-----------------------
Start of variable list:
-----------------------
Sample_ID:
IS_M3
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 11:36:29 EDT 2017
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9395313
Current job name : Step_08b_IS_M3
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9395313.1.linga

Loading required modules...


List files in scratch directory:

total 1.8G
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 17 11:36 .
drwxrwxrwt. 69 root   root        92K Jun 17 11:36 ..
-rw-r--r--   1 kkarri montilab-p    0 Jun 17 11:36 IS_M3_featureCounts.out
-rw-r--r--   1 kkarri montilab-p 1.8G Jun 17 11:36 IS_M3_primary_unique.bam
-rwxr-xr-x   1 kkarri montilab-p  52M Jun 17 11:36 genes.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 0 -g gene_id -t exon -a genes.gtf -o IS_M3_featureCounts.out IS_M3'_sorted'.bam

Ending featureCounts


List files in scratch

total 4.4G
drwxr-xr-x   2 kkarri montilab-p  20K Jun 17 11:58 .
drwxrwxrwt. 70 root   root        92K Jun 17 11:49 ..
-rw-r--r--   1 kkarri montilab-p 164K Jun 17 11:58 IS_M3_featureCounts.out
-rw-r--r--   1 kkarri montilab-p  295 Jun 17 11:58 IS_M3_featureCounts.out.summary
-rw-r--r--   1 kkarri montilab-p 1.8G Jun 17 11:36 IS_M3_primary_unique.bam
-rw-r--r--   1 kkarri montilab-p 2.6G Jun 17 11:53 IS_M3_sorted.bam
-rwxr-xr-x   1 kkarri montilab-p  52M Jun 17 11:36 genes.gtf
==========================================================
Finished on : Sat Jun 17 11:58:52 EDT 2017
0 hours, 22 minutes and 23 seconds elapsed.
==========================================================