-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M1
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 19:21:27 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/07b_Extract_Counts_featureCounts
Current job ID : 6138923
Current job name : Step_07b_LZ_M1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6138923.1.linga

Loading required modules...


List files in scratch directory:

total 605M
drwx------   2 kkarri waxmanlab 4.0K May  9 19:21 .
drwxrwxrwt. 58 root   root      112K May  9 19:21 ..
-rw-r--r--   1 kkarri waxmanlab    0 May  9 19:21 LZ_M1_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 351M May  9 19:21 LZ_M1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 254M May  9 19:21 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_M1_featureCounts.out LZ_M1'_sorted'.bam

Ending featureCounts


List files in scratch

total 1.2G
drwx------   2 kkarri waxmanlab 4.0K May  9 19:27 .
drwxrwxrwt. 62 root   root      112K May  9 19:25 ..
-rw-r--r--   1 kkarri waxmanlab 698K May  9 19:27 LZ_M1_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  293 May  9 19:27 LZ_M1_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 351M May  9 19:21 LZ_M1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 576M May  9 19:26 LZ_M1_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 254M May  9 19:21 ncRNA_exon_for_counting.gtf
==========================================================
Finished on : Wed May  9 19:27:08 EDT 2018
0 hours, 5 minutes and 41 seconds elapsed.
==========================================================