-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M16
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:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Dec 18 23:04:25 EST 2018
Running on node : scc-tk4
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 366191
Current job name : Step_08b_G123_M16
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/366191.1.linga

Loading required modules...


List files in scratch directory:

total 1.7G
drwx------  2 kkarri waxmanlab 4.0K Dec 18 23:04 .
drwxrwxrwt. 9 root   root       52K Dec 18 23:04 ..
-rw-r--r--  1 kkarri waxmanlab    0 Dec 18 23:04 G123_M16_featureCounts.out
-rw-r--r--  1 kkarri waxmanlab 1.6G Dec 18 23:04 G123_M16_primary_unique.bam
-rw-r--r--  1 kkarri waxmanlab  72M Dec 18 23:04 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
WARNING: ignoring environment value of R_HOME
Running assign_all_features counting
featureCounts -O -p -T 16 -s 2 -g gene_id -t exon -a GeneSym_assign_all_features.gtf -o G123_M16_assign_all_features.out G123_M16'_sorted'.bam
Running assign_only1_feature counting
featureCounts -p -T 16 -s 2 -g gene_id -t exon -a GeneSym_assign_only1_feature.gtf -o G123_M16_assign_only1_feature.out G123_M16'_sorted'.bam
Processing *_assign_*.out
Done processing file.

Ending featureCounts


List files in scratch

total 4.0G
-rw-r--r--  1 kkarri waxmanlab    0 Dec 18 23:18 *_assign_*.out
drwx------  2 kkarri waxmanlab 4.0K Dec 18 23:18 .
drwxrwxrwt. 8 root   root       52K Dec 18 23:18 ..
-rw-r--r--  1 kkarri waxmanlab    0 Dec 18 23:18 G123_M16_featureCounts.out
-rw-r--r--  1 kkarri waxmanlab   67 Dec 18 23:18 G123_M16_featureCounts.out.summary
-rw-r--r--  1 kkarri waxmanlab 1.6G Dec 18 23:04 G123_M16_primary_unique.bam
-rw-r--r--  1 kkarri waxmanlab 2.3G Dec 18 23:18 G123_M16_sorted.bam
-rw-r--r--  1 kkarri waxmanlab  14K Dec 18 23:18 GeneSym_List.txt
-rwxr-xr-x  1 kkarri waxmanlab 6.8K Dec 18 23:18 Parse_GTF.R
-rw-r--r--  1 kkarri waxmanlab  72M Dec 18 23:04 RefSeq_GeneBody.gtf
==========================================================
Finished on : Tue Dec 18 23:18:05 EST 2018
0 hours, 13 minutes and 40 seconds elapsed.
==========================================================