-----------------------
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:
exonic_only_gene_models_ncRNA_for_counting.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Aug 30 23:21:48 EDT 2017
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 474075
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/474075.1.linga

Loading required modules...


List files in scratch directory:

total 1.5G
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 23:21 .
drwxrwxrwt. 53 root   root     92K Aug 30 23:21 ..
-rw-r--r--   1 kkarri pulmseq    0 Aug 30 23:21 G160_M55_featureCounts.out
-rw-r--r--   1 kkarri pulmseq 1.5G Aug 30 23:21 G160_M55_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq  19M Aug 30 23:21 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri pulmseq  17M Aug 30 23:21 exonic_only_gene_models_ncRNA_for_counting.gtf

Starting to run my commands


Starting featureCounts


Starting Intron_Only_Regions read overlap filter


Ending Intron_Only_Regions read overlap filter

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

Ending featureCounts


List files in scratch

total 3.0G
drwxr-xr-x   2 kkarri pulmseq  20K Aug 30 23:43 .
drwxrwxrwt. 53 root   root     92K Aug 30 23:38 ..
-rw-r--r--   1 kkarri pulmseq 694K Aug 30 23:43 G160_M55_featureCounts.out
-rw-r--r--   1 kkarri pulmseq  297 Aug 30 23:43 G160_M55_featureCounts.out.summary
-rw-r--r--   1 kkarri pulmseq 593M Aug 30 23:29 G160_M55_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri pulmseq 1.5G Aug 30 23:21 G160_M55_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq 918M Aug 30 23:39 G160_M55_sorted.bam
-rw-r--r--   1 kkarri pulmseq  19M Aug 30 23:21 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri pulmseq  17M Aug 30 23:21 exonic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Wed Aug 30 23:43:48 EDT 2017
0 hours, 22 minutes and 0 seconds elapsed.
==========================================================