-----------------------
Start of variable list:
-----------------------
Sample_ID:
G166_M2
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_exon_for_counting.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Apr 23 10:52:58 EDT 2019
Running on node : scc-kb8
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 5542324
Current job name : Step_08b_G166_M2
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5542324.1.linga

Loading required modules...


List files in scratch directory:

total 1.4G
drwx------   2 kkarri waxmanlab 4.0K Apr 23 10:53 .
drwxrwxrwt. 14 root   root      112K Apr 23 10:52 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 23 10:53 G166_M2_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 1.2G Apr 23 10:53 G166_M2_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 254M Apr 23 10:53 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 G166_M2_featureCounts.out G166_M2'_sorted'.bam

Ending featureCounts


List files in scratch

total 3.6G
drwx------   2 kkarri waxmanlab  20K Apr 23 11:39 .
drwxrwxrwt. 11 root   root      112K Apr 23 11:39 ..
-rw-r--r--   1 kkarri waxmanlab 705K Apr 23 11:39 G166_M2_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  299 Apr 23 11:39 G166_M2_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 1.2G Apr 23 10:53 G166_M2_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 2.2G Apr 23 11:17 G166_M2_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 254M Apr 23 10:53 ncRNA_exon_for_counting.gtf
==========================================================
Finished on : Tue Apr 23 11:39:34 EDT 2019
0 hours, 46 minutes and 36 seconds elapsed.
==========================================================