-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M20
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 20:16:27 EDT 2019
Running on node : scc-ph4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9162239
Current job name : Step_08b_G170_M20
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9162239.1.p16

Loading required modules...


List files in scratch directory:

total 2.0G
drwx------   2 kkarri waxmanlab 4.0K Sep  5 20:17 .
drwxrwxrwt. 17 root   root      4.0K Sep  5 20:16 ..
-rw-r--r--   1 kkarri waxmanlab    0 Sep  5 20:17 G170_M20_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 2.0G Sep  5 20:17 G170_M20_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  19M Sep  5 20:17 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_M20_featureCounts.out G170_M20'_sorted'.bam

Ending featureCounts


List files in scratch

total 5.3G
drwx------   2 kkarri waxmanlab  20K Sep  5 20:42 .
drwxrwxrwt. 17 root   root      4.0K Sep  5 20:16 ..
-rw-r--r--   1 kkarri waxmanlab 341K Sep  5 20:42 G170_M20_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  298 Sep  5 20:42 G170_M20_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 1.2G Sep  5 20:27 G170_M20_primary_no_splice.bam
-rw-r--r--   1 kkarri waxmanlab 2.0G Sep  5 20:17 G170_M20_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 2.2G Sep  5 20:38 G170_M20_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  19M Sep  5 20:17 intronic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Thu Sep  5 20:42:29 EDT 2019
0 hours, 26 minutes and 2 seconds elapsed.
==========================================================