-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M10
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:
Intron_Only_Regions.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Dec 18 22:16:14 EST 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 366142
Current job name : Step_08b_G123_M10
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/366142.1.linga

Loading required modules...


List files in scratch directory:

total 1.3G
drwx------   2 kkarri waxmanlab 4.0K Dec 18 22:16 .
drwxrwxrwt. 32 root   root      112K Dec 18 22:16 ..
-rw-r--r--   1 kkarri waxmanlab    0 Dec 18 22:16 G123_M10_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 1.3G Dec 18 22:16 G123_M10_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  18M Dec 18 22:16 Intron_Only_Regions.gtf

Starting to run my commands


Starting featureCounts


Starting splice read filter


Ending splice read filter

GTF file name: Intron_Only_Regions
Rscript Parse_GTF.R Intron_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 Intronic_Only -a GeneSym_assign_all_features.gtf -o G123_M10_assign_all_features.out G123_M10'_sorted'.bam
Running assign_only1_feature counting
featureCounts -p -T 16 -s 2 -g gene_id -t Intronic_Only -a GeneSym_assign_only1_feature.gtf -o G123_M10_assign_only1_feature.out G123_M10'_sorted'.bam
Processing *_assign_*.out
Done processing file.

Ending featureCounts


List files in scratch

total 3.9G
-rw-r--r--   1 kkarri waxmanlab    0 Dec 18 22:44 *_assign_*.out
drwx------   2 kkarri waxmanlab 4.0K Dec 18 22:44 .
drwxrwxrwt. 32 root   root      112K Dec 18 22:16 ..
-rw-r--r--   1 kkarri waxmanlab  38K Dec 18 22:44 G123_M10_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab   67 Dec 18 22:44 G123_M10_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 1.2G Dec 18 22:27 G123_M10_primary_no_splice.bam
-rw-r--r--   1 kkarri waxmanlab 1.3G Dec 18 22:16 G123_M10_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.6G Dec 18 22:44 G123_M10_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 4.0K Dec 18 22:44 GeneSym_List.txt
-rw-r--r--   1 kkarri waxmanlab  18M Dec 18 22:16 Intron_Only_Regions.gtf
-rwxr-xr-x   1 kkarri waxmanlab 6.8K Dec 18 22:44 Parse_GTF.R
-rwxr-xr-x   1 kkarri waxmanlab  38K Dec 18 22:44 RefSeq_Genes_Zero_Count.txt
==========================================================
Finished on : Tue Dec 18 22:44:11 EST 2018
0 hours, 27 minutes and 57 seconds elapsed.
==========================================================