-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M19
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:
intronic_only_gene_models_ncRNA_for_counting.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun Apr 21 02:35:05 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 : 5412500
Current job name : Step_08b_G168_G169_M19
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5412500.1.linga

Loading required modules...


List files in scratch directory:

total 1.8G
drwx------   2 kkarri waxmanlab 4.0K Apr 21 02:35 .
drwxrwxrwt. 70 root   root      116K Apr 21 02:35 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 21 02:35 G168_G169_M19_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 1.8G Apr 21 02:35 G168_G169_M19_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  19M Apr 21 02:35 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 G168_G169_M19_featureCounts.out G168_G169_M19'_sorted'.bam

Ending featureCounts


List files in scratch

total 4.5G
drwx------   2 kkarri waxmanlab  20K Apr 21 03:15 .
drwxrwxrwt. 64 root   root      116K Apr 21 03:12 ..
-rw-r--r--   1 kkarri waxmanlab 339K Apr 21 03:14 G168_G169_M19_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  303 Apr 21 03:14 G168_G169_M19_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 950M Apr 21 02:52 G168_G169_M19_primary_no_splice.bam
-rw-r--r--   1 kkarri waxmanlab 1.8G Apr 21 02:35 G168_G169_M19_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.7G Apr 21 03:09 G168_G169_M19_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  19M Apr 21 02:35 intronic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Sun Apr 21 03:15:00 EDT 2019
0 hours, 39 minutes and 55 seconds elapsed.
==========================================================