-----------------------
Start of variable list:
-----------------------
Sample_ID:
E12-MAA100138-3_56_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:
genes.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun Oct 14 17:52:32 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 8813064
Current job name : Step_08b_E12-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8813064.1.linga

Loading required modules...


List files in scratch directory:

total 75M
drwx------    2 kkarri waxmanlab 4.0K Oct 14 17:52 .
drwxrwxrwt. 123 root   root      116K Oct 14 17:52 ..
-rw-r--r--    1 kkarri waxmanlab    0 Oct 14 17:52 E12-MAA100138-3_56_F-1-1_featureCounts.out
-rw-r--r--    1 kkarri waxmanlab  15M Oct 14 17:52 E12-MAA100138-3_56_F-1-1_primary_unique.bam
-rwxr-xr-x    1 kkarri waxmanlab  60M Oct 14 17:52 genes.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 0 -g gene_id -t exon -a genes.gtf -o E12-MAA100138-3_56_F-1-1_featureCounts.out E12-MAA100138-3_56_F-1-1'_sorted'.bam

Ending featureCounts


List files in scratch

total 107M
drwx------    2 kkarri waxmanlab  20K Oct 14 17:53 .
drwxrwxrwt. 123 root   root      116K Oct 14 17:52 ..
-rw-r--r--    1 kkarri waxmanlab 161K Oct 14 17:53 E12-MAA100138-3_56_F-1-1_featureCounts.out
-rw-r--r--    1 kkarri waxmanlab  309 Oct 14 17:53 E12-MAA100138-3_56_F-1-1_featureCounts.out.summary
-rw-r--r--    1 kkarri waxmanlab  15M Oct 14 17:52 E12-MAA100138-3_56_F-1-1_primary_unique.bam
-rw-r--r--    1 kkarri waxmanlab  33M Oct 14 17:52 E12-MAA100138-3_56_F-1-1_sorted.bam
-rwxr-xr-x    1 kkarri waxmanlab  60M Oct 14 17:52 genes.gtf
==========================================================
Finished on : Sun Oct 14 17:53:19 EDT 2018
0 hours, 0 minutes and 47 seconds elapsed.
==========================================================