-----------------------
Start of variable list:
-----------------------
Sample_ID:
PB_M1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/restricted/projectnb/waxmanlab/kkarri/GTF_Files1
STRANDEDNESS_featureCount:
0
FEATURE_ID:
gene_id
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
genes.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sat Jun 17 12:09:48 EDT 2017
Running on node : scc-ka1
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9395325
Current job name : Step_08b_PB_M1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9395325.1.linga

Loading required modules...


List files in scratch directory:

total 2.2G
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 17 12:09 .
drwxrwxrwt. 201 root   root       124K Jun 17 12:09 ..
-rw-r--r--    1 kkarri montilab-p    0 Jun 17 12:09 PB_M1_featureCounts.out
-rw-r--r--    1 kkarri montilab-p 2.1G Jun 17 12:09 PB_M1_primary_unique.bam
-rwxr-xr-x    1 kkarri montilab-p  52M Jun 17 12:09 genes.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 0 -g gene_id -t exon -a genes.gtf -o PB_M1_featureCounts.out PB_M1'_sorted'.bam

Ending featureCounts


List files in scratch

total 5.3G
drwxr-xr-x    2 kkarri montilab-p  20K Jun 17 12:35 .
drwxrwxrwt. 201 root   root       124K Jun 17 12:09 ..
-rw-r--r--    1 kkarri montilab-p 165K Jun 17 12:35 PB_M1_featureCounts.out
-rw-r--r--    1 kkarri montilab-p  296 Jun 17 12:35 PB_M1_featureCounts.out.summary
-rw-r--r--    1 kkarri montilab-p 2.1G Jun 17 12:09 PB_M1_primary_unique.bam
-rw-r--r--    1 kkarri montilab-p 3.2G Jun 17 12:29 PB_M1_sorted.bam
-rwxr-xr-x    1 kkarri montilab-p  52M Jun 17 12:09 genes.gtf
==========================================================
Finished on : Sat Jun 17 12:35:53 EDT 2017
0 hours, 26 minutes and 5 seconds elapsed.
==========================================================