-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M11
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/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/Scripts/07b_Extract_Counts_featureCounts
ANNOTATION_FILE:
ncRNA_genebodies_for_counting.gtf
FEATURE_TYPE:
gene_body
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed May  9 20:02:37 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/07b_Extract_Counts_featureCounts
Current job ID : 6139004
Current job name : Step_07b_LZ_M11
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6139004.1.linga

Loading required modules...


List files in scratch directory:

total 271M
drwx------   2 kkarri waxmanlab 4.0K May  9 20:02 .
drwxrwxrwt. 61 root   root      112K May  9 20:02 ..
-rw-r--r--   1 kkarri waxmanlab    0 May  9 20:02 LZ_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 268M May  9 20:02 LZ_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M May  9 20:02 ncRNA_genebodies_for_counting.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 2 -g gene_id -t gene_body -a ncRNA_genebodies_for_counting.gtf -o LZ_M11_featureCounts.out LZ_M11'_sorted'.bam

Ending featureCounts


List files in scratch

total 708M
drwx------   2 kkarri waxmanlab 4.0K May  9 20:07 .
drwxrwxrwt. 62 root   root      112K May  9 20:03 ..
-rw-r--r--   1 kkarri waxmanlab 697K May  9 20:07 LZ_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  295 May  9 20:07 LZ_M11_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 268M May  9 20:02 LZ_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 436M May  9 20:07 LZ_M11_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M May  9 20:02 ncRNA_genebodies_for_counting.gtf
==========================================================
Finished on : Wed May  9 20:07:18 EDT 2018
0 hours, 4 minutes and 41 seconds elapsed.
==========================================================