-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M6
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/unprotected/projects/waxmanlab/routines/GTF_Files
MODE:
intersection-nonempty
STRANDEDNESS_HTSeq:
reverse
FEATURE_ID:
gene_id
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
Exon_Only_Regions.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Jul 18 13:43:14 EDT 2018
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 6966611
Current job name : Step_08a_G167_M6
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6966611.1.linga

Loading required modules...


List files in scratch directory:

total 692M
drwx------    2 kkarri waxmanlab 4.0K Jul 18 13:43 .
drwxrwxrwt. 139 root   root      168K Jul 18 13:43 ..
-rw-r--r--    1 kkarri waxmanlab  19M Jul 18 13:43 Exon_Only_Regions.gtf
-rw-r--r--    1 kkarri waxmanlab    0 Jul 18 13:43 G167_M6_HTSeq.out
-rw-r--r--    1 kkarri waxmanlab 656M Jul 18 13:43 G167_M6_primary_unique.bam
-rw-r--r--    1 kkarri waxmanlab  18M Jul 18 13:43 Intron_Only_Regions.gtf

Starting to run my commands


Starting samtools and htseq-count


Starting Intron_Only_Regions read overlap filter


Ending Intron_Only_Regions read overlap filter

samtools view G167_M6'_sorted'.bam | htseq-count --stranded=reverse --type=Exonic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Exon_Only_Regions.gtf  > G167_M6_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 1.5G
drwx------    2 kkarri waxmanlab 4.0K Jul 18 13:52 .
drwxrwxrwt. 140 root   root      168K Jul 18 13:52 ..
-rw-r--r--    1 kkarri waxmanlab  19M Jul 18 13:43 Exon_Only_Regions.gtf
-rw-r--r--    1 kkarri waxmanlab    0 Jul 18 13:52 G167_M6_HTSeq.out
-rw-r--r--    1 kkarri waxmanlab 269M Jul 18 13:47 G167_M6_primary_no_Intron_Only.bam
-rw-r--r--    1 kkarri waxmanlab 656M Jul 18 13:43 G167_M6_primary_unique.bam
-rw-r--r--    1 kkarri waxmanlab 514M Jul 18 13:52 G167_M6_sorted.bam
-rw-r--r--    1 kkarri waxmanlab  18M Jul 18 13:43 Intron_Only_Regions.gtf
==========================================================
Finished on : Wed Jul 18 13:52:44 EDT 2018
0 hours, 9 minutes and 30 seconds elapsed.
==========================================================