-----------------------
Start of variable list:
-----------------------
Sample_ID:
NSM_IP2
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/restricted/projectnb/waxmanlab/kkarri/GTF_Files1
STRANDEDNESS_featureCount:
0
FEATURE_ID:
gene_id
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Jun 15 10:14:40 EDT 2017
Running on node : scc-pf1
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9333839
Current job name : Step_08b_NSM_IP2
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9333839.1.p8

Loading required modules...


List files in scratch directory:

total 1.9G
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 10:14 .
drwxrwxrwt. 33 root   root       4.0K Jun 15 10:14 ..
-rw-r--r--   1 kkarri montilab-p    0 Jun 15 10:14 NSM_IP2_featureCounts.out
-rw-r--r--   1 kkarri montilab-p 1.9G Jun 15 10:14 NSM_IP2_primary_unique.bam
-rwx------   1 kkarri montilab-p  41M Jun 15 10:14 RefSeq_GeneBody.gtf

Starting to run my commands


Starting featureCounts

GTF file name: RefSeq_GeneBody
Rscript Parse_GTF.R RefSeq_GeneBody.gtf GeneSym_List.txt
[1] "Print arguments:"
[1] "-----------------"
[1] "GTF_File:"
[1] "RefSeq_GeneBody.gtf"
[1] "Subset_List:"
[1] "GeneSym_List.txt"
[1] "-----------------"
[1] "Loading RefSeq_GeneBody.gtf"
[1] "Loading GeneSym_List.txt"
Running assign_all_features counting
featureCounts -O -p -T 16 -s 0 -g gene_id -t exon -a GeneSym_assign_all_features.gtf -o NSM_IP2_assign_all_features.out NSM_IP2'_sorted'.bam
Running assign_only1_feature counting
featureCounts -p -T 16 -s 0 -g gene_id -t exon -a GeneSym_assign_only1_feature.gtf -o NSM_IP2_assign_only1_feature.out NSM_IP2'_sorted'.bam
Processing *_assign_*.out
Done processing file.

Ending featureCounts


List files in scratch

total 4.7G
-rw-r--r--   1 kkarri montilab-p    0 Jun 15 10:26 *_assign_*.out
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 10:26 .
drwxrwxrwt. 33 root   root       4.0K Jun 15 10:14 ..
-rw-r--r--   1 kkarri montilab-p    0 Jun 15 10:26 NSM_IP2_featureCounts.out
-rw-r--r--   1 kkarri montilab-p   65 Jun 15 10:26 NSM_IP2_featureCounts.out.summary
-rw-r--r--   1 kkarri montilab-p 1.9G Jun 15 10:14 NSM_IP2_primary_unique.bam
-rw-r--r--   1 kkarri montilab-p 2.8G Jun 15 10:26 NSM_IP2_sorted.bam
-rwxr-xr-x   1 kkarri montilab-p 6.8K Jun 15 10:26 Parse_GTF.R
-rwx------   1 kkarri montilab-p  41M Jun 15 10:14 RefSeq_GeneBody.gtf
==========================================================
Finished on : Thu Jun 15 10:26:20 EDT 2017
0 hours, 11 minutes and 40 seconds elapsed.
==========================================================