-----------------------
Start of variable list:
-----------------------
Sample_ID:
KI10
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 04:09:31 EDT 2019
Running on node : scc-ka6
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 5790522
Current job name : Step_08b_KI10
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5790522.1.linga

Loading required modules...


List files in scratch directory:

total 304M
drwx------   2 kkarri waxmanlab 4.0K May  1 04:09 .
drwxrwxrwt. 72 root   root       92K May  1 04:09 ..
-rw-r--r--   1 kkarri waxmanlab  19M May  1 04:09 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab    0 May  1 04:09 KI10_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 269M May  1 04:09 KI10_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  17M May  1 04:09 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 KI10_featureCounts.out KI10'_sorted'.bam

Ending featureCounts


List files in scratch

total 800M
drwx------   2 kkarri waxmanlab  20K May  1 04:16 .
drwxrwxrwt. 59 root   root       92K May  1 04:15 ..
-rw-r--r--   1 kkarri waxmanlab  19M May  1 04:09 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab 689K May  1 04:16 KI10_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  291 May  1 04:16 KI10_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 193M May  1 04:12 KI10_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri waxmanlab 269M May  1 04:09 KI10_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 303M May  1 04:15 KI10_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  17M May  1 04:09 exonic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Wed May  1 04:16:26 EDT 2019
0 hours, 6 minutes and 55 seconds elapsed.
==========================================================