-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M13
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/unprotected/projects/waxmanlab/routines/GTF_Files
STRANDEDNESS_featureCount:
2
FEATURE_ID:
gene_id
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/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 : Thu Sep  5 18:23:37 EDT 2019
Running on node : scc-ka5
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9162181
Current job name : Step_08b_G170_M13
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9162181.1.linga

Loading required modules...


List files in scratch directory:

total 2.0G
drwx------   2 kkarri waxmanlab 4.0K Sep  5 18:23 .
drwxrwxrwt. 40 root   root      4.0K Sep  5 18:23 ..
-rw-r--r--   1 kkarri waxmanlab    0 Sep  5 18:23 G170_M13_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 2.0G Sep  5 18:23 G170_M13_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  19M Sep  5 18:23 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab  17M Sep  5 18:23 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 G170_M13_featureCounts.out G170_M13'_sorted'.bam

Ending featureCounts


List files in scratch

total 4.7G
drwx------   2 kkarri waxmanlab  20K Sep  5 18:50 .
drwxrwxrwt. 38 root   root      4.0K Sep  5 18:34 ..
-rw-r--r--   1 kkarri waxmanlab 700K Sep  5 18:50 G170_M13_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  296 Sep  5 18:50 G170_M13_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 934M Sep  5 18:32 G170_M13_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri waxmanlab 2.0G Sep  5 18:23 G170_M13_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.9G Sep  5 18:46 G170_M13_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  19M Sep  5 18:23 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab  17M Sep  5 18:23 exonic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Thu Sep  5 18:50:42 EDT 2019
0 hours, 27 minutes and 5 seconds elapsed.
==========================================================