-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M10
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:
exonic_only_gene_models_ncRNA_for_counting.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed May  9 19:54:49 EDT 2018
Running on node : scc-ka1
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/07b_Extract_Counts_featureCounts
Current job ID : 6138992
Current job name : Step_07b_LZ_M10
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6138992.1.linga

Loading required modules...


List files in scratch directory:

total 369M
drwx------   2 kkarri waxmanlab 4.0K May  9 19:54 .
drwxrwxrwt. 60 root   root      124K May  9 19:54 ..
-rw-r--r--   1 kkarri waxmanlab  19M May  9 19:54 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab    0 May  9 19:54 LZ_M10_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 334M May  9 19:54 LZ_M10_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  17M May  9 19:54 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_M10_featureCounts.out LZ_M10'_sorted'.bam

Ending featureCounts


List files in scratch

total 1008M
drwx------   2 kkarri waxmanlab 4.0K May  9 20:01 .
drwxrwxrwt. 49 root   root      124K May  9 20:00 ..
-rw-r--r--   1 kkarri waxmanlab  19M May  9 19:54 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab 695K May  9 20:01 LZ_M10_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  291 May  9 20:01 LZ_M10_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 243M May  9 19:57 LZ_M10_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri waxmanlab 334M May  9 19:54 LZ_M10_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 397M May  9 20:01 LZ_M10_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  17M May  9 19:54 exonic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Wed May  9 20:01:25 EDT 2018
0 hours, 6 minutes and 36 seconds elapsed.
==========================================================