-----------------------
Start of variable list:
-----------------------
Sample_ID:
E4-MAA100042-3_9_M-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 18:09:47 EDT 2018
Running on node : scc-kb8
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 8813147
Current job name : Step_08b_E4-MAA100042-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8813147.1.linga

Loading required modules...


List files in scratch directory:

total 87M
drwx------   2 kkarri waxmanlab 4.0K Oct 14 18:10 .
drwxrwxrwt. 65 root   root      112K Oct 14 18:09 ..
-rw-r--r--   1 kkarri waxmanlab    0 Oct 14 18:10 E4-MAA100042-3_9_M-1-1_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  84M Oct 14 18:10 E4-MAA100042-3_9_M-1-1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Oct 14 18:10 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 E4-MAA100042-3_9_M-1-1_featureCounts.out E4-MAA100042-3_9_M-1-1'_sorted'.bam

Ending featureCounts


List files in scratch

total 299M
drwx------   2 kkarri waxmanlab  20K Oct 14 18:12 .
drwxrwxrwt. 66 root   root      112K Oct 14 18:12 ..
-rw-r--r--   1 kkarri waxmanlab 680K Oct 14 18:12 E4-MAA100042-3_9_M-1-1_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  311 Oct 14 18:12 E4-MAA100042-3_9_M-1-1_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab  84M Oct 14 18:10 E4-MAA100042-3_9_M-1-1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 211M Oct 14 18:11 E4-MAA100042-3_9_M-1-1_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.4M Oct 14 18:10 ncRNA_genebodies_for_counting.gtf
==========================================================
Finished on : Sun Oct 14 18:12:58 EDT 2018
0 hours, 3 minutes and 11 seconds elapsed.
==========================================================