-----------------------
Start of variable list:
-----------------------
Sample_ID:
G166_M6
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files
STRANDEDNESS_featureCount:
2
FEATURE_ID:
gene_id
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
ncRNA_genebodies_for_counting.gtf
FEATURE_TYPE:
gene_body
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Apr 23 11:43:13 EDT 2019
Running on node : scc-pg7
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 5542349
Current job name : Step_08b_G166_M6
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5542349.1.p16

Loading required modules...


List files in scratch directory:

total 103M
drwx------   2 kkarri waxmanlab 4.0K Apr 23 11:43 .
drwxrwxrwt. 26 root   root      364K Apr 23 11:43 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 23 11:43 G166_M6_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  99M Apr 23 11:43 G166_M6_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Apr 23 11:43 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 G166_M6_featureCounts.out G166_M6'_sorted'.bam

Ending featureCounts


List files in scratch

total 242M
drwx------   2 kkarri waxmanlab  20K Apr 23 11:44 .
drwxrwxrwt. 26 root   root      364K Apr 23 11:43 ..
-rw-r--r--   1 kkarri waxmanlab 687K Apr 23 11:44 G166_M6_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  295 Apr 23 11:44 G166_M6_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab  99M Apr 23 11:43 G166_M6_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 139M Apr 23 11:44 G166_M6_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Apr 23 11:43 ncRNA_genebodies_for_counting.gtf
==========================================================
Finished on : Tue Apr 23 11:44:35 EDT 2019
0 hours, 1 minutes and 22 seconds elapsed.
==========================================================