----------------------- Start of variable list: ----------------------- Sample_ID: G168_G169_M16 Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP Sample_Labels_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/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/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/08b_Extract_Counts_featureCounts ANNOTATION_FILE: Exon_Only_Regions.gtf FEATURE_TYPE: Exonic_Only ----------------------- End of variable list ----------------------- ========================================================== Starting on : Sun Apr 21 01:30:58 EDT 2019 Running on node : scc-ca7 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/08b_Extract_Counts_featureCounts Current job ID : 5412471 Current job name : Step_08b_G168_G169_M16 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5412471.1.c Loading required modules... List files in scratch directory: total 2.2G drwx------ 2 kkarri waxmanlab 4.0K Apr 21 01:31 . drwxrwxrwt. 8 root root 100K Apr 21 01:30 .. -rw-r--r-- 1 kkarri waxmanlab 19M Apr 21 01:31 Exon_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 0 Apr 21 01:31 G168_G169_M16_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 2.2G Apr 21 01:31 G168_G169_M16_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 18M Apr 21 01:31 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 G168_G169_M16_assign_all_features.out G168_G169_M16'_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 G168_G169_M16_assign_only1_feature.out G168_G169_M16'_sorted'.bam Processing G168_G169_M16_assign_all_features.out Done processing file. Processing G168_G169_M16_assign_only1_feature.out Done processing file. Ending featureCounts List files in scratch total 4.9G drwx------ 2 kkarri waxmanlab 20K Apr 21 01:55 . drwxrwxrwt. 8 root root 100K Apr 21 01:30 .. -rw-r--r-- 1 kkarri waxmanlab 19M Apr 21 01:31 Exon_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 17K Apr 21 01:55 G168_G169_M16_assign_all_features.out -rw-r--r-- 1 kkarri waxmanlab 297 Apr 21 01:51 G168_G169_M16_assign_all_features.out.summary -rw-r--r-- 1 kkarri waxmanlab 224K Apr 21 01:55 G168_G169_M16_assign_only1_feature.out -rw-r--r-- 1 kkarri waxmanlab 302 Apr 21 01:55 G168_G169_M16_assign_only1_feature.out.summary -rw-r--r-- 1 kkarri waxmanlab 241K Apr 21 01:55 G168_G169_M16_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 676 Apr 21 01:55 G168_G169_M16_featureCounts.out.summary -rw-r--r-- 1 kkarri waxmanlab 954M Apr 21 01:38 G168_G169_M16_primary_no_Intron_Only.bam -rw-r--r-- 1 kkarri waxmanlab 2.2G Apr 21 01:31 G168_G169_M16_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 1.8G Apr 21 01:47 G168_G169_M16_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 14K Apr 21 01:48 GeneSym_List.txt -rw-r--r-- 1 kkarri waxmanlab 503K Apr 21 01:48 GeneSym_assign_all_features.gtf -rw-r--r-- 1 kkarri waxmanlab 18M Apr 21 01:48 GeneSym_assign_only1_feature.gtf -rw-r--r-- 1 kkarri waxmanlab 18M Apr 21 01:31 Intron_Only_Regions.gtf -rwxr-xr-x 1 kkarri waxmanlab 6.8K Apr 21 01:48 Parse_GTF.R ========================================================== Finished on : Sun Apr 21 01:55:31 EDT 2019 0 hours, 24 minutes and 33 seconds elapsed. ==========================================================