-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M1
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/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/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
ncRNA_genebodies_for_counting.gtf
FEATURE_TYPE:
gene_body
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sat Apr 20 21:16:48 EDT 2019
Running on node : scc-kb7
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 5412353
Current job name : Step_08b_G168_G169_M1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5412353.1.linga

Loading required modules...


List files in scratch directory:

total 1.6G
drwx------   2 kkarri waxmanlab 4.0K Apr 20 21:18 .
drwxrwxrwt. 57 root   root      168K Apr 20 21:16 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 20 21:18 G168_G169_M1_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 1.6G Apr 20 21:18 G168_G169_M1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Apr 20 21:18 ncRNA_genebodies_for_counting.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 2 -g gene_id -t gene_body -a ncRNA_genebodies_for_counting.gtf -o G168_G169_M1_featureCounts.out G168_G169_M1'_sorted'.bam

Ending featureCounts


List files in scratch

total 4.5G
drwx------   2 kkarri waxmanlab  20K Apr 20 21:51 .
drwxrwxrwt. 51 root   root      168K Apr 20 21:51 ..
-rw-r--r--   1 kkarri waxmanlab 700K Apr 20 21:51 G168_G169_M1_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  302 Apr 20 21:51 G168_G169_M1_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 1.6G Apr 20 21:18 G168_G169_M1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 2.9G Apr 20 21:43 G168_G169_M1_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Apr 20 21:18 ncRNA_genebodies_for_counting.gtf
==========================================================
Finished on : Sat Apr 20 21:51:29 EDT 2019
0 hours, 34 minutes and 41 seconds elapsed.
==========================================================