-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M7
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_exon_for_counting.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Sep  5 16:22:28 EDT 2019
Running on node : scc-tl2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9162136
Current job name : Step_08b_G170_M7
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9162136.1.linga

Loading required modules...


List files in scratch directory:

total 2.0G
drwx------   2 kkarri waxmanlab 4.0K Sep  5 16:27 .
drwxrwxrwt. 17 root   root      4.0K Sep  5 16:04 ..
-rw-r--r--   1 kkarri waxmanlab    0 Sep  5 16:27 G170_M7_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 1.8G Sep  5 16:27 G170_M7_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 254M Sep  5 16:27 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 G170_M7_featureCounts.out G170_M7'_sorted'.bam

Ending featureCounts


List files in scratch

total 5.4G
drwx------   2 kkarri waxmanlab  20K Sep  5 16:56 .
drwxrwxrwt. 17 root   root      4.0K Sep  5 16:04 ..
-rw-r--r--   1 kkarri waxmanlab 705K Sep  5 16:56 G170_M7_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  297 Sep  5 16:56 G170_M7_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 1.8G Sep  5 16:27 G170_M7_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.4G Sep  5 16:49 G170_M7_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 254M Sep  5 16:27 ncRNA_exon_for_counting.gtf
==========================================================
Finished on : Thu Sep  5 16:56:46 EDT 2019
0 hours, 34 minutes and 19 seconds elapsed.
==========================================================