-----------------------
Start of variable list:
-----------------------
Sample_ID:
KI3
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:
ncRNA_genebodies_for_counting.gtf
FEATURE_TYPE:
gene_body
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed May  1 03:42:49 EDT 2019
Running on node : scc-pg8
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 5790404
Current job name : Step_08b_KI3
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5790404.1.p16

Loading required modules...


List files in scratch directory:

total 293M
drwx------   2 kkarri waxmanlab 4.0K May  1 03:42 .
drwxrwxrwt. 27 root   root      4.0K May  1 03:42 ..
-rw-r--r--   1 kkarri waxmanlab    0 May  1 03:42 KI3_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 290M May  1 03:42 KI3_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M May  1 03:42 ncRNA_genebodies_for_counting.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 2 -g gene_id -t gene_body -a ncRNA_genebodies_for_counting.gtf -o KI3_featureCounts.out KI3'_sorted'.bam

Ending featureCounts


List files in scratch

total 747M
drwx------   2 kkarri waxmanlab  20K May  1 03:46 .
drwxrwxrwt. 27 root   root      4.0K May  1 03:42 ..
-rw-r--r--   1 kkarri waxmanlab 693K May  1 03:46 KI3_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  292 May  1 03:46 KI3_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 290M May  1 03:42 KI3_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 454M May  1 03:45 KI3_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M May  1 03:42 ncRNA_genebodies_for_counting.gtf
==========================================================
Finished on : Wed May  1 03:46:52 EDT 2019
0 hours, 4 minutes and 3 seconds elapsed.
==========================================================