-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M30
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:
genes.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Sep  5 22:20:59 EDT 2019
Running on node : scc-tm3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9162318
Current job name : Step_08b_G170_M30
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9162318.1.linga

Loading required modules...


List files in scratch directory:

total 1.8G
drwx------   2 kkarri waxmanlab 4.0K Sep  5 22:21 .
drwxrwxrwt. 14 root   root      4.0K Sep  5 22:20 ..
-rw-r--r--   1 kkarri waxmanlab    0 Sep  5 22:21 G170_M30_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 1.7G Sep  5 22:21 G170_M30_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M Sep  5 22:21 genes.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 2 -g gene_id -t exon -a genes.gtf -o G170_M30_featureCounts.out G170_M30'_sorted'.bam

Ending featureCounts


List files in scratch

total 5.0G
drwx------   2 kkarri waxmanlab  20K Sep  5 22:46 .
drwxrwxrwt. 14 root   root      4.0K Sep  5 22:45 ..
-rw-r--r--   1 kkarri waxmanlab 242K Sep  5 22:46 G170_M30_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  299 Sep  5 22:46 G170_M30_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 1.7G Sep  5 22:21 G170_M30_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.3G Sep  5 22:38 G170_M30_sorted.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M Sep  5 22:21 genes.gtf
==========================================================
Finished on : Thu Sep  5 22:46:08 EDT 2019
0 hours, 25 minutes and 10 seconds elapsed.
==========================================================