-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M3
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/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/liver_zonation/Scripts/07a_Extract_Counts_HTSeq
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed May  9 18:45:23 EDT 2018
Running on node : scc-ka7
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/07a_Extract_Counts_HTSeq
Current job ID : 6138163
Current job name : Step_07a_LZ_M3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6138163.1.linga

Loading required modules...


List files in scratch directory:

total 379M
drwx------   2 kkarri waxmanlab 4.0K May  9 18:45 .
drwxrwxrwt. 53 root   root      340K May  9 18:45 ..
-rw-r--r--   1 kkarri waxmanlab    0 May  9 18:45 LZ_M3_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 308M May  9 18:45 LZ_M3_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  72M May  9 18:45 RefSeq_GeneBody.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view LZ_M3'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > LZ_M3_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 882M
drwx------   2 kkarri waxmanlab 4.0K May  9 18:50 .
drwxrwxrwt. 47 root   root      340K May  9 19:12 ..
-rw-r--r--   1 kkarri waxmanlab 241K May  9 19:13 LZ_M3_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 308M May  9 18:45 LZ_M3_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 503M May  9 18:50 LZ_M3_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  72M May  9 18:45 RefSeq_GeneBody.gtf
==========================================================
Finished on : Wed May  9 19:13:30 EDT 2018
0 hours, 28 minutes and 7 seconds elapsed.
==========================================================