-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M4
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/unprotected/projects/waxmanlab/routines/GTF_Files
STRANDEDNESS_featureCount:
2
FEATURE_ID:
gene_id
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
Exon_Only_Regions.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Dec 18 21:15:08 EST 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 366093
Current job name : Step_08b_G123_M4
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/366093.1.linga

Loading required modules...


List files in scratch directory:

total 1.9G
drwx------   2 kkarri waxmanlab 4.0K Dec 18 21:15 .
drwxrwxrwt. 45 root   root       92K Dec 18 21:15 ..
-rw-r--r--   1 kkarri waxmanlab  19M Dec 18 21:15 Exon_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab    0 Dec 18 21:15 G123_M4_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 1.8G Dec 18 21:15 G123_M4_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  18M Dec 18 21:15 Intron_Only_Regions.gtf

Starting to run my commands


Starting featureCounts


Starting Intron_Only_Regions read overlap filter


Ending Intron_Only_Regions read overlap filter

GTF file name: Exon_Only_Regions
Rscript Parse_GTF.R Exon_Only_Regions.gtf GeneSym_List.txt
WARNING: ignoring environment value of R_HOME
Running assign_all_features counting
featureCounts -O -p -T 16 -s 2 -g gene_id -t Exonic_Only -a GeneSym_assign_all_features.gtf -o G123_M4_assign_all_features.out G123_M4'_sorted'.bam
Running assign_only1_feature counting
featureCounts -p -T 16 -s 2 -g gene_id -t Exonic_Only -a GeneSym_assign_only1_feature.gtf -o G123_M4_assign_only1_feature.out G123_M4'_sorted'.bam
Processing *_assign_*.out
Done processing file.

Ending featureCounts


List files in scratch

total 1.9G
-rw-r--r--   1 kkarri waxmanlab    0 Dec 18 21:15 *_assign_*.out
drwx------   2 kkarri waxmanlab 4.0K Dec 18 21:15 .
drwxrwxrwt. 45 root   root       92K Dec 18 21:15 ..
-rw-r--r--   1 kkarri waxmanlab  19M Dec 18 21:15 Exon_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab    0 Dec 18 21:15 G123_M4_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab   65 Dec 18 21:15 G123_M4_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab    0 Dec 18 21:15 G123_M4_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri waxmanlab 1.8G Dec 18 21:15 G123_M4_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  14K Dec 18 21:15 GeneSym_List.txt
-rw-r--r--   1 kkarri waxmanlab  18M Dec 18 21:15 Intron_Only_Regions.gtf
-rwxr-xr-x   1 kkarri waxmanlab 6.8K Dec 18 21:15 Parse_GTF.R
==========================================================
Finished on : Tue Dec 18 21:15:38 EST 2018
0 hours, 0 minutes and 30 seconds elapsed.
==========================================================