-----------------------
Start of variable list:
-----------------------
Sample_ID:
WT10
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/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/CAR_Project_Data/GSE96650_LxRKo/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
genes.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed May  1 03:16:55 EDT 2019
Running on node : scc-pf4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 5790317
Current job name : Step_08b_WT10
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5790317.1.p8

Loading required modules...


List files in scratch directory:

total 344M
drwx------   2 kkarri waxmanlab 4.0K May  1 03:17 .
drwxrwxrwt. 26 root   root      4.0K May  1 03:16 ..
-rw-r--r--   1 kkarri waxmanlab    0 May  1 03:17 WT10_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 264M May  1 03:17 WT10_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M May  1 03:17 genes.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 2 -g gene_id -t exon -a genes.gtf -o WT10_featureCounts.out WT10'_sorted'.bam

Ending featureCounts


List files in scratch

total 754M
drwx------   2 kkarri waxmanlab  20K May  1 03:20 .
drwxrwxrwt. 26 root   root      4.0K May  1 03:16 ..
-rw-r--r--   1 kkarri waxmanlab 229K May  1 03:20 WT10_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  292 May  1 03:20 WT10_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 264M May  1 03:17 WT10_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 411M May  1 03:19 WT10_sorted.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M May  1 03:17 genes.gtf
==========================================================
Finished on : Wed May  1 03:20:40 EDT 2019
0 hours, 3 minutes and 46 seconds elapsed.
==========================================================