----------------------- Start of variable list: ----------------------- Sample_ID: G170_M13 Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170 Sample_Labels_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/00_Setup_Pipeline GTF_Files_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files STRANDEDNESS_featureCount: 2 FEATURE_ID: gene_id SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts ANNOTATION_FILE: Exon_Only_Regions.gtf FEATURE_TYPE: Exonic_Only ----------------------- End of variable list ----------------------- ========================================================== Starting on : Thu Sep 5 18:18:33 EDT 2019 Running on node : scc-kb7 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts Current job ID : 9162178 Current job name : Step_08b_G170_M13 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9162178.1.linga Loading required modules... List files in scratch directory: total 2.0G drwx------ 2 kkarri waxmanlab 4.0K Sep 5 18:18 . drwxrwxrwt. 52 root root 4.0K Sep 5 18:18 .. -rw-r--r-- 1 kkarri waxmanlab 19M Sep 5 18:18 Exon_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 0 Sep 5 18:18 G170_M13_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 2.0G Sep 5 18:18 G170_M13_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 18M Sep 5 18:18 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 G170_M13_assign_all_features.out G170_M13'_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 G170_M13_assign_only1_feature.out G170_M13'_sorted'.bam Processing G170_M13_assign_all_features.out Done processing file. Processing G170_M13_assign_only1_feature.out Done processing file. Ending featureCounts List files in scratch total 4.5G drwx------ 2 kkarri waxmanlab 20K Sep 5 18:49 . drwxrwxrwt. 53 root root 4.0K Sep 5 18:43 .. -rw-r--r-- 1 kkarri waxmanlab 19M Sep 5 18:18 Exon_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 18K Sep 5 18:49 G170_M13_assign_all_features.out -rw-r--r-- 1 kkarri waxmanlab 292 Sep 5 18:44 G170_M13_assign_all_features.out.summary -rw-r--r-- 1 kkarri waxmanlab 228K Sep 5 18:49 G170_M13_assign_only1_feature.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 5 18:49 G170_M13_assign_only1_feature.out.summary -rw-r--r-- 1 kkarri waxmanlab 245K Sep 5 18:49 G170_M13_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 656 Sep 5 18:49 G170_M13_featureCounts.out.summary -rw-r--r-- 1 kkarri waxmanlab 857M Sep 5 18:28 G170_M13_primary_no_Intron_Only.bam -rw-r--r-- 1 kkarri waxmanlab 2.0G Sep 5 18:18 G170_M13_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 1.7G Sep 5 18:40 G170_M13_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 14K Sep 5 18:40 GeneSym_List.txt -rw-r--r-- 1 kkarri waxmanlab 503K Sep 5 18:40 GeneSym_assign_all_features.gtf -rw-r--r-- 1 kkarri waxmanlab 18M Sep 5 18:40 GeneSym_assign_only1_feature.gtf -rw-r--r-- 1 kkarri waxmanlab 18M Sep 5 18:18 Intron_Only_Regions.gtf -rwxr-xr-x 1 kkarri waxmanlab 6.8K Sep 5 18:40 Parse_GTF.R ========================================================== Finished on : Thu Sep 5 18:49:10 EDT 2019 0 hours, 30 minutes and 37 seconds elapsed. ==========================================================