-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M11
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/unprotected/projects/waxmanlab/routines/GTF_Files
STRANDEDNESS_featureCount:
2
FEATURE_ID:
gene_id
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
genes.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun Apr 21 00:18:38 EDT 2019
Running on node : scc-tk2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 5412435
Current job name : Step_08b_G168_G169_M11
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5412435.1.linga

Loading required modules...


List files in scratch directory:

total 2.2G
drwx------   2 kkarri waxmanlab 4.0K Apr 21 00:19 .
drwxrwxrwt. 11 root   root       36K Apr 21 00:18 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 21 00:19 G168_G169_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 2.2G Apr 21 00:18 G168_G169_M11_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M Apr 21 00:18 genes.gtf

Starting to run my commands


Starting featureCounts

featureCounts -p  -T 16 -s 2 -g gene_id -t exon -a genes.gtf -o G168_G169_M11_featureCounts.out G168_G169_M11'_sorted'.bam

Ending featureCounts


List files in scratch

total 6.4G
drwx------   2 kkarri waxmanlab  20K Apr 21 00:50 .
drwxrwxrwt. 14 root   root       36K Apr 21 00:45 ..
-rw-r--r--   1 kkarri waxmanlab 239K Apr 21 00:50 G168_G169_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  304 Apr 21 00:50 G168_G169_M11_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 2.2G Apr 21 00:18 G168_G169_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 4.2G Apr 21 00:39 G168_G169_M11_sorted.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M Apr 21 00:18 genes.gtf
==========================================================
Finished on : Sun Apr 21 00:50:04 EDT 2019
0 hours, 31 minutes and 26 seconds elapsed.
==========================================================