-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M31
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/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/liver_zonation/infusion_rerun/Scripts/07b_Extract_Counts_featureCounts
ANNOTATION_FILE:
intronic_only_gene_models_ncRNA_for_counting.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun May 13 15:47:24 EDT 2018
Running on node : scc-ph5
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/07b_Extract_Counts_featureCounts
Current job ID : 6184785
Current job name : Step_07b_LZ_M31
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6184785.1.p16

Loading required modules...


List files in scratch directory:

total 353M
drwx------   2 kkarri waxmanlab 4.0K May 13 15:47 .
drwxrwxrwt. 13 root   root      4.0K May 13 15:47 ..
-rw-r--r--   1 kkarri waxmanlab    0 May 13 15:47 LZ_M31_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 335M May 13 15:47 LZ_M31_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  19M May 13 15:47 intronic_only_gene_models_ncRNA_for_counting.gtf

Starting to run my commands


Starting featureCounts


Starting splice read filter


Ending splice read filter

featureCounts -p  -T 16 -s 2 -g gene_id -t Intronic_Only -a intronic_only_gene_models_ncRNA_for_counting.gtf -o LZ_M31_featureCounts.out LZ_M31'_sorted'.bam

Ending featureCounts


List files in scratch

total 1.1G
drwx------   2 kkarri waxmanlab 4.0K May 13 15:51 .
drwxrwxrwt. 13 root   root      4.0K May 13 15:47 ..
-rw-r--r--   1 kkarri waxmanlab 337K May 13 15:51 LZ_M31_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  297 May 13 15:51 LZ_M31_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 296M May 13 15:49 LZ_M31_primary_no_splice.bam
-rw-r--r--   1 kkarri waxmanlab 335M May 13 15:47 LZ_M31_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 464M May 13 15:51 LZ_M31_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  19M May 13 15:47 intronic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Sun May 13 15:51:51 EDT 2018
0 hours, 4 minutes and 27 seconds elapsed.
==========================================================