-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M8
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 16:46:19 EDT 2019
Running on node : scc-kb4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9162143
Current job name : Step_08b_G170_M8
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9162143.1.linga

Loading required modules...


List files in scratch directory:

total 2.7G
drwx------   2 kkarri waxmanlab 4.0K Sep  5 16:46 .
drwxrwxrwt. 47 root   root      4.0K Sep  5 16:46 ..
-rw-r--r--   1 kkarri waxmanlab    0 Sep  5 16:46 G170_M8_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 2.7G Sep  5 16:46 G170_M8_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  19M Sep  5 16:46 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_M8_featureCounts.out G170_M8'_sorted'.bam

Ending featureCounts


List files in scratch

total 7.3G
drwx------   2 kkarri waxmanlab  20K Sep  5 17:41 .
drwxrwxrwt. 46 root   root      4.0K Sep  5 17:30 ..
-rw-r--r--   1 kkarri waxmanlab 348K Sep  5 17:41 G170_M8_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  297 Sep  5 17:41 G170_M8_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 1.6G Sep  5 17:08 G170_M8_primary_no_splice.bam
-rw-r--r--   1 kkarri waxmanlab 2.7G Sep  5 16:46 G170_M8_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.0G Sep  5 17:32 G170_M8_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  19M Sep  5 16:46 intronic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Thu Sep  5 17:41:19 EDT 2019
0 hours, 55 minutes and 0 seconds elapsed.
==========================================================