-----------------------
Start of variable list:
-----------------------
Sample_ID:
TA_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 09:56:00 EDT 2017
Running on node : scc-ka1
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9333831
Current job name : Step_08b_TA_IP1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9333831.1.linga

Loading required modules...


List files in scratch directory:

total 2.3G
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 15 09:56 .
drwxrwxrwt. 213 root   root       124K Jun 15 09:56 ..
-rwx------    1 kkarri montilab-p  41M Jun 15 09:56 RefSeq_GeneBody.gtf
-rw-r--r--    1 kkarri montilab-p    0 Jun 15 09:56 TA_IP1_featureCounts.out
-rw-r--r--    1 kkarri montilab-p 2.2G Jun 15 09:56 TA_IP1_primary_unique.bam

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 TA_IP1_assign_all_features.out TA_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 TA_IP1_assign_only1_feature.out TA_IP1'_sorted'.bam
Processing *_assign_*.out
Done processing file.

Ending featureCounts


List files in scratch

total 5.5G
-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. 213 root   root       124K Jun 15 10:19 ..
-rwxr-xr-x    1 kkarri montilab-p 6.8K Jun 15 10:20 Parse_GTF.R
-rwx------    1 kkarri montilab-p  41M Jun 15 09:56 RefSeq_GeneBody.gtf
-rw-r--r--    1 kkarri montilab-p    0 Jun 15 10:20 TA_IP1_featureCounts.out
-rw-r--r--    1 kkarri montilab-p   63 Jun 15 10:20 TA_IP1_featureCounts.out.summary
-rw-r--r--    1 kkarri montilab-p 2.2G Jun 15 09:56 TA_IP1_primary_unique.bam
-rw-r--r--    1 kkarri montilab-p 3.3G Jun 15 10:20 TA_IP1_sorted.bam
==========================================================
Finished on : Thu Jun 15 10:20:17 EDT 2017
0 hours, 24 minutes and 17 seconds elapsed.
==========================================================