-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M19
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 15:13:35 EDT 2018
Running on node : scc-kb5
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/07b_Extract_Counts_featureCounts
Current job ID : 6184688
Current job name : Step_07b_LZ_M19
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6184688.1.linga

Loading required modules...


List files in scratch directory:

total 375M
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 13 15:13 .
drwxrwxrwt. 50 root   root      268K May 13 15:13 ..
-rw-r--r--   1 kkarri waxmanlab    0 May 13 15:13 LZ_M19_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 295M May 13 15:13 LZ_M19_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M May 13 15:13 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_M19_featureCounts.out LZ_M19'_sorted'.bam

Ending featureCounts


List files in scratch

total 867M
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 13 15:18 .
drwxrwxrwt. 50 root   root      268K May 13 15:13 ..
-rw-r--r--   1 kkarri waxmanlab 235K May 13 15:18 LZ_M19_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  296 May 13 15:18 LZ_M19_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 295M May 13 15:13 LZ_M19_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 492M May 13 15:17 LZ_M19_sorted.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M May 13 15:13 genes.gtf
==========================================================
Finished on : Sun May 13 15:18:05 EDT 2018
0 hours, 4 minutes and 30 seconds elapsed.
==========================================================