-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M27
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/unprotected/projects/waxmanlab/routines/GTF_Files
STRANDEDNESS_featureCount:
2
FEATURE_ID:
gene_id
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
ncRNA_genebodies_for_counting.gtf
FEATURE_TYPE:
gene_body
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Sep  5 21:47:31 EDT 2019
Running on node : scc-ka8
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9162297
Current job name : Step_08b_G170_M27
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9162297.1.linga

Loading required modules...


List files in scratch directory:

total 2.0G
drwx------   2 kkarri waxmanlab 4.0K Sep  5 21:47 .
drwxrwxrwt. 55 root   root       12K Sep  5 21:47 ..
-rw-r--r--   1 kkarri waxmanlab    0 Sep  5 21:47 G170_M27_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 2.0G Sep  5 21:47 G170_M27_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Sep  5 21:47 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 G170_M27_featureCounts.out G170_M27'_sorted'.bam

Ending featureCounts


List files in scratch

total 6.0G
drwx------   2 kkarri waxmanlab  20K Sep  5 22:25 .
drwxrwxrwt. 56 root   root       12K Sep  5 22:13 ..
-rw-r--r--   1 kkarri waxmanlab 705K Sep  5 22:25 G170_M27_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  299 Sep  5 22:25 G170_M27_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 2.0G Sep  5 21:47 G170_M27_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 4.0G Sep  5 22:16 G170_M27_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Sep  5 21:47 ncRNA_genebodies_for_counting.gtf
==========================================================
Finished on : Thu Sep  5 22:25:46 EDT 2019
0 hours, 38 minutes and 15 seconds elapsed.
==========================================================