-----------------------
Start of variable list:
-----------------------
Sample_ID:
G166_M11
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files
STRANDEDNESS_featureCount:
2
FEATURE_ID:
gene_id
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
intronic_only_gene_models_ncRNA_for_counting.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Apr 23 12:52:52 EDT 2019
Running on node : scc-ka2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 5542387
Current job name : Step_08b_G166_M11
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5542387.1.linga

Loading required modules...


List files in scratch directory:

total 760M
drwx------   2 kkarri waxmanlab 4.0K Apr 23 12:53 .
drwxrwxrwt. 75 root   root      116K Apr 23 12:52 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 23 12:53 G166_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 742M Apr 23 12:53 G166_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  19M Apr 23 12:53 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 G166_M11_featureCounts.out G166_M11'_sorted'.bam

Ending featureCounts


List files in scratch

total 2.6G
drwx------   2 kkarri waxmanlab  20K Apr 23 13:16 .
drwxrwxrwt. 60 root   root      116K Apr 23 13:00 ..
-rw-r--r--   1 kkarri waxmanlab 350K Apr 23 13:16 G166_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  298 Apr 23 13:16 G166_M11_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 717M Apr 23 13:00 G166_M11_primary_no_splice.bam
-rw-r--r--   1 kkarri waxmanlab 742M Apr 23 12:53 G166_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.2G Apr 23 13:12 G166_M11_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  19M Apr 23 12:53 intronic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Tue Apr 23 13:16:25 EDT 2019
0 hours, 23 minutes and 33 seconds elapsed.
==========================================================