-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M29
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 17:38:20 EDT 2018
Running on node : scc-tk3
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/07b_Extract_Counts_featureCounts
Current job ID : 6179023
Current job name : Step_07b_LZ_M29
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6179023.1.linga

Loading required modules...


List files in scratch directory:

total 642M
drwx------   2 kkarri waxmanlab 4.0K May 11 17:38 .
drwxrwxrwt. 21 root   root       20K May 11 17:38 ..
-rw-r--r--   1 kkarri waxmanlab    0 May 11 17:38 LZ_M29_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 389M May 11 17:38 LZ_M29_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 254M May 11 17:38 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_M29_featureCounts.out LZ_M29'_sorted'.bam

Ending featureCounts


List files in scratch

total 1.3G
drwx------   2 kkarri waxmanlab 4.0K May 11 17:42 .
drwxrwxrwt. 21 root   root       20K May 11 17:38 ..
-rw-r--r--   1 kkarri waxmanlab 698K May 11 17:42 LZ_M29_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  294 May 11 17:42 LZ_M29_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 389M May 11 17:38 LZ_M29_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 628M May 11 17:41 LZ_M29_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 254M May 11 17:38 ncRNA_exon_for_counting.gtf
==========================================================
Finished on : Fri May 11 17:42:09 EDT 2018
0 hours, 3 minutes and 49 seconds elapsed.
==========================================================