----------------------- Start of variable list: ----------------------- Sample_ID: LZ_M11 Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation Sample_Labels_DIR: /restricted/projectnb/waxmanlab/kkarri/liver_zonation/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/liver_zonation/Scripts/07b_Extract_Counts_featureCounts ANNOTATION_FILE: Exon_Only_Regions.gtf FEATURE_TYPE: Exonic_Only ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed May 9 20:01:38 EDT 2018 Running on node : scc-kb7 Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/07b_Extract_Counts_featureCounts Current job ID : 6138997 Current job name : Step_07b_LZ_M11 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/6138997.1.linga Loading required modules... List files in scratch directory: total 304M drwx------ 2 kkarri waxmanlab 4.0K May 9 20:01 . drwxrwxrwt. 48 root root 168K May 9 20:01 .. -rw-r--r-- 1 kkarri waxmanlab 19M May 9 20:01 Exon_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 18M May 9 20:01 Intron_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 0 May 9 20:01 LZ_M11_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 268M May 9 20:01 LZ_M11_primary_unique.bam 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 LZ_M11_assign_all_features.out LZ_M11'_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 LZ_M11_assign_only1_feature.out LZ_M11'_sorted'.bam Processing LZ_M11_assign_all_features.out Done processing file. Processing LZ_M11_assign_only1_feature.out Done processing file. Ending featureCounts List files in scratch total 855M drwx------ 2 kkarri waxmanlab 4.0K May 9 20:07 . drwxrwxrwt. 47 root root 168K May 9 20:07 .. -rw-r--r-- 1 kkarri waxmanlab 19M May 9 20:01 Exon_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 14K May 9 20:07 GeneSym_List.txt -rw-r--r-- 1 kkarri waxmanlab 503K May 9 20:07 GeneSym_assign_all_features.gtf -rw-r--r-- 1 kkarri waxmanlab 18M May 9 20:07 GeneSym_assign_only1_feature.gtf -rw-r--r-- 1 kkarri waxmanlab 18M May 9 20:01 Intron_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 17K May 9 20:07 LZ_M11_assign_all_features.out -rw-r--r-- 1 kkarri waxmanlab 289 May 9 20:07 LZ_M11_assign_all_features.out.summary -rw-r--r-- 1 kkarri waxmanlab 222K May 9 20:07 LZ_M11_assign_only1_feature.out -rw-r--r-- 1 kkarri waxmanlab 294 May 9 20:07 LZ_M11_assign_only1_feature.out.summary -rw-r--r-- 1 kkarri waxmanlab 239K May 9 20:07 LZ_M11_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 646 May 9 20:07 LZ_M11_featureCounts.out.summary -rw-r--r-- 1 kkarri waxmanlab 203M May 9 20:03 LZ_M11_primary_no_Intron_Only.bam -rw-r--r-- 1 kkarri waxmanlab 268M May 9 20:01 LZ_M11_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 331M May 9 20:06 LZ_M11_sorted.bam -rwxr-xr-x 1 kkarri waxmanlab 6.8K May 9 20:07 Parse_GTF.R ========================================================== Finished on : Wed May 9 20:07:25 EDT 2018 0 hours, 5 minutes and 47 seconds elapsed. ==========================================================