-----------------------
Start of variable list:
-----------------------
Sample_ID:
A4-MAA100140-3_57_F-1-1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/GTF_Files
STRANDEDNESS_featureCount:
0
FEATURE_ID:
gene_id
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
ncRNA_genebodies_for_counting.gtf
FEATURE_TYPE:
gene_body
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun Oct 14 14:22:41 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 8812225
Current job name : Step_08b_A4-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8812225.1.linga

Loading required modules...


List files in scratch directory:

total 56M
drwx------   2 kkarri waxmanlab 4.0K Oct 14 14:22 .
drwxrwxrwt. 47 root   root      108K Oct 14 14:22 ..
-rw-r--r--   1 kkarri waxmanlab    0 Oct 14 14:22 A4-MAA100140-3_57_F-1-1_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  52M Oct 14 14:22 A4-MAA100140-3_57_F-1-1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Oct 14 14:22 ncRNA_genebodies_for_counting.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 0 -g gene_id -t gene_body -a ncRNA_genebodies_for_counting.gtf -o A4-MAA100140-3_57_F-1-1_featureCounts.out A4-MAA100140-3_57_F-1-1'_sorted'.bam

Ending featureCounts


List files in scratch

total 163M
drwx------   2 kkarri waxmanlab  20K Oct 14 14:23 .
drwxrwxrwt. 48 root   root      108K Oct 14 14:23 ..
-rw-r--r--   1 kkarri waxmanlab 681K Oct 14 14:23 A4-MAA100140-3_57_F-1-1_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  310 Oct 14 14:23 A4-MAA100140-3_57_F-1-1_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab  52M Oct 14 14:22 A4-MAA100140-3_57_F-1-1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 107M Oct 14 14:23 A4-MAA100140-3_57_F-1-1_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Oct 14 14:22 ncRNA_genebodies_for_counting.gtf
==========================================================
Finished on : Sun Oct 14 14:23:46 EDT 2018
0 hours, 1 minutes and 5 seconds elapsed.
==========================================================