-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M13
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_rerun/Scripts/07b_Extract_Counts_featureCounts
ANNOTATION_FILE:
exonic_only_gene_models_ncRNA_for_counting.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun May 13 14:56:27 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/07b_Extract_Counts_featureCounts
Current job ID : 6184639
Current job name : Step_07b_LZ_M13
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6184639.1.linga

Loading required modules...


List files in scratch directory:

total 510M
drwx------   2 kkarri waxmanlab 4.0K May 13 14:56 .
drwxrwxrwt. 54 root   root       84K May 13 14:56 ..
-rw-r--r--   1 kkarri waxmanlab  19M May 13 14:56 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab    0 May 13 14:56 LZ_M13_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 475M May 13 14:56 LZ_M13_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  17M May 13 14:56 exonic_only_gene_models_ncRNA_for_counting.gtf

Starting to run my commands


Starting featureCounts


Starting Intron_Only_Regions read overlap filter


Ending Intron_Only_Regions read overlap filter

featureCounts -p  -T 16 -s 2 -g gene_id -t Exonic_Only -a exonic_only_gene_models_ncRNA_for_counting.gtf -o LZ_M13_featureCounts.out LZ_M13'_sorted'.bam

Ending featureCounts


List files in scratch

total 1.4G
drwx------   2 kkarri waxmanlab 4.0K May 13 15:04 .
drwxrwxrwt. 53 root   root       84K May 13 15:02 ..
-rw-r--r--   1 kkarri waxmanlab  19M May 13 14:56 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab 696K May 13 15:04 LZ_M13_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  292 May 13 15:04 LZ_M13_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 340M May 13 14:59 LZ_M13_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri waxmanlab 475M May 13 14:56 LZ_M13_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 552M May 13 15:03 LZ_M13_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  17M May 13 14:56 exonic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Sun May 13 15:04:14 EDT 2018
0 hours, 7 minutes and 47 seconds elapsed.
==========================================================