-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M11
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:
exonic_only_gene_models_ncRNA_for_counting.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun Apr 21 00:16:28 EDT 2019
Running on node : scc-ka2
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 : 5412434
Current job name : Step_08b_G168_G169_M11
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5412434.1.linga

Loading required modules...


List files in scratch directory:

total 2.2G
drwx------   2 kkarri waxmanlab 4.0K Apr 21 00:16 .
drwxrwxrwt. 71 root   root      116K Apr 21 00:16 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 21 00:16 G168_G169_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 2.2G Apr 21 00:16 G168_G169_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  19M Apr 21 00:16 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab  17M Apr 21 00:16 exonic_only_gene_models_ncRNA_for_counting.gtf

Starting to run my commands


Starting featureCounts


Starting Intron_Only_Regions read overlap filter


Ending Intron_Only_Regions read overlap filter

featureCounts -p  -T 16 -s 2 -g gene_id -t Exonic_Only -a exonic_only_gene_models_ncRNA_for_counting.gtf -o G168_G169_M11_featureCounts.out G168_G169_M11'_sorted'.bam

Ending featureCounts


List files in scratch

total 4.9G
drwx------   2 kkarri waxmanlab  20K Apr 21 00:48 .
drwxrwxrwt. 77 root   root      116K Apr 21 00:48 ..
-rw-r--r--   1 kkarri waxmanlab 696K Apr 21 00:48 G168_G169_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  301 Apr 21 00:48 G168_G169_M11_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 941M Apr 21 00:28 G168_G169_M11_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri waxmanlab 2.2G Apr 21 00:16 G168_G169_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.8G Apr 21 00:43 G168_G169_M11_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  19M Apr 21 00:16 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab  17M Apr 21 00:16 exonic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Sun Apr 21 00:48:59 EDT 2019
0 hours, 32 minutes and 31 seconds elapsed.
==========================================================