----------------------- Start of variable list: ----------------------- Sample_ID: D1-MAA100039-3_11_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 17:13:54 EDT 2018 Running on node : scc-ka5 Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/08b_Extract_Counts_featureCounts Current job ID : 8812866 Current job name : Step_08b_D1-MAA100039-3_11_M-1-1 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/8812866.1.linga Loading required modules... List files in scratch directory: total 118M drwx------ 2 kkarri waxmanlab 4.0K Oct 14 17:14 . drwxrwxrwt. 94 root root 128K Oct 14 17:13 .. -rw-r--r-- 1 kkarri waxmanlab 0 Oct 14 17:14 D1-MAA100039-3_11_M-1-1_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 46M Oct 14 17:13 D1-MAA100039-3_11_M-1-1_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 72M Oct 14 17:13 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 D1-MAA100039-3_11_M-1-1_assign_all_features.out D1-MAA100039-3_11_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 D1-MAA100039-3_11_M-1-1_assign_only1_feature.out D1-MAA100039-3_11_M-1-1'_sorted'.bam Processing D1-MAA100039-3_11_M-1-1_assign_all_features.out Done processing file. Processing D1-MAA100039-3_11_M-1-1_assign_only1_feature.out Done processing file. Ending featureCounts List files in scratch total 280M drwx------ 2 kkarri waxmanlab 20K Oct 14 17:19 . drwxrwxrwt. 94 root root 128K Oct 14 17:13 .. -rw-r--r-- 1 kkarri waxmanlab 17K Oct 14 17:19 D1-MAA100039-3_11_M-1-1_assign_all_features.out -rw-r--r-- 1 kkarri waxmanlab 305 Oct 14 17:17 D1-MAA100039-3_11_M-1-1_assign_all_features.out.summary -rw-r--r-- 1 kkarri waxmanlab 210K Oct 14 17:19 D1-MAA100039-3_11_M-1-1_assign_only1_feature.out -rw-r--r-- 1 kkarri waxmanlab 308 Oct 14 17:18 D1-MAA100039-3_11_M-1-1_assign_only1_feature.out.summary -rw-r--r-- 1 kkarri waxmanlab 227K Oct 14 17:19 D1-MAA100039-3_11_M-1-1_featureCounts.out -rw-r--r-- 1 kkarri waxmanlab 710 Oct 14 17:19 D1-MAA100039-3_11_M-1-1_featureCounts.out.summary -rw-r--r-- 1 kkarri waxmanlab 46M Oct 14 17:13 D1-MAA100039-3_11_M-1-1_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 94M Oct 14 17:14 D1-MAA100039-3_11_M-1-1_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 14K Oct 14 17:15 GeneSym_List.txt -rw-r--r-- 1 kkarri waxmanlab 1.3M Oct 14 17:16 GeneSym_assign_all_features.gtf -rw-r--r-- 1 kkarri waxmanlab 67M Oct 14 17:16 GeneSym_assign_only1_feature.gtf -rwxr-xr-x 1 kkarri waxmanlab 6.8K Oct 14 17:15 Parse_GTF.R -rw-r--r-- 1 kkarri waxmanlab 72M Oct 14 17:13 RefSeq_GeneBody.gtf ========================================================== Finished on : Sun Oct 14 17:19:56 EDT 2018 0 hours, 6 minutes and 4 seconds elapsed. ==========================================================