-----------------------
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:
ncRNA_genebodies_for_counting.gtf
FEATURE_TYPE:
gene_body
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed May  1 03:22:57 EDT 2019
Running on node : scc-ca4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 5790342
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/5790342.1.c

Loading required modules...


List files in scratch directory:

total 267M
drwx------   2 kkarri waxmanlab 4.0K May  1 03:23 .
drwxrwxrwt. 12 root   root      4.0K 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 3.4M May  1 03:23 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 WT11_featureCounts.out WT11'_sorted'.bam

Ending featureCounts


List files in scratch

total 677M
drwx------   2 kkarri waxmanlab  20K May  1 03:26 .
drwxrwxrwt. 12 root   root      4.0K May  1 03:22 ..
-rw-r--r--   1 kkarri waxmanlab 692K May  1 03:26 WT11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  293 May  1 03:26 WT11_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 264M May  1 03:23 WT11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 410M May  1 03:25 WT11_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M May  1 03:23 ncRNA_genebodies_for_counting.gtf
==========================================================
Finished on : Wed May  1 03:26:41 EDT 2019
0 hours, 3 minutes and 44 seconds elapsed.
==========================================================