-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M33
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:
genes.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Aug 30 22:30:56 EDT 2017
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 474044
Current job name : Step_08b_G160_M33
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/474044.1.linga

Loading required modules...


List files in scratch directory:

total 1.9G
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 22:31 .
drwxrwxrwt. 42 root   root    180K Aug 30 22:30 ..
-rw-r--r--   1 kkarri pulmseq    0 Aug 30 22:31 G160_M33_featureCounts.out
-rw-r--r--   1 kkarri pulmseq 1.8G Aug 30 22:31 G160_M33_primary_unique.bam
-rwxr-xr-x   1 kkarri pulmseq  81M Aug 30 22:31 genes.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 2 -g gene_id -t exon -a genes.gtf -o G160_M33_featureCounts.out G160_M33'_sorted'.bam

Ending featureCounts


List files in scratch

total 4.2G
drwxr-xr-x   2 kkarri pulmseq  20K Aug 30 23:10 .
drwxrwxrwt. 49 root   root    180K Aug 30 22:50 ..
-rw-r--r--   1 kkarri pulmseq 236K Aug 30 23:10 G160_M33_featureCounts.out
-rw-r--r--   1 kkarri pulmseq  298 Aug 30 23:10 G160_M33_featureCounts.out.summary
-rw-r--r--   1 kkarri pulmseq 1.8G Aug 30 22:31 G160_M33_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq 2.4G Aug 30 22:59 G160_M33_sorted.bam
-rwxr-xr-x   1 kkarri pulmseq  81M Aug 30 22:31 genes.gtf
==========================================================
Finished on : Wed Aug 30 23:10:01 EDT 2017
0 hours, 39 minutes and 5 seconds elapsed.
==========================================================