-----------------------
Start of variable list:
-----------------------
Sample_ID:
TA_IP2
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_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/IP_Saline/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
genes.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Jun 15 09:56:00 EDT 2017
Running on node : scc-pf1
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9333834
Current job name : Step_08b_TA_IP2
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9333834.1.p8

Loading required modules...


List files in scratch directory:

total 2.4G
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 09:56 .
drwxrwxrwt. 33 root   root       4.0K Jun 15 09:56 ..
-rw-r--r--   1 kkarri montilab-p    0 Jun 15 09:56 TA_IP2_featureCounts.out
-rw-r--r--   1 kkarri montilab-p 2.3G Jun 15 09:56 TA_IP2_primary_unique.bam
-rwxr-xr-x   1 kkarri montilab-p  52M Jun 15 09:56 genes.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 0 -g gene_id -t exon -a genes.gtf -o TA_IP2_featureCounts.out TA_IP2'_sorted'.bam

Ending featureCounts


List files in scratch

total 5.7G
drwxr-xr-x   2 kkarri montilab-p  20K Jun 15 10:14 .
drwxrwxrwt. 33 root   root       4.0K Jun 15 09:56 ..
-rw-r--r--   1 kkarri montilab-p 167K Jun 15 10:14 TA_IP2_featureCounts.out
-rw-r--r--   1 kkarri montilab-p  297 Jun 15 10:14 TA_IP2_featureCounts.out.summary
-rw-r--r--   1 kkarri montilab-p 2.3G Jun 15 09:56 TA_IP2_primary_unique.bam
-rw-r--r--   1 kkarri montilab-p 3.4G Jun 15 10:09 TA_IP2_sorted.bam
-rwxr-xr-x   1 kkarri montilab-p  52M Jun 15 09:56 genes.gtf
==========================================================
Finished on : Thu Jun 15 10:14:01 EDT 2017
0 hours, 18 minutes and 1 seconds elapsed.
==========================================================