-----------------------
Start of variable list:
-----------------------
Sample_ID:
E5-MAA100040-3_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:
exonic_only_gene_models_ncRNA_for_counting.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun Oct 14 18:13:19 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 : 8813159
Current job name : Step_08b_E5-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8813159.1.linga

Loading required modules...


List files in scratch directory:

total 38M
drwx------   2 kkarri waxmanlab 4.0K Oct 14 18:13 .
drwxrwxrwt. 92 root   root      128K Oct 14 18:12 ..
-rw-r--r--   1 kkarri waxmanlab    0 Oct 14 18:13 E5-MAA100040-3_11_M-1-1_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  22M Oct 14 18:13 E5-MAA100040-3_11_M-1-1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  17M Oct 14 18:13 exonic_only_gene_models_ncRNA_for_counting.gtf

Starting to run my commands


Starting featureCounts


Starting Intron_Only_Regions read overlap filter


Ending Intron_Only_Regions read overlap filter

featureCounts -p  -T 16 -s 0 -g gene_id -t Exonic_Only -a exonic_only_gene_models_ncRNA_for_counting.gtf -o E5-MAA100040-3_11_M-1-1_featureCounts.out E5-MAA100040-3_11_M-1-1'_sorted'.bam

Ending featureCounts


List files in scratch

total 39M
drwx------   2 kkarri waxmanlab 4.0K Oct 14 18:13 .
drwxrwxrwt. 92 root   root      128K Oct 14 18:12 ..
-rw-r--r--   1 kkarri waxmanlab 777K Oct 14 18:13 E5-MAA100040-3_11_M-1-1_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  239 Oct 14 18:13 E5-MAA100040-3_11_M-1-1_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab    0 Oct 14 18:13 E5-MAA100040-3_11_M-1-1_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri waxmanlab  22M Oct 14 18:13 E5-MAA100040-3_11_M-1-1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  17M Oct 14 18:13 exonic_only_gene_models_ncRNA_for_counting.gtf
==========================================================
Finished on : Sun Oct 14 18:14:06 EDT 2018
0 hours, 0 minutes and 48 seconds elapsed.
==========================================================