-----------------------
Start of variable list:
-----------------------
Sample_ID:
WT2
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files
STRANDEDNESS_featureCount:
2
FEATURE_ID:
gene_id
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/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 : Wed May  1 02:03:02 EDT 2019
Running on node : scc-ka2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 5790183
Current job name : Step_08b_WT2
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5790183.1.linga

Loading required modules...


List files in scratch directory:

total 292M
drwx------   2 kkarri waxmanlab 4.0K May  1 02:03 .
drwxrwxrwt. 76 root   root      116K May  1 02:03 ..
-rw-r--r--   1 kkarri waxmanlab  19M May  1 02:03 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab    0 May  1 02:03 WT2_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 257M May  1 02:03 WT2_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  17M May  1 02:03 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 WT2_featureCounts.out WT2'_sorted'.bam

Ending featureCounts


List files in scratch

total 782M
drwx------   2 kkarri waxmanlab  20K May  1 02:09 .
drwxrwxrwt. 77 root   root      116K May  1 02:09 ..
-rw-r--r--   1 kkarri waxmanlab  19M May  1 02:03 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab 689K May  1 02:09 WT2_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  290 May  1 02:09 WT2_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 190M May  1 02:05 WT2_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri waxmanlab 257M May  1 02:03 WT2_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 301M May  1 02:08 WT2_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  17M May  1 02:03 exonic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Wed May  1 02:09:43 EDT 2019
0 hours, 6 minutes and 41 seconds elapsed.
==========================================================