-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
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Sample_ID:
G160_M22
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:
genes.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Aug 30 20:41:55 EDT 2017
Running on node : scc-kb5
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 473955
Current job name : Step_08a_G160_M22
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/473955.1.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. 60 root   root    268K Aug 30 20:41 ..
-rw-r--r--   1 kkarri pulmseq    0 Aug 30 20:42 G160_M22_HTSeq.out
-rw-r--r--   1 kkarri pulmseq 1.8G Aug 30 20:42 G160_M22_primary_unique.bam
-rwxr-xr-x   1 kkarri pulmseq  81M Aug 30 20:42 genes.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view G160_M22'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - genes.gtf  > G160_M22_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 4.2G
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 21:12 .
drwxrwxrwt. 59 root   root    268K Aug 30 22:43 ..
-rw-r--r--   1 kkarri pulmseq 237K Aug 30 22:44 G160_M22_HTSeq.out
-rw-r--r--   1 kkarri pulmseq 1.8G Aug 30 20:42 G160_M22_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq 2.4G Aug 30 21:12 G160_M22_sorted.bam
-rwxr-xr-x   1 kkarri pulmseq  81M Aug 30 20:42 genes.gtf
==========================================================
Finished on : Wed Aug 30 22:44:04 EDT 2017
2 hours, 2 minutes and 9 seconds elapsed.
==========================================================