-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M33
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:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Aug 30 20:42:06 EDT 2017
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 473962
Current job name : Step_08a_G160_M33
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/473962.1.linga

Loading required modules...


List files in scratch directory:

total 1.9G
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 20:42 .
drwxrwxrwt. 57 root   root    180K Aug 30 20:42 ..
-rw-r--r--   1 kkarri pulmseq    0 Aug 30 20:42 G160_M33_HTSeq.out
-rw-r--r--   1 kkarri pulmseq 1.8G Aug 30 20:42 G160_M33_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq  72M Aug 30 20:42 RefSeq_GeneBody.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view G160_M33'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > G160_M33_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 4.2G
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 21:10 .
drwxrwxrwt. 40 root   root    180K Aug 30 22:33 ..
-rw-r--r--   1 kkarri pulmseq 241K Aug 30 22:34 G160_M33_HTSeq.out
-rw-r--r--   1 kkarri pulmseq 1.8G Aug 30 20:42 G160_M33_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq 2.4G Aug 30 21:10 G160_M33_sorted.bam
-rw-r--r--   1 kkarri pulmseq  72M Aug 30 20:42 RefSeq_GeneBody.gtf
==========================================================
Finished on : Wed Aug 30 22:34:00 EDT 2017
1 hours, 51 minutes and 54 seconds elapsed.
==========================================================