----------------------- Start of variable list: ----------------------- Sample_ID: G160_M33 Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G160_Samples Sample_Labels_DIR: /restricted/projectnb/waxmanlab/kkarri/G160_Samples/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/G160_Samples/Scripts/08b_Extract_Counts_featureCounts ANNOTATION_FILE: Exon_Only_Regions.gtf FEATURE_TYPE: Exonic_Only ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed Aug 30 22:22:39 EDT 2017 Running on node : scc-ph7 Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/08b_Extract_Counts_featureCounts Current job ID : 474040 Current job name : Step_08b_G160_M33 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/474040.1.p16 Loading required modules... List files in scratch directory: total 1.8G drwxr-xr-x 2 kkarri pulmseq 4.0K Aug 30 22:22 . drwxrwxrwt. 61 root root 4.0K Aug 30 22:22 .. -rw-r--r-- 1 kkarri pulmseq 19M Aug 30 22:22 Exon_Only_Regions.gtf -rw-r--r-- 1 kkarri pulmseq 0 Aug 30 22:22 G160_M33_featureCounts.out -rw-r--r-- 1 kkarri pulmseq 1.8G Aug 30 22:22 G160_M33_primary_unique.bam -rw-r--r-- 1 kkarri pulmseq 18M Aug 30 22:22 Intron_Only_Regions.gtf Starting to run my commands Starting featureCounts Starting Intron_Only_Regions read overlap filter Ending Intron_Only_Regions read overlap filter GTF file name: Exon_Only_Regions Rscript Parse_GTF.R Exon_Only_Regions.gtf GeneSym_List.txt [1] "Print arguments:" [1] "-----------------" [1] "GTF_File:" [1] "Exon_Only_Regions.gtf" [1] "Subset_List:" [1] "GeneSym_List.txt" [1] "-----------------" [1] "Loading Exon_Only_Regions.gtf" [1] "Loading GeneSym_List.txt" [1] "Number of gene symbols in common:" [1] "1725" [1] "Percentage overlap:" [1] "100%" [1] "How many GeneSym in the GTF list and not in Subset list:" [1] "(Expect high number)" [1] 22472 [1] "How many GeneSym in the Subset list and not in GTF list:" [1] "(Due to updated RefSeq gene annotations)" [1] 0 [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 Exonic_Only -a GeneSym_assign_all_features.gtf -o G160_M33_assign_all_features.out G160_M33'_sorted'.bam Running assign_only1_feature counting featureCounts -p -T 16 -s 2 -g gene_id -t Exonic_Only -a GeneSym_assign_only1_feature.gtf -o G160_M33_assign_only1_feature.out G160_M33'_sorted'.bam Processing G160_M33_assign_all_features.out Done processing file. Processing G160_M33_assign_only1_feature.out Done processing file. Ending featureCounts List files in scratch total 3.2G drwxr-xr-x 2 kkarri pulmseq 24K Aug 30 22:34 . drwxrwxrwt. 61 root root 4.0K Aug 30 22:22 .. -rw-r--r-- 1 kkarri pulmseq 19M Aug 30 22:22 Exon_Only_Regions.gtf -rw-r--r-- 1 kkarri pulmseq 17K Aug 30 22:34 G160_M33_assign_all_features.out -rw-r--r-- 1 kkarri pulmseq 291 Aug 30 22:33 G160_M33_assign_all_features.out.summary -rw-r--r-- 1 kkarri pulmseq 223K Aug 30 22:34 G160_M33_assign_only1_feature.out -rw-r--r-- 1 kkarri pulmseq 297 Aug 30 22:34 G160_M33_assign_only1_feature.out.summary -rw-r--r-- 1 kkarri pulmseq 240K Aug 30 22:34 G160_M33_featureCounts.out -rw-r--r-- 1 kkarri pulmseq 655 Aug 30 22:34 G160_M33_featureCounts.out.summary -rw-r--r-- 1 kkarri pulmseq 542M Aug 30 22:26 G160_M33_primary_no_Intron_Only.bam -rw-r--r-- 1 kkarri pulmseq 1.8G Aug 30 22:22 G160_M33_primary_unique.bam -rw-r--r-- 1 kkarri pulmseq 793M Aug 30 22:31 G160_M33_sorted.bam -rw-r--r-- 1 kkarri pulmseq 14K Aug 30 22:31 GeneSym_List.txt -rw-r--r-- 1 kkarri pulmseq 503K Aug 30 22:31 GeneSym_assign_all_features.gtf -rw-r--r-- 1 kkarri pulmseq 18M Aug 30 22:31 GeneSym_assign_only1_feature.gtf -rw-r--r-- 1 kkarri pulmseq 18M Aug 30 22:22 Intron_Only_Regions.gtf -rwxr-xr-x 1 kkarri pulmseq 6.8K Aug 30 22:31 Parse_GTF.R ========================================================== Finished on : Wed Aug 30 22:34:51 EDT 2017 0 hours, 12 minutes and 12 seconds elapsed. ==========================================================