----------------------- Start of variable list: ----------------------- Sample_ID: G170_M15 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 18:50:43 EDT 2019 Running on node : scc-tm2 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts Current job ID : 9162194 Current job name : Step_08b_G170_M15 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9162194.1.linga Loading required modules... List files in scratch directory: total 2.1G drwx------ 2 kkarri waxmanlab 4.0K Sep 5 18:51 . drwxrwxrwt. 13 root root 4.0K Sep 5 18:50 .. -rw-r--r-- 1 kkarri waxmanlab 19M Sep 5 18:51 Exon_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 0 Sep 5 18:51 G170_M15_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 2.1G Sep 5 18:51 G170_M15_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 18M Sep 5 18:51 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_M15_assign_all_features.out G170_M15'_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_M15_assign_only1_feature.out G170_M15'_sorted'.bam Processing G170_M15_assign_all_features.out Done processing file. Processing G170_M15_assign_only1_feature.out Done processing file. Ending featureCounts List files in scratch total 5.0G drwx------ 2 kkarri waxmanlab 24K Sep 5 19:16 . drwxrwxrwt. 13 root root 4.0K Sep 5 18:50 .. -rw-r--r-- 1 kkarri waxmanlab 19M Sep 5 18:51 Exon_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 18K Sep 5 19:16 G170_M15_assign_all_features.out -rw-r--r-- 1 kkarri waxmanlab 292 Sep 5 19:12 G170_M15_assign_all_features.out.summary -rw-r--r-- 1 kkarri waxmanlab 229K Sep 5 19:16 G170_M15_assign_only1_feature.out -rw-r--r-- 1 kkarri waxmanlab 298 Sep 5 19:16 G170_M15_assign_only1_feature.out.summary -rw-r--r-- 1 kkarri waxmanlab 246K Sep 5 19:16 G170_M15_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 657 Sep 5 19:16 G170_M15_featureCounts.out.summary -rw-r--r-- 1 kkarri waxmanlab 959M Sep 5 18:56 G170_M15_primary_no_Intron_Only.bam -rw-r--r-- 1 kkarri waxmanlab 2.1G Sep 5 18:51 G170_M15_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 1.9G Sep 5 19:07 G170_M15_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 14K Sep 5 19:07 GeneSym_List.txt -rw-r--r-- 1 kkarri waxmanlab 503K Sep 5 19:07 GeneSym_assign_all_features.gtf -rw-r--r-- 1 kkarri waxmanlab 18M Sep 5 19:07 GeneSym_assign_only1_feature.gtf -rw-r--r-- 1 kkarri waxmanlab 18M Sep 5 18:51 Intron_Only_Regions.gtf -rwxr-xr-x 1 kkarri waxmanlab 6.8K Sep 5 19:07 Parse_GTF.R ========================================================== Finished on : Thu Sep 5 19:16:57 EDT 2019 0 hours, 26 minutes and 14 seconds elapsed. ==========================================================