-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M24
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:
intronic_only_gene_models_ncRNA_for_counting.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Sep  5 21:09:00 EDT 2019
Running on node : scc-pa1
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9162271
Current job name : Step_08b_G170_M24
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9162271.1.p-long

Loading required modules...


List files in scratch directory:

total 1.6G
drwx------  2 kkarri waxmanlab 4.0K Sep  5 21:09 .
drwxrwxrwt. 9 root   root      4.0K Sep  5 21:09 ..
-rw-r--r--  1 kkarri waxmanlab    0 Sep  5 21:09 G170_M24_featureCounts.out
-rw-r--r--  1 kkarri waxmanlab 1.6G Sep  5 21:09 G170_M24_primary_unique.bam
-rw-r--r--  1 kkarri waxmanlab  19M Sep  5 21:09 intronic_only_gene_models_ncRNA_for_counting.gtf

Starting to run my commands


Starting featureCounts


Starting splice read filter


Ending splice read filter

featureCounts -p  -T 16 -s 2 -g gene_id -t Intronic_Only -a intronic_only_gene_models_ncRNA_for_counting.gtf -o G170_M24_featureCounts.out G170_M24'_sorted'.bam

Ending featureCounts


List files in scratch

total 4.3G
drwx------  2 kkarri waxmanlab  20K Sep  5 21:29 .
drwxrwxrwt. 9 root   root      4.0K Sep  5 21:09 ..
-rw-r--r--  1 kkarri waxmanlab 340K Sep  5 21:29 G170_M24_featureCounts.out
-rw-r--r--  1 kkarri waxmanlab  298 Sep  5 21:29 G170_M24_featureCounts.out.summary
-rw-r--r--  1 kkarri waxmanlab 966M Sep  5 21:17 G170_M24_primary_no_splice.bam
-rw-r--r--  1 kkarri waxmanlab 1.6G Sep  5 21:09 G170_M24_primary_unique.bam
-rw-r--r--  1 kkarri waxmanlab 1.8G Sep  5 21:26 G170_M24_sorted.bam
-rw-r--r--  1 kkarri waxmanlab  19M Sep  5 21:09 intronic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Thu Sep  5 21:29:18 EDT 2019
0 hours, 20 minutes and 18 seconds elapsed.
==========================================================