-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M28
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/unprotected/projects/waxmanlab/routines/GTF_Files
STRANDEDNESS_featureCount:
2
FEATURE_ID:
gene_id
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/07b_Extract_Counts_featureCounts
ANNOTATION_FILE:
genes.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun May 13 15:37:49 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/07b_Extract_Counts_featureCounts
Current job ID : 6184760
Current job name : Step_07b_LZ_M28
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6184760.1.linga

Loading required modules...


List files in scratch directory:

total 453M
drwx------   2 kkarri waxmanlab 4.0K May 13 15:37 .
drwxrwxrwt. 56 root   root       84K May 13 15:37 ..
-rw-r--r--   1 kkarri waxmanlab    0 May 13 15:37 LZ_M28_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 372M May 13 15:37 LZ_M28_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M May 13 15:37 genes.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 2 -g gene_id -t exon -a genes.gtf -o LZ_M28_featureCounts.out LZ_M28'_sorted'.bam

Ending featureCounts


List files in scratch

total 1.1G
drwx------   2 kkarri waxmanlab 4.0K May 13 15:42 .
drwxrwxrwt. 56 root   root       84K May 13 15:37 ..
-rw-r--r--   1 kkarri waxmanlab 236K May 13 15:42 LZ_M28_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  296 May 13 15:42 LZ_M28_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 372M May 13 15:37 LZ_M28_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 597M May 13 15:42 LZ_M28_sorted.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M May 13 15:37 genes.gtf
==========================================================
Finished on : Sun May 13 15:42:56 EDT 2018
0 hours, 5 minutes and 7 seconds elapsed.
==========================================================