-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M34
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:
Exon_Only_Regions.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri May 11 15:13:40 EDT 2018
Running on node : scc-ka1
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/07a_Extract_Counts_HTSeq
Current job ID : 6178538
Current job name : Step_07a_LZ_M34
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6178538.1.linga

Loading required modules...


List files in scratch directory:

total 482M
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  19M May 11 15:13 Exon_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab  18M May 11 15:13 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab    0 May 11 15:13 LZ_M34_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 447M May 11 15:13 LZ_M34_primary_unique.bam

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 LZ_M34'_sorted'.bam | htseq-count --stranded=reverse --type=Exonic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Exon_Only_Regions.gtf  > LZ_M34_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 1.4G
drwx------   2 kkarri waxmanlab 4.0K May 11 15:23 .
drwxrwxrwt. 57 root   root      124K May 11 15:50 ..
-rw-r--r--   1 kkarri waxmanlab  19M May 11 15:13 Exon_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab  18M May 11 15:13 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab 241K May 11 15:50 LZ_M34_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 337M May 11 15:18 LZ_M34_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri waxmanlab 447M May 11 15:13 LZ_M34_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 549M May 11 15:23 LZ_M34_sorted.bam
==========================================================
Finished on : Fri May 11 15:50:49 EDT 2018
0 hours, 37 minutes and 9 seconds elapsed.
==========================================================