-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M1
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 21:07:21 EDT 2017
Running on node : scc-ca8
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 474007
Current job name : Step_08b_G160_M1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/474007.1.c

Loading required modules...


List files in scratch directory:

total 1.1G
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 21:07 .
drwxrwxrwt. 29 root   root    4.0K Aug 30 21:07 ..
-rw-r--r--   1 kkarri pulmseq    0 Aug 30 21:07 G160_M1_featureCounts.out
-rw-r--r--   1 kkarri pulmseq 1.1G Aug 30 21:07 G160_M1_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq 3.4M Aug 30 21:07 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_M1_featureCounts.out G160_M1'_sorted'.bam

Ending featureCounts


List files in scratch

total 2.6G
drwxr-xr-x   2 kkarri pulmseq  20K Aug 30 21:19 .
drwxrwxrwt. 29 root   root    4.0K Aug 30 21:07 ..
-rw-r--r--   1 kkarri pulmseq 702K Aug 30 21:19 G160_M1_featureCounts.out
-rw-r--r--   1 kkarri pulmseq  298 Aug 30 21:19 G160_M1_featureCounts.out.summary
-rw-r--r--   1 kkarri pulmseq 1.1G Aug 30 21:07 G160_M1_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq 1.5G Aug 30 21:16 G160_M1_sorted.bam
-rw-r--r--   1 kkarri pulmseq 3.4M Aug 30 21:07 ncRNA_genebodies_for_counting.gtf
==========================================================
Finished on : Wed Aug 30 21:19:49 EDT 2017
0 hours, 12 minutes and 28 seconds elapsed.
==========================================================