-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M3
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples/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/G160_Samples/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
Exon_Only_Regions.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Aug 30 20:41:53 EDT 2017
Running on node : scc-ka7
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 473956
Current job name : Step_08a_G160_M3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/473956.1.linga

Loading required modules...


List files in scratch directory:

total 1.8G
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 20:42 .
drwxrwxrwt. 65 root   root    340K Aug 30 20:41 ..
-rw-r--r--   1 kkarri pulmseq  19M Aug 30 20:42 Exon_Only_Regions.gtf
-rw-r--r--   1 kkarri pulmseq    0 Aug 30 20:42 G160_M3_HTSeq.out
-rw-r--r--   1 kkarri pulmseq 1.8G Aug 30 20:42 G160_M3_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq  18M Aug 30 20:42 Intron_Only_Regions.gtf

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 G160_M3'_sorted'.bam | htseq-count --stranded=reverse --type=Exonic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Exon_Only_Regions.gtf  > G160_M3_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 3.1G
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 21:00 .
drwxrwxrwt. 74 root   root    340K Aug 30 21:29 ..
-rw-r--r--   1 kkarri pulmseq  19M Aug 30 20:42 Exon_Only_Regions.gtf
-rw-r--r--   1 kkarri pulmseq 240K Aug 30 21:36 G160_M3_HTSeq.out
-rw-r--r--   1 kkarri pulmseq 542M Aug 30 20:51 G160_M3_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri pulmseq 1.8G Aug 30 20:42 G160_M3_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq 793M Aug 30 21:00 G160_M3_sorted.bam
-rw-r--r--   1 kkarri pulmseq  18M Aug 30 20:42 Intron_Only_Regions.gtf
==========================================================
Finished on : Wed Aug 30 21:36:24 EDT 2017
0 hours, 54 minutes and 31 seconds elapsed.
==========================================================