-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M11
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New/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_New/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
ncRNA_genebodies_for_counting.gtf
FEATURE_TYPE:
gene_body
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Dec  7 23:00:32 EST 2018
Running on node : scc-kb8
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 27880
Current job name : Step_08b_G123_M11
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/27880.1.linga

Loading required modules...


List files in scratch directory:

total 1.1G
drwx------   2 kkarri waxmanlab 4.0K Dec  7 23:00 .
drwxrwxrwt. 41 root   root      112K Dec  7 23:00 ..
-rw-r--r--   1 kkarri waxmanlab    0 Dec  7 23:00 G123_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 1.1G Dec  7 23:00 G123_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Dec  7 23:00 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_M11_featureCounts.out G123_M11'_sorted'.bam

Ending featureCounts


List files in scratch

total 2.5G
drwx------   2 kkarri waxmanlab  20K Dec  7 23:19 .
drwxrwxrwt. 42 root   root      112K Dec  7 23:19 ..
-rw-r--r--   1 kkarri waxmanlab 702K Dec  7 23:19 G123_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  298 Dec  7 23:19 G123_M11_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 1.1G Dec  7 23:00 G123_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.5G Dec  7 23:15 G123_M11_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Dec  7 23:00 ncRNA_genebodies_for_counting.gtf
==========================================================
Finished on : Fri Dec  7 23:19:47 EST 2018
0 hours, 19 minutes and 15 seconds elapsed.
==========================================================