-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M9
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_exon_for_counting.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed May  9 19:53:32 EDT 2018
Running on node : scc-ka6
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/07b_Extract_Counts_featureCounts
Current job ID : 6138987
Current job name : Step_07b_LZ_M9
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6138987.1.linga

Loading required modules...


List files in scratch directory:

total 588M
drwx------   2 kkarri waxmanlab 4.0K May  9 19:53 .
drwxrwxrwt. 51 root   root       92K May  9 19:53 ..
-rw-r--r--   1 kkarri waxmanlab    0 May  9 19:53 LZ_M9_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 335M May  9 19:53 LZ_M9_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 254M May  9 19:53 ncRNA_exon_for_counting.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 2 -g gene_id -t exon -a ncRNA_exon_for_counting.gtf -o LZ_M9_featureCounts.out LZ_M9'_sorted'.bam

Ending featureCounts


List files in scratch

total 1.2G
drwx------   2 kkarri waxmanlab 4.0K May  9 19:59 .
drwxrwxrwt. 53 root   root       92K May  9 19:56 ..
-rw-r--r--   1 kkarri waxmanlab 698K May  9 19:59 LZ_M9_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  293 May  9 19:59 LZ_M9_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 335M May  9 19:53 LZ_M9_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 549M May  9 19:58 LZ_M9_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 254M May  9 19:53 ncRNA_exon_for_counting.gtf
==========================================================
Finished on : Wed May  9 19:59:12 EDT 2018
0 hours, 5 minutes and 40 seconds elapsed.
==========================================================