----------------------- Start of variable list: ----------------------- Sample_ID: LZ_M6 Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation Sample_Labels_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/00_Setup_Pipeline GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files STRANDEDNESS_featureCount: 2 FEATURE_ID: gene_id SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/07b_Extract_Counts_featureCounts ANNOTATION_FILE: RefSeq_GeneBody.gtf FEATURE_TYPE: exon ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed May 9 19:39:34 EDT 2018 Running on node : scc-pf4 Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/07b_Extract_Counts_featureCounts Current job ID : 6138959 Current job name : Step_07b_LZ_M6 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/6138959.1.p8 Loading required modules... List files in scratch directory: total 351M drwx------ 2 kkarri waxmanlab 4.0K May 9 19:39 . drwxrwxrwt. 24 root root 4.0K May 9 19:39 .. -rw-r--r-- 1 kkarri waxmanlab 0 May 9 19:39 LZ_M6_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 280M May 9 19:39 LZ_M6_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 72M May 9 19:39 RefSeq_GeneBody.gtf 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 LZ_M6_assign_all_features.out LZ_M6'_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 LZ_M6_assign_only1_feature.out LZ_M6'_sorted'.bam Processing LZ_M6_assign_all_features.out Done processing file. Processing LZ_M6_assign_only1_feature.out Done processing file. Ending featureCounts List files in scratch total 882M drwx------ 2 kkarri waxmanlab 4.0K May 9 19:42 . drwxrwxrwt. 24 root root 4.0K May 9 19:39 .. -rw-r--r-- 1 kkarri waxmanlab 14K May 9 19:42 GeneSym_List.txt -rw-r--r-- 1 kkarri waxmanlab 1.3M May 9 19:42 GeneSym_assign_all_features.gtf -rw-r--r-- 1 kkarri waxmanlab 67M May 9 19:42 GeneSym_assign_only1_feature.gtf -rw-r--r-- 1 kkarri waxmanlab 17K May 9 19:42 LZ_M6_assign_all_features.out -rw-r--r-- 1 kkarri waxmanlab 289 May 9 19:42 LZ_M6_assign_all_features.out.summary -rw-r--r-- 1 kkarri waxmanlab 224K May 9 19:42 LZ_M6_assign_only1_feature.out -rw-r--r-- 1 kkarri waxmanlab 294 May 9 19:42 LZ_M6_assign_only1_feature.out.summary -rw-r--r-- 1 kkarri waxmanlab 241K May 9 19:42 LZ_M6_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 644 May 9 19:42 LZ_M6_featureCounts.out.summary -rw-r--r-- 1 kkarri waxmanlab 280M May 9 19:39 LZ_M6_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 463M May 9 19:42 LZ_M6_sorted.bam -rwxr-xr-x 1 kkarri waxmanlab 6.8K May 9 19:42 Parse_GTF.R -rw-r--r-- 1 kkarri waxmanlab 72M May 9 19:39 RefSeq_GeneBody.gtf ========================================================== Finished on : Wed May 9 19:42:34 EDT 2018 0 hours, 3 minutes and 0 seconds elapsed. ==========================================================