-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M13
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/unprotected/projects/waxmanlab/routines/GTF_Files
STRANDEDNESS_featureCount:
2
FEATURE_ID:
gene_id
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
ncRNA_genebodies_for_counting.gtf
FEATURE_TYPE:
gene_body
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Dec 18 22:44:46 EST 2018
Running on node : scc-ka1
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 366172
Current job name : Step_08b_G123_M13
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/366172.1.linga

Loading required modules...


List files in scratch directory:

total 1.4G
drwx------   2 kkarri waxmanlab 4.0K Dec 18 22:44 .
drwxrwxrwt. 50 root   root      124K Dec 18 22:44 ..
-rw-r--r--   1 kkarri waxmanlab    0 Dec 18 22:44 G123_M13_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 1.4G Dec 18 22:44 G123_M13_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Dec 18 22:44 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 G123_M13_featureCounts.out G123_M13'_sorted'.bam

Ending featureCounts


List files in scratch

total 3.4G
drwx------   2 kkarri waxmanlab  20K Dec 18 23:12 .
drwxrwxrwt. 28 root   root      124K Dec 18 23:11 ..
-rw-r--r--   1 kkarri waxmanlab 705K Dec 18 23:12 G123_M13_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  298 Dec 18 23:12 G123_M13_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 1.4G Dec 18 22:44 G123_M13_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 2.0G Dec 18 23:06 G123_M13_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Dec 18 22:44 ncRNA_genebodies_for_counting.gtf
==========================================================
Finished on : Tue Dec 18 23:12:58 EST 2018
0 hours, 28 minutes and 12 seconds elapsed.
==========================================================