----------------------- Start of variable list: ----------------------- Sample_ID: G7-MAA100042-3_9_M-1-1 Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq Sample_Labels_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/00_Setup_Pipeline GTF_Files_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/GTF_Files STRANDEDNESS_featureCount: 0 FEATURE_ID: gene_id SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/08b_Extract_Counts_featureCounts ANNOTATION_FILE: RefSeq_GeneBody.gtf FEATURE_TYPE: exon ----------------------- End of variable list ----------------------- ========================================================== Starting on : Sun Oct 14 19:35:33 EDT 2018 Running on node : scc-kb4 Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/08b_Extract_Counts_featureCounts Current job ID : 8813599 Current job name : Step_08b_G7-MAA100042-3_9_M-1-1 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/8813599.1.linga Loading required modules... List files in scratch directory: total 131M drwx------ 2 kkarri waxmanlab 4.0K Oct 14 19:35 . drwxrwxrwt. 88 root root 164K Oct 14 19:35 .. -rw-r--r-- 1 kkarri waxmanlab 0 Oct 14 19:35 G7-MAA100042-3_9_M-1-1_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 59M Oct 14 19:35 G7-MAA100042-3_9_M-1-1_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 72M Oct 14 19:35 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] 22576 [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 0 -g gene_id -t exon -a GeneSym_assign_all_features.gtf -o G7-MAA100042-3_9_M-1-1_assign_all_features.out G7-MAA100042-3_9_M-1-1'_sorted'.bam Running assign_only1_feature counting featureCounts -p -T 16 -s 0 -g gene_id -t exon -a GeneSym_assign_only1_feature.gtf -o G7-MAA100042-3_9_M-1-1_assign_only1_feature.out G7-MAA100042-3_9_M-1-1'_sorted'.bam Processing G7-MAA100042-3_9_M-1-1_assign_all_features.out Done processing file. Processing G7-MAA100042-3_9_M-1-1_assign_only1_feature.out Done processing file. Ending featureCounts List files in scratch total 327M drwx------ 2 kkarri waxmanlab 24K Oct 14 19:38 . drwxrwxrwt. 73 root root 164K Oct 14 19:37 .. -rw-r--r-- 1 kkarri waxmanlab 17K Oct 14 19:38 G7-MAA100042-3_9_M-1-1_assign_all_features.out -rw-r--r-- 1 kkarri waxmanlab 305 Oct 14 19:37 G7-MAA100042-3_9_M-1-1_assign_all_features.out.summary -rw-r--r-- 1 kkarri waxmanlab 211K Oct 14 19:38 G7-MAA100042-3_9_M-1-1_assign_only1_feature.out -rw-r--r-- 1 kkarri waxmanlab 308 Oct 14 19:38 G7-MAA100042-3_9_M-1-1_assign_only1_feature.out.summary -rw-r--r-- 1 kkarri waxmanlab 227K Oct 14 19:38 G7-MAA100042-3_9_M-1-1_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 708 Oct 14 19:38 G7-MAA100042-3_9_M-1-1_featureCounts.out.summary -rw-r--r-- 1 kkarri waxmanlab 59M Oct 14 19:35 G7-MAA100042-3_9_M-1-1_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 128M Oct 14 19:36 G7-MAA100042-3_9_M-1-1_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 14K Oct 14 19:36 GeneSym_List.txt -rw-r--r-- 1 kkarri waxmanlab 1.3M Oct 14 19:36 GeneSym_assign_all_features.gtf -rw-r--r-- 1 kkarri waxmanlab 67M Oct 14 19:36 GeneSym_assign_only1_feature.gtf -rwxr-xr-x 1 kkarri waxmanlab 6.8K Oct 14 19:36 Parse_GTF.R -rw-r--r-- 1 kkarri waxmanlab 72M Oct 14 19:35 RefSeq_GeneBody.gtf ========================================================== Finished on : Sun Oct 14 19:38:10 EDT 2018 0 hours, 2 minutes and 37 seconds elapsed. ==========================================================