-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M25
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_rerun/Scripts/07a_Extract_Counts_HTSeq
ANNOTATION_FILE:
Exon_Only_Regions.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun May 13 14:10:46 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/07a_Extract_Counts_HTSeq
Current job ID : 6184482
Current job name : Step_07a_LZ_M25
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6184482.1.linga

Loading required modules...


List files in scratch directory:

total 358M
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 13 14:10 .
drwxrwxrwt. 53 root   root      108K May 13 14:10 ..
-rw-r--r--   1 kkarri waxmanlab  19M May 13 14:10 Exon_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab  18M May 13 14:10 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab    0 May 13 14:10 LZ_M25_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 322M May 13 14:10 LZ_M25_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_M25'_sorted'.bam | htseq-count --stranded=reverse --type=Exonic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Exon_Only_Regions.gtf  > LZ_M25_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 1013M
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 13 14:17 .
drwxrwxrwt. 53 root   root      108K May 13 14:33 ..
-rw-r--r--   1 kkarri waxmanlab  19M May 13 14:10 Exon_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab  18M May 13 14:10 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab 240K May 13 14:33 LZ_M25_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 242M May 13 14:13 LZ_M25_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri waxmanlab 322M May 13 14:10 LZ_M25_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 413M May 13 14:17 LZ_M25_sorted.bam
==========================================================
Finished on : Sun May 13 14:33:56 EDT 2018
0 hours, 23 minutes and 10 seconds elapsed.
==========================================================