-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
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Sample_ID:
LZ_M31
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/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/infusion/Scripts/07a_Extract_Counts_HTSeq
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri May 11 15:13:38 EDT 2018
Running on node : scc-ka1
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/07a_Extract_Counts_HTSeq
Current job ID : 6178528
Current job name : Step_07a_LZ_M31
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6178528.1.linga

Loading required modules...


List files in scratch directory:

total 406M
drwx------   2 kkarri waxmanlab 4.0K May 11 15:13 .
drwxrwxrwt. 55 root   root      124K May 11 15:13 ..
-rw-r--r--   1 kkarri waxmanlab    0 May 11 15:13 LZ_M31_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 335M May 11 15:13 LZ_M31_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  72M May 11 15:13 RefSeq_GeneBody.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view LZ_M31'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > LZ_M31_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 943M
drwx------   2 kkarri waxmanlab 4.0K May 11 15:20 .
drwxrwxrwt. 58 root   root      124K May 11 15:47 ..
-rw-r--r--   1 kkarri waxmanlab 241K May 11 15:47 LZ_M31_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 335M May 11 15:13 LZ_M31_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 537M May 11 15:20 LZ_M31_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  72M May 11 15:13 RefSeq_GeneBody.gtf
==========================================================
Finished on : Fri May 11 15:47:58 EDT 2018
0 hours, 34 minutes and 20 seconds elapsed.
==========================================================