-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M9
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 17:02:04 EDT 2019
Running on node : scc-ph5
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9162152
Current job name : Step_08b_G170_M9
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9162152.1.p16

Loading required modules...


List files in scratch directory:

total 2.9G
drwx------   2 kkarri waxmanlab 4.0K Sep  5 17:02 .
drwxrwxrwt. 16 root   root      4.0K Sep  5 17:02 ..
-rw-r--r--   1 kkarri waxmanlab    0 Sep  5 17:02 G170_M9_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 2.6G Sep  5 17:02 G170_M9_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 254M Sep  5 17:02 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_M9_featureCounts.out G170_M9'_sorted'.bam

Ending featureCounts


List files in scratch

total 8.0G
drwx------   2 kkarri waxmanlab  24K Sep  5 17:35 .
drwxrwxrwt. 16 root   root      4.0K Sep  5 17:02 ..
-rw-r--r--   1 kkarri waxmanlab 708K Sep  5 17:35 G170_M9_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  297 Sep  5 17:35 G170_M9_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 2.6G Sep  5 17:02 G170_M9_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 5.2G Sep  5 17:26 G170_M9_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 254M Sep  5 17:02 ncRNA_exon_for_counting.gtf
==========================================================
Finished on : Thu Sep  5 17:35:43 EDT 2019
0 hours, 33 minutes and 39 seconds elapsed.
==========================================================