-----------------------
Start of variable list:
-----------------------
Sample_ID:
B14-MAA000907-3_11_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:
genes.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun Oct 14 10:27:42 EDT 2018
Running on node : scc-ka5
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 8811163
Current job name : Step_08b_B14-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8811163.1.linga

Loading required modules...


List files in scratch directory:

total 76M
drwx------   2 kkarri waxmanlab 4.0K Oct 14 10:27 .
drwxrwxrwt. 71 root   root      128K Oct 14 10:27 ..
-rw-r--r--   1 kkarri waxmanlab    0 Oct 14 10:27 B14-MAA000907-3_11_M-1-1_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  17M Oct 14 10:27 B14-MAA000907-3_11_M-1-1_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab  60M Oct 14 10:27 genes.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 0 -g gene_id -t exon -a genes.gtf -o B14-MAA000907-3_11_M-1-1_featureCounts.out B14-MAA000907-3_11_M-1-1'_sorted'.bam

Ending featureCounts


List files in scratch

total 108M
drwx------   2 kkarri waxmanlab  20K Oct 14 10:28 .
drwxrwxrwt. 71 root   root      128K Oct 14 10:27 ..
-rw-r--r--   1 kkarri waxmanlab 162K Oct 14 10:28 B14-MAA000907-3_11_M-1-1_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  309 Oct 14 10:28 B14-MAA000907-3_11_M-1-1_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab  17M Oct 14 10:27 B14-MAA000907-3_11_M-1-1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  32M Oct 14 10:27 B14-MAA000907-3_11_M-1-1_sorted.bam
-rwxr-xr-x   1 kkarri waxmanlab  60M Oct 14 10:27 genes.gtf
==========================================================
Finished on : Sun Oct 14 10:28:12 EDT 2018
0 hours, 0 minutes and 30 seconds elapsed.
==========================================================