-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M11
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/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/G123_Env/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
exonic_only_gene_models_ncRNA_for_counting.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Dec 18 22:25:25 EST 2018
Running on node : scc-ka1
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 366152
Current job name : Step_08b_G123_M11
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/366152.1.linga

Loading required modules...


List files in scratch directory:

total 1.1G
drwx------   2 kkarri waxmanlab 4.0K Dec 18 22:25 .
drwxrwxrwt. 50 root   root      124K Dec 18 22:25 ..
-rw-r--r--   1 kkarri waxmanlab    0 Dec 18 22:25 G123_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 1.1G Dec 18 22:25 G123_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  19M Dec 18 22:25 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab  17M Dec 18 22:25 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 G123_M11_featureCounts.out G123_M11'_sorted'.bam

Ending featureCounts


List files in scratch

total 1.1G
drwx------   2 kkarri waxmanlab 4.0K Dec 18 22:25 .
drwxrwxrwt. 50 root   root      124K Dec 18 22:25 ..
-rw-r--r--   1 kkarri waxmanlab 777K Dec 18 22:25 G123_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  239 Dec 18 22:25 G123_M11_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab    0 Dec 18 22:25 G123_M11_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri waxmanlab 1.1G Dec 18 22:25 G123_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  19M Dec 18 22:25 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab  17M Dec 18 22:25 exonic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Tue Dec 18 22:25:29 EST 2018
0 hours, 0 minutes and 4 seconds elapsed.
==========================================================