----------------------- Start of variable list: ----------------------- Sample_ID: LZ_M5 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: Intron_Only_Regions.gtf FEATURE_TYPE: Intronic_Only ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed May 9 19:36:23 EDT 2018 Running on node : scc-kb2 Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/07b_Extract_Counts_featureCounts Current job ID : 6138950 Current job name : Step_07b_LZ_M5 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/6138950.1.linga Loading required modules... List files in scratch directory: total 294M drwx------ 2 kkarri waxmanlab 4.0K May 9 19:36 . drwxrwxrwt. 53 root root 92K May 9 19:36 .. -rw-r--r-- 1 kkarri waxmanlab 18M May 9 19:36 Intron_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 0 May 9 19:36 LZ_M5_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 276M May 9 19:36 LZ_M5_primary_unique.bam 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 LZ_M5_assign_all_features.out LZ_M5'_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 LZ_M5_assign_only1_feature.out LZ_M5'_sorted'.bam Processing LZ_M5_assign_all_features.out Done processing file. Processing LZ_M5_assign_only1_feature.out Done processing file. Ending featureCounts List files in scratch total 949M drwx------ 2 kkarri waxmanlab 4.0K May 9 19:43 . drwxrwxrwt. 51 root root 92K May 9 19:39 .. -rw-r--r-- 1 kkarri waxmanlab 4.0K May 9 19:42 GeneSym_List.txt -rw-r--r-- 1 kkarri waxmanlab 348K May 9 19:43 GeneSym_assign_all_features.gtf -rw-r--r-- 1 kkarri waxmanlab 17M May 9 19:43 GeneSym_assign_only1_feature.gtf -rw-r--r-- 1 kkarri waxmanlab 18M May 9 19:36 Intron_Only_Regions.gtf -rw-r--r-- 1 kkarri waxmanlab 5.1K May 9 19:43 LZ_M5_assign_all_features.out -rw-r--r-- 1 kkarri waxmanlab 289 May 9 19:43 LZ_M5_assign_all_features.out.summary -rw-r--r-- 1 kkarri waxmanlab 188K May 9 19:43 LZ_M5_assign_only1_feature.out -rw-r--r-- 1 kkarri waxmanlab 292 May 9 19:43 LZ_M5_assign_only1_feature.out.summary -rw-r--r-- 1 kkarri waxmanlab 230K May 9 19:43 LZ_M5_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 642 May 9 19:43 LZ_M5_featureCounts.out.summary -rw-r--r-- 1 kkarri waxmanlab 245M May 9 19:39 LZ_M5_primary_no_splice.bam -rw-r--r-- 1 kkarri waxmanlab 276M May 9 19:36 LZ_M5_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 395M May 9 19:42 LZ_M5_sorted.bam -rwxr-xr-x 1 kkarri waxmanlab 6.8K May 9 19:42 Parse_GTF.R -rwxr-xr-x 1 kkarri waxmanlab 38K May 9 19:43 RefSeq_Genes_Zero_Count.txt ========================================================== Finished on : Wed May 9 19:43:21 EDT 2018 0 hours, 6 minutes and 58 seconds elapsed. ==========================================================