-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M31
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 17:46:46 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/07b_Extract_Counts_featureCounts
Current job ID : 6179039
Current job name : Step_07b_LZ_M31
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6179039.1.linga

Loading required modules...


List files in scratch directory:

total 588M
drwx------   2 kkarri waxmanlab 4.0K May 11 17:46 .
drwxrwxrwt. 40 root   root       92K May 11 17:46 ..
-rw-r--r--   1 kkarri waxmanlab    0 May 11 17:46 LZ_M31_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 335M May 11 17:46 LZ_M31_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 254M May 11 17:46 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_M31_featureCounts.out LZ_M31'_sorted'.bam

Ending featureCounts


List files in scratch

total 1.1G
drwx------   2 kkarri waxmanlab 4.0K May 11 17:52 .
drwxrwxrwt. 39 root   root       92K May 11 17:52 ..
-rw-r--r--   1 kkarri waxmanlab 697K May 11 17:52 LZ_M31_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  294 May 11 17:52 LZ_M31_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 335M May 11 17:46 LZ_M31_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 537M May 11 17:51 LZ_M31_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 254M May 11 17:46 ncRNA_exon_for_counting.gtf
==========================================================
Finished on : Fri May 11 17:52:07 EDT 2018
0 hours, 5 minutes and 21 seconds elapsed.
==========================================================