-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
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Sample_ID:
NSM_IP1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/restricted/projectnb/waxmanlab/kkarri/GTF_Files1
MODE:
intersection-nonempty
STRANDEDNESS_HTSeq:
no
FEATURE_ID:
gene_id
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
genes.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Jun 15 06:27:17 EDT 2017
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 9332966
Current job name : Step_08a_NSM_IP1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9332966.1.linga

Loading required modules...


List files in scratch directory:

total 1.9G
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 06:27 .
drwxrwxrwt. 85 root   root       168K Jun 15 06:27 ..
-rw-r--r--   1 kkarri montilab-p    0 Jun 15 06:27 NSM_IP1_HTSeq.out
-rw-r--r--   1 kkarri montilab-p 1.9G Jun 15 06:27 NSM_IP1_primary_unique.bam
-rwxr-xr-x   1 kkarri montilab-p  52M Jun 15 06:27 genes.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view NSM_IP1'_sorted'.bam | htseq-count --stranded=no --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - genes.gtf  > NSM_IP1_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 4.6G
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 06:44 .
drwxrwxrwt. 84 root   root       168K Jun 15 07:26 ..
-rw-r--r--   1 kkarri montilab-p 167K Jun 15 07:29 NSM_IP1_HTSeq.out
-rw-r--r--   1 kkarri montilab-p 1.9G Jun 15 06:27 NSM_IP1_primary_unique.bam
-rw-r--r--   1 kkarri montilab-p 2.7G Jun 15 06:44 NSM_IP1_sorted.bam
-rwxr-xr-x   1 kkarri montilab-p  52M Jun 15 06:27 genes.gtf
==========================================================
Finished on : Thu Jun 15 07:29:46 EDT 2017
1 hours, 2 minutes and 29 seconds elapsed.
==========================================================