----------------------- Start of variable list: ----------------------- Sample_ID: G160_M66 Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G160_Samples Sample_Labels_DIR: /restricted/projectnb/waxmanlab/kkarri/G160_Samples/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/G160_Samples/Scripts/08b_Extract_Counts_featureCounts ANNOTATION_FILE: RefSeq_GeneBody.gtf FEATURE_TYPE: exon ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed Aug 30 23:49:33 EDT 2017 Running on node : scc-ca8 Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/08b_Extract_Counts_featureCounts Current job ID : 474090 Current job name : Step_08b_G160_M66 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/474090.1.c Loading required modules... List files in scratch directory: total 885M drwxr-xr-x 2 kkarri pulmseq 4.0K Aug 30 23:49 . drwxrwxrwt. 29 root root 4.0K Aug 30 23:49 .. -rw-r--r-- 1 kkarri pulmseq 0 Aug 30 23:49 G160_M66_featureCounts.out -rw-r--r-- 1 kkarri pulmseq 814M Aug 30 23:49 G160_M66_primary_unique.bam -rw-r--r-- 1 kkarri pulmseq 72M Aug 30 23:49 RefSeq_GeneBody.gtf Starting to run my commands Starting featureCounts GTF file name: RefSeq_GeneBody Rscript Parse_GTF.R RefSeq_GeneBody.gtf GeneSym_List.txt [1] "Print arguments:" [1] "-----------------" [1] "GTF_File:" [1] "RefSeq_GeneBody.gtf" [1] "Subset_List:" [1] "GeneSym_List.txt" [1] "-----------------" [1] "Loading RefSeq_GeneBody.gtf" [1] "Loading GeneSym_List.txt" [1] "Number of gene symbols in common:" [1] "1713" [1] "Percentage overlap:" [1] "98%" [1] "How many GeneSym in the GTF list and not in Subset list:" [1] "(Expect high number)" [1] 22484 [1] "How many GeneSym in the Subset list and not in GTF list:" [1] "(Due to updated RefSeq gene annotations)" [1] 27 [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 exon -a GeneSym_assign_all_features.gtf -o G160_M66_assign_all_features.out G160_M66'_sorted'.bam Running assign_only1_feature counting featureCounts -p -T 16 -s 2 -g gene_id -t exon -a GeneSym_assign_only1_feature.gtf -o G160_M66_assign_only1_feature.out G160_M66'_sorted'.bam Processing G160_M66_assign_all_features.out Done processing file. Processing G160_M66_assign_only1_feature.out Done processing file. Ending featureCounts List files in scratch total 2.3G drwxr-xr-x 2 kkarri pulmseq 24K Aug 31 00:05 . drwxrwxrwt. 29 root root 4.0K Aug 30 23:49 .. -rw-r--r-- 1 kkarri pulmseq 17K Aug 31 00:05 G160_M66_assign_all_features.out -rw-r--r-- 1 kkarri pulmseq 293 Aug 31 00:02 G160_M66_assign_all_features.out.summary -rw-r--r-- 1 kkarri pulmseq 213K Aug 31 00:05 G160_M66_assign_only1_feature.out -rw-r--r-- 1 kkarri pulmseq 298 Aug 31 00:05 G160_M66_assign_only1_feature.out.summary -rw-r--r-- 1 kkarri pulmseq 230K Aug 31 00:05 G160_M66_featureCounts.out -rw-r--r-- 1 kkarri pulmseq 658 Aug 31 00:05 G160_M66_featureCounts.out.summary -rw-r--r-- 1 kkarri pulmseq 814M Aug 30 23:49 G160_M66_primary_unique.bam -rw-r--r-- 1 kkarri pulmseq 1.4G Aug 30 23:58 G160_M66_sorted.bam -rw-r--r-- 1 kkarri pulmseq 14K Aug 30 23:58 GeneSym_List.txt -rw-r--r-- 1 kkarri pulmseq 1.3M Aug 30 23:58 GeneSym_assign_all_features.gtf -rw-r--r-- 1 kkarri pulmseq 67M Aug 30 23:58 GeneSym_assign_only1_feature.gtf -rwxr-xr-x 1 kkarri pulmseq 6.8K Aug 30 23:58 Parse_GTF.R -rw-r--r-- 1 kkarri pulmseq 72M Aug 30 23:49 RefSeq_GeneBody.gtf ========================================================== Finished on : Thu Aug 31 00:05:57 EDT 2017 0 hours, 16 minutes and 24 seconds elapsed. ==========================================================