-----------------------
Need shift 1 command (have more than 9 arguments):
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-----------------------
Start of variable list:
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Sample_ID:
LZ_M28
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 15:13:23 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/07a_Extract_Counts_HTSeq
Current job ID : 6178516
Current job name : Step_07a_LZ_M28
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6178516.1.linga

Loading required modules...


List files in scratch directory:

total 444M
drwx------   2 kkarri waxmanlab 4.0K May 11 15:13 .
drwxrwxrwt. 84 root   root       84K May 11 15:13 ..
-rw-r--r--   1 kkarri waxmanlab    0 May 11 15:13 LZ_M28_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 372M May 11 15:13 LZ_M28_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_M28'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > LZ_M28_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 1.1G
drwx------   2 kkarri waxmanlab 4.0K May 11 15:19 .
drwxrwxrwt. 83 root   root       84K May 11 15:52 ..
-rw-r--r--   1 kkarri waxmanlab 242K May 11 15:52 LZ_M28_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 372M May 11 15:13 LZ_M28_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 597M May 11 15:19 LZ_M28_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  72M May 11 15:13 RefSeq_GeneBody.gtf
==========================================================
Finished on : Fri May 11 15:52:27 EDT 2018
0 hours, 39 minutes and 4 seconds elapsed.
==========================================================