----------------------- Start of variable list: ----------------------- Sample_ID: G170_M12 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: Intron_Only_Regions.gtf FEATURE_TYPE: Intronic_Only ----------------------- End of variable list ----------------------- ========================================================== Starting on : Thu Sep 5 18:00:46 EDT 2019 Running on node : scc-ca4 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts Current job ID : 9162171 Current job name : Step_08b_G170_M12 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9162171.1.c Loading required modules... List files in scratch directory: total 2.2G drwx------ 2 kkarri waxmanlab 4.0K Sep 5 18:01 . drwxrwxrwt. 18 root root 4.0K Sep 5 18:00 .. -rw-r--r-- 1 kkarri waxmanlab 0 Sep 5 18:01 G170_M12_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 2.1G Sep 5 18:01 G170_M12_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 18M Sep 5 18:01 Intron_Only_Regions.gtf Starting to run my commands Starting featureCounts Starting splice read filter Ending splice read filter GTF file name: Intron_Only_Regions Rscript Parse_GTF.R Intron_Only_Regions.gtf GeneSym_List.txt [1] "Print arguments:" [1] "-----------------" [1] "GTF_File:" [1] "Intron_Only_Regions.gtf" [1] "Subset_List:" [1] "GeneSym_List.txt" [1] "-----------------" [1] "Loading Intron_Only_Regions.gtf" [1] "Loading GeneSym_List.txt" [1] "Number of gene symbols in common:" [1] "524" [1] "Percentage overlap:" [1] "100%" [1] "How many GeneSym in the GTF list and not in Subset list:" [1] "(Expect high number)" [1] 19957 [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 Intronic_Only -a GeneSym_assign_all_features.gtf -o G170_M12_assign_all_features.out G170_M12'_sorted'.bam Running assign_only1_feature counting featureCounts -p -T 16 -s 2 -g gene_id -t Intronic_Only -a GeneSym_assign_only1_feature.gtf -o G170_M12_assign_only1_feature.out G170_M12'_sorted'.bam Processing G170_M12_assign_all_features.out Done processing file. Processing G170_M12_assign_only1_feature.out Done processing file. Ending featureCounts List files in scratch total 5.7G drwx------ 2 kkarri waxmanlab 20K Sep 5 18:34 . drwxrwxrwt. 18 root root 4.0K Sep 5 18:00 .. -rw-r--r-- 1 kkarri waxmanlab 5.3K Sep 5 18:34 G170_M12_assign_all_features.out -rw-r--r-- 1 kkarri waxmanlab 292 Sep 5 18:29 G170_M12_assign_all_features.out.summary -rw-r--r-- 1 kkarri waxmanlab 198K Sep 5 18:34 G170_M12_assign_only1_feature.out -rw-r--r-- 1 kkarri waxmanlab 297 Sep 5 18:34 G170_M12_assign_only1_feature.out.summary -rw-r--r-- 1 kkarri waxmanlab 240K Sep 5 18:34 G170_M12_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 656 Sep 5 18:34 G170_M12_featureCounts.out.summary -rw-r--r-- 1 kkarri waxmanlab 1.3G Sep 5 18:12 G170_M12_primary_no_splice.bam -rw-r--r-- 1 kkarri waxmanlab 2.1G Sep 5 18:01 G170_M12_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 2.3G Sep 5 18:24 G170_M12_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 4.0K Sep 5 18:24 GeneSym_List.txt -rw-r--r-- 1 kkarri waxmanlab 348K Sep 5 18:24 GeneSym_assign_all_features.gtf -rw-r--r-- 1 kkarri waxmanlab 17M Sep 5 18:24 GeneSym_assign_only1_feature.gtf -rw-r--r-- 1 kkarri waxmanlab 18M Sep 5 18:01 Intron_Only_Regions.gtf -rwxr-xr-x 1 kkarri waxmanlab 6.8K Sep 5 18:24 Parse_GTF.R -rwxr-xr-x 1 kkarri waxmanlab 38K Sep 5 18:34 RefSeq_Genes_Zero_Count.txt ========================================================== Finished on : Thu Sep 5 18:34:14 EDT 2019 0 hours, 33 minutes and 28 seconds elapsed. ==========================================================