-----------------------
Start of variable list:
-----------------------
Sample_ID:
NSM_IP1
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 10:09:57 EDT 2017
Running on node : scc-pg2
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9333837
Current job name : Step_08b_NSM_IP1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9333837.1.p16

Loading required modules...


List files in scratch directory:

total 1.9G
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 10:10 .
drwxrwxrwt. 27 root   root       4.0K Jun 15 10:09 ..
-rw-r--r--   1 kkarri montilab-p    0 Jun 15 10:10 NSM_IP1_featureCounts.out
-rw-r--r--   1 kkarri montilab-p 1.9G Jun 15 10:10 NSM_IP1_primary_unique.bam
-rwx------   1 kkarri montilab-p  41M Jun 15 10:10 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_IP1_assign_all_features.out NSM_IP1'_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_IP1_assign_only1_feature.out NSM_IP1'_sorted'.bam
Processing *_assign_*.out
Done processing file.

Ending featureCounts


List files in scratch

total 4.6G
-rw-r--r--   1 kkarri montilab-p    0 Jun 15 10:20 *_assign_*.out
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 10:20 .
drwxrwxrwt. 27 root   root       4.0K Jun 15 10:09 ..
-rw-r--r--   1 kkarri montilab-p    0 Jun 15 10:20 NSM_IP1_featureCounts.out
-rw-r--r--   1 kkarri montilab-p   65 Jun 15 10:20 NSM_IP1_featureCounts.out.summary
-rw-r--r--   1 kkarri montilab-p 1.9G Jun 15 10:10 NSM_IP1_primary_unique.bam
-rw-r--r--   1 kkarri montilab-p 2.7G Jun 15 10:20 NSM_IP1_sorted.bam
-rwxr-xr-x   1 kkarri montilab-p 6.8K Jun 15 10:20 Parse_GTF.R
-rwx------   1 kkarri montilab-p  41M Jun 15 10:10 RefSeq_GeneBody.gtf
==========================================================
Finished on : Thu Jun 15 10:20:49 EDT 2017
0 hours, 10 minutes and 52 seconds elapsed.
==========================================================