-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M6
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_exon_for_counting.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Dec 18 21:36:36 EST 2018
Running on node : scc-kb8
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 366115
Current job name : Step_08b_G123_M6
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/366115.1.linga

Loading required modules...


List files in scratch directory:

total 1.9G
drwx------   2 kkarri waxmanlab 4.0K Dec 18 21:36 .
drwxrwxrwt. 45 root   root      112K Dec 18 21:36 ..
-rw-r--r--   1 kkarri waxmanlab    0 Dec 18 21:36 G123_M6_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 1.6G Dec 18 21:36 G123_M6_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 254M Dec 18 21:36 ncRNA_exon_for_counting.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 2 -g gene_id -t exon -a ncRNA_exon_for_counting.gtf -o G123_M6_featureCounts.out G123_M6'_sorted'.bam

Ending featureCounts


List files in scratch

total 4.1G
drwx------   2 kkarri waxmanlab  20K Dec 18 22:11 .
drwxrwxrwt. 46 root   root      112K Dec 18 22:08 ..
-rw-r--r--   1 kkarri waxmanlab 706K Dec 18 22:11 G123_M6_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  298 Dec 18 22:11 G123_M6_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 1.6G Dec 18 21:36 G123_M6_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 2.3G Dec 18 22:03 G123_M6_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 254M Dec 18 21:36 ncRNA_exon_for_counting.gtf
==========================================================
Finished on : Tue Dec 18 22:11:45 EST 2018
0 hours, 35 minutes and 9 seconds elapsed.
==========================================================