-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M11
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/unprotected/projects/waxmanlab/routines/GTF_Files
STRANDEDNESS_featureCount:
2
FEATURE_ID:
gene_id
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/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 Jul 15 20:43:07 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 6944968
Current job name : Step_08b_G167_M11
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6944968.1.linga

Loading required modules...


List files in scratch directory:

total 934M
drwx------    2 kkarri waxmanlab 4.0K Jul 15 20:43 .
drwxrwxrwt. 117 root   root      116K Jul 15 20:43 ..
-rw-r--r--    1 kkarri waxmanlab    0 Jul 15 20:43 G167_M11_featureCounts.out
-rw-r--r--    1 kkarri waxmanlab 916M Jul 15 20:43 G167_M11_primary_unique.bam
-rw-r--r--    1 kkarri waxmanlab  19M Jul 15 20:43 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 G167_M11_featureCounts.out G167_M11'_sorted'.bam

Ending featureCounts


List files in scratch

total 2.2G
drwx------    2 kkarri waxmanlab  20K Jul 15 21:01 .
drwxrwxrwt. 117 root   root      116K Jul 15 20:58 ..
-rw-r--r--    1 kkarri waxmanlab 329K Jul 15 21:01 G167_M11_featureCounts.out
-rw-r--r--    1 kkarri waxmanlab  296 Jul 15 21:01 G167_M11_featureCounts.out.summary
-rw-r--r--    1 kkarri waxmanlab 420M Jul 15 20:50 G167_M11_primary_no_splice.bam
-rw-r--r--    1 kkarri waxmanlab 916M Jul 15 20:43 G167_M11_primary_unique.bam
-rw-r--r--    1 kkarri waxmanlab 816M Jul 15 20:58 G167_M11_sorted.bam
-rw-r--r--    1 kkarri waxmanlab  19M Jul 15 20:43 intronic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Sun Jul 15 21:01:22 EDT 2018
0 hours, 18 minutes and 16 seconds elapsed.
==========================================================