-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M8
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 23:34:08 EDT 2019
Running on node : scc-tl3
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 : 5412414
Current job name : Step_08b_G168_G169_M8
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5412414.1.linga

Loading required modules...


List files in scratch directory:

total 1.9G
drwx------   2 kkarri waxmanlab 4.0K Apr 20 23:34 .
drwxrwxrwt. 16 root   root      132K Apr 20 23:34 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 20 23:34 G168_G169_M8_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 1.9G Apr 20 23:34 G168_G169_M8_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Apr 20 23:34 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_M8_featureCounts.out G168_G169_M8'_sorted'.bam

Ending featureCounts


List files in scratch

total 5.7G
drwx------   2 kkarri waxmanlab  20K Apr 21 00:03 .
drwxrwxrwt. 16 root   root      132K Apr 21 00:02 ..
-rw-r--r--   1 kkarri waxmanlab 701K Apr 21 00:03 G168_G169_M8_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  303 Apr 21 00:03 G168_G169_M8_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 1.9G Apr 20 23:34 G168_G169_M8_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.8G Apr 20 23:54 G168_G169_M8_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Apr 20 23:34 ncRNA_genebodies_for_counting.gtf
==========================================================
Finished on : Sun Apr 21 00:03:08 EDT 2019
0 hours, 29 minutes and 0 seconds elapsed.
==========================================================