-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M32
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/Scripts/07b_Extract_Counts_featureCounts
ANNOTATION_FILE:
ncRNA_exon_for_counting.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri May 11 17:48:05 EDT 2018
Running on node : scc-ka1
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/07b_Extract_Counts_featureCounts
Current job ID : 6179047
Current job name : Step_07b_LZ_M32
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6179047.1.linga

Loading required modules...


List files in scratch directory:

total 697M
drwx------   2 kkarri waxmanlab 4.0K May 11 17:48 .
drwxrwxrwt. 62 root   root      124K May 11 17:48 ..
-rw-r--r--   1 kkarri waxmanlab    0 May 11 17:48 LZ_M32_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 443M May 11 17:48 LZ_M32_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 254M May 11 17:48 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_M32_featureCounts.out LZ_M32'_sorted'.bam

Ending featureCounts


List files in scratch

total 1.4G
drwx------   2 kkarri waxmanlab 4.0K May 11 17:56 .
drwxrwxrwt. 61 root   root      124K May 11 17:55 ..
-rw-r--r--   1 kkarri waxmanlab 699K May 11 17:56 LZ_M32_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  294 May 11 17:56 LZ_M32_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 443M May 11 17:48 LZ_M32_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 718M May 11 17:56 LZ_M32_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 254M May 11 17:48 ncRNA_exon_for_counting.gtf
==========================================================
Finished on : Fri May 11 17:56:50 EDT 2018
0 hours, 8 minutes and 45 seconds elapsed.
==========================================================