-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M10
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:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Dec  7 19:06:10 EST 2018
Running on node : scc-tm3
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 27228
Current job name : Step_08a_G123_M10
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/27228.1.linga

Loading required modules...


List files in scratch directory:

total 1.3G
drwx------   2 kkarri waxmanlab 4.0K Dec  7 19:06 .
drwxrwxrwt. 21 root   root       36K Dec  7 19:06 ..
-rw-r--r--   1 kkarri waxmanlab    0 Dec  7 19:06 G123_M10_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.3G Dec  7 19:06 G123_M10_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  72M Dec  7 19:06 RefSeq_GeneBody.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view G123_M10'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > G123_M10_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 3.0G
drwx------   2 kkarri waxmanlab 4.0K Dec  7 19:17 .
drwxrwxrwt. 17 root   root       36K Dec  7 19:40 ..
-rw-r--r--   1 kkarri waxmanlab 244K Dec  7 19:41 G123_M10_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.3G Dec  7 19:06 G123_M10_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.8G Dec  7 19:17 G123_M10_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  72M Dec  7 19:06 RefSeq_GeneBody.gtf
==========================================================
Finished on : Fri Dec  7 19:41:56 EST 2018
0 hours, 35 minutes and 46 seconds elapsed.
==========================================================