefSeq gene annotations)" [1] 27 [1] "Check out GeneSym_assign_all_features.gtf!" [1] "GeneSym_assign_only1_feature.gtf!" Running assign_all_features counting featureCounts -O -p -T 16 -s 2 -g gene_id -t exon -a GeneSym_assign_all_features.gtf -o WT11_assign_all_features.out WT11'_sorted'.bam Running assign_only1_feature counting featureCounts -p -T 16 -s 2 -g gene_id -t exon -a GeneSym_assign_only1_feature.gtf -o WT11_assign_only1_feature.out WT11'_sorted'.bam Processing WT11_assign_all_features.out Done processing file. Processing WT11_assign_only1_feature.out Done processing file. Ending featureCounts List files in scratch total 813M drwx------ 2 kkarri waxmanlab 20K May 1 03:30 . drwxrwxrwt. 67 root root 124K May 1 03:27 .. -rw-r--r-- 1 kkarri waxmanlab 14K May 1 03:26 GeneSym_List.txt -rw-r--r-- 1 kkarri waxmanlab 1.3M May 1 03:26 GeneSym_assign_all_features.gtf -rw-r--r-- 1 kkarri waxmanlab 67M May 1 03:27 GeneSym_assign_only1_feature.gtf -rwxr-xr-x 1 kkarri waxmanlab 6.8K May 1 03:26 Parse_GTF.R -rw-r--r-- 1 kkarri waxmanlab 72M May 1 03:22 RefSeq_GeneBody.gtf -rw-r--r-- 1 kkarri waxmanlab 17K May 1 03:30 WT11_assign_all_features.out -rw-r--r-- 1 kkarri waxmanlab 287 May 1 03:28 WT11_assign_all_features.out.summary -rw-r--r-- 1 kkarri waxmanlab 218K May 1 03:30 WT11_assign_only1_feature.out -rw-r--r-- 1 kkarri waxmanlab 291 May 1 03:30 WT11_assign_only1_feature.out.summary -rw-r--r-- 1 kkarri waxmanlab 235K May 1 03:30 WT11_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 637 May 1 03:30 WT11_featureCounts.out.summary -rw-r--r-- 1 kkarri waxmanlab 264M May 1 03:22 WT11_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 410M May 1 03:26 WT11_sorted.bam ========================================================== Finished on : Wed May 1 03:30:28 EDT 2019 0 hours, 8 minutes and 30 seconds elapsed. ==========================================================