-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M1
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
MODE:
intersection-nonempty
STRANDEDNESS_HTSeq:
reverse
FEATURE_ID:
gene_id
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
Exon_Only_Regions.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Dec 18 18:53:44 EST 2018
Running on node : scc-tm2
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 365151
Current job name : Step_08a_G123_M1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/365151.1.linga

Loading required modules...


List files in scratch directory:

total 1.4G
drwx------  2 kkarri waxmanlab 4.0K Dec 18 18:54 .
drwxrwxrwt. 8 root   root      116K Dec 18 18:53 ..
-rw-r--r--  1 kkarri waxmanlab  19M Dec 18 18:54 Exon_Only_Regions.gtf
-rw-r--r--  1 kkarri waxmanlab    0 Dec 18 18:54 G123_M1_HTSeq.out
-rw-r--r--  1 kkarri waxmanlab 1.3G Dec 18 18:54 G123_M1_primary_unique.bam
-rw-r--r--  1 kkarri waxmanlab  18M Dec 18 18:54 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 G123_M1'_sorted'.bam | htseq-count --stranded=reverse --type=Exonic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Exon_Only_Regions.gtf  > G123_M1_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 1.4G
drwx------  2 kkarri waxmanlab 4.0K Dec 18 18:54 .
drwxrwxrwt. 8 root   root      116K Dec 18 18:53 ..
-rw-r--r--  1 kkarri waxmanlab  19M Dec 18 18:54 Exon_Only_Regions.gtf
-rw-r--r--  1 kkarri waxmanlab    0 Dec 18 18:54 G123_M1_HTSeq.out
-rw-r--r--  1 kkarri waxmanlab    0 Dec 18 18:54 G123_M1_primary_no_Intron_Only.bam
-rw-r--r--  1 kkarri waxmanlab 1.3G Dec 18 18:54 G123_M1_primary_unique.bam
-rw-r--r--  1 kkarri waxmanlab  18M Dec 18 18:54 Intron_Only_Regions.gtf
==========================================================
Finished on : Tue Dec 18 18:55:30 EST 2018
0 hours, 1 minutes and 46 seconds elapsed.
==========================================================