-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M11
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 21:24:28 EDT 2017
Running on node : scc-pf2
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 474012
Current job name : Step_08b_G160_M11
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/474012.1.p8

Loading required modules...


List files in scratch directory:

total 1.2G
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 21:24 .
drwxrwxrwt. 75 root   root    4.0K Aug 30 21:24 ..
-rw-r--r--   1 kkarri pulmseq    0 Aug 30 21:24 G160_M11_featureCounts.out
-rw-r--r--   1 kkarri pulmseq 1.1G Aug 30 21:24 G160_M11_primary_unique.bam
-rwxr-xr-x   1 kkarri pulmseq  81M Aug 30 21:24 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_M11_featureCounts.out G160_M11'_sorted'.bam

Ending featureCounts


List files in scratch

total 2.7G
drwxr-xr-x   2 kkarri pulmseq  20K Aug 30 21:36 .
drwxrwxrwt. 75 root   root    4.0K Aug 30 21:24 ..
-rw-r--r--   1 kkarri pulmseq 235K Aug 30 21:36 G160_M11_featureCounts.out
-rw-r--r--   1 kkarri pulmseq  297 Aug 30 21:36 G160_M11_featureCounts.out.summary
-rw-r--r--   1 kkarri pulmseq 1.1G Aug 30 21:24 G160_M11_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq 1.5G Aug 30 21:33 G160_M11_sorted.bam
-rwxr-xr-x   1 kkarri pulmseq  81M Aug 30 21:24 genes.gtf
==========================================================
Finished on : Wed Aug 30 21:36:17 EDT 2017
0 hours, 11 minutes and 49 seconds elapsed.
==========================================================