-----------------------
Start of variable list:
-----------------------
Sample_ID:
MM_M3
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_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/Water_Saline/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sat Jun 17 11:59:08 EDT 2017
Running on node : scc-ka6
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9395322
Current job name : Step_08b_MM_M3
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9395322.1.linga

Loading required modules...


List files in scratch directory:

total 2.5G
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 17 11:59 .
drwxrwxrwt. 125 root   root        92K Jun 17 11:59 ..
-rw-r--r--    1 kkarri montilab-p    0 Jun 17 11:59 MM_M3_featureCounts.out
-rw-r--r--    1 kkarri montilab-p 2.5G Jun 17 11:59 MM_M3_primary_unique.bam
-rwx------    1 kkarri montilab-p  41M Jun 17 11:59 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 MM_M3_assign_all_features.out MM_M3'_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 MM_M3_assign_only1_feature.out MM_M3'_sorted'.bam
Processing *_assign_*.out
Done processing file.

Ending featureCounts


List files in scratch

total 6.3G
-rw-r--r--    1 kkarri montilab-p    0 Jun 17 12:28 *_assign_*.out
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 17 12:28 .
drwxrwxrwt. 124 root   root        92K Jun 17 12:28 ..
-rw-r--r--    1 kkarri montilab-p    0 Jun 17 12:28 MM_M3_featureCounts.out
-rw-r--r--    1 kkarri montilab-p   61 Jun 17 12:28 MM_M3_featureCounts.out.summary
-rw-r--r--    1 kkarri montilab-p 2.5G Jun 17 11:59 MM_M3_primary_unique.bam
-rw-r--r--    1 kkarri montilab-p 3.8G Jun 17 12:28 MM_M3_sorted.bam
-rwxr-xr-x    1 kkarri montilab-p 6.8K Jun 17 12:28 Parse_GTF.R
-rwx------    1 kkarri montilab-p  41M Jun 17 11:59 RefSeq_GeneBody.gtf
==========================================================
Finished on : Sat Jun 17 12:28:17 EDT 2017
0 hours, 29 minutes and 9 seconds elapsed.
==========================================================