-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M55
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_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/G160_Samples/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
ncRNA_genebodies_for_counting.gtf
FEATURE_TYPE:
gene_body
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Aug 30 23:27:14 EDT 2017
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 474079
Current job name : Step_08b_G160_M55
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/474079.1.linga

Loading required modules...


List files in scratch directory:

total 1.5G
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 23:27 .
drwxrwxrwt. 48 root   root    168K Aug 30 23:27 ..
-rw-r--r--   1 kkarri pulmseq    0 Aug 30 23:27 G160_M55_featureCounts.out
-rw-r--r--   1 kkarri pulmseq 1.5G Aug 30 23:27 G160_M55_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq 3.4M Aug 30 23:27 ncRNA_genebodies_for_counting.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 2 -g gene_id -t gene_body -a ncRNA_genebodies_for_counting.gtf -o G160_M55_featureCounts.out G160_M55'_sorted'.bam

Ending featureCounts


List files in scratch

total 3.5G
drwxr-xr-x   2 kkarri pulmseq  20K Aug 30 23:59 .
drwxrwxrwt. 48 root   root    168K Aug 30 23:53 ..
-rw-r--r--   1 kkarri pulmseq 702K Aug 30 23:59 G160_M55_featureCounts.out
-rw-r--r--   1 kkarri pulmseq  300 Aug 30 23:59 G160_M55_featureCounts.out.summary
-rw-r--r--   1 kkarri pulmseq 1.5G Aug 30 23:27 G160_M55_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq 2.1G Aug 30 23:50 G160_M55_sorted.bam
-rw-r--r--   1 kkarri pulmseq 3.4M Aug 30 23:27 ncRNA_genebodies_for_counting.gtf
==========================================================
Finished on : Wed Aug 30 23:59:40 EDT 2017
0 hours, 32 minutes and 26 seconds elapsed.
==========================================================