-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New/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_New/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
Exon_Only_Regions.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Dec  7 19:06:09 EST 2018
Running on node : scc-tm2
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 27190
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/27190.1.linga

Loading required modules...


List files in scratch directory:

total 1.4G
drwx------   2 kkarri waxmanlab 4.0K Dec  7 19:06 .
drwxrwxrwt. 13 root   root      116K Dec  7 19:06 ..
-rw-r--r--   1 kkarri waxmanlab  19M Dec  7 19:06 Exon_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab    0 Dec  7 19:06 G123_M1_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.3G Dec  7 19:06 G123_M1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  18M Dec  7 19:06 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 3.0G
drwx------   2 kkarri waxmanlab 4.0K Dec  7 19:15 .
drwxrwxrwt. 13 root   root      116K Dec  7 19:11 ..
-rw-r--r--   1 kkarri waxmanlab  19M Dec  7 19:06 Exon_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab 243K Dec  7 19:28 G123_M1_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 680M Dec  7 19:10 G123_M1_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri waxmanlab 1.3G Dec  7 19:06 G123_M1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 990M Dec  7 19:15 G123_M1_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  18M Dec  7 19:06 Intron_Only_Regions.gtf
==========================================================
Finished on : Fri Dec  7 19:28:22 EST 2018
0 hours, 22 minutes and 13 seconds elapsed.
==========================================================