-----------------------
Start of variable list:
-----------------------
Sample_ID:
WT11
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files
STRANDEDNESS_featureCount:
2
FEATURE_ID:
gene_id
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
intronic_only_gene_models_ncRNA_for_counting.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed May  1 03:22:57 EDT 2019
Running on node : scc-ka5
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 5790338
Current job name : Step_08b_WT11
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5790338.1.linga

Loading required modules...


List files in scratch directory:

total 282M
drwx------   2 kkarri waxmanlab 4.0K May  1 03:23 .
drwxrwxrwt. 80 root   root      128K May  1 03:22 ..
-rw-r--r--   1 kkarri waxmanlab    0 May  1 03:23 WT11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 264M May  1 03:23 WT11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  19M May  1 03:23 intronic_only_gene_models_ncRNA_for_counting.gtf

Starting to run my commands


Starting featureCounts


Starting splice read filter


Ending splice read filter

featureCounts -p  -T 16 -s 2 -g gene_id -t Intronic_Only -a intronic_only_gene_models_ncRNA_for_counting.gtf -o WT11_featureCounts.out WT11'_sorted'.bam

Ending featureCounts


List files in scratch

total 845M
drwx------   2 kkarri waxmanlab  20K May  1 03:31 .
drwxrwxrwt. 80 root   root      128K May  1 03:29 ..
-rw-r--r--   1 kkarri waxmanlab 332K May  1 03:31 WT11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  292 May  1 03:31 WT11_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 223M May  1 03:25 WT11_primary_no_splice.bam
-rw-r--r--   1 kkarri waxmanlab 264M May  1 03:23 WT11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 341M May  1 03:29 WT11_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  19M May  1 03:23 intronic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Wed May  1 03:31:06 EDT 2019
0 hours, 8 minutes and 9 seconds elapsed.
==========================================================