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Need shift 1 command (have more than 9 arguments):
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-----------------------
Start of variable list:
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Sample_ID:
WT3
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files
MODE:
intersection-nonempty
STRANDEDNESS_HTSeq:
reverse
FEATURE_ID:
gene_id
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
genes.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
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==========================================================
Starting on : Tue Apr 30 05:29:42 EDT 2019
Running on node : scc-kb2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 5782293
Current job name : Step_08a_WT3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5782293.1.linga

Loading required modules...


List files in scratch directory:

total 339M
drwx------   2 kkarri waxmanlab 4.0K Apr 30 05:41 .
drwxrwxrwt. 83 root   root       92K Apr 30 05:33 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 30 05:41 WT3_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 259M Apr 30 05:35 WT3_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M Apr 30 05:35 genes.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view WT3'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - genes.gtf  > WT3_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 748M
drwx------   2 kkarri waxmanlab 4.0K Apr 30 05:45 .
drwxrwxrwt. 78 root   root       92K Apr 30 06:00 ..
-rw-r--r--   1 kkarri waxmanlab 229K Apr 30 06:01 WT3_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 259M Apr 30 05:35 WT3_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 409M Apr 30 05:45 WT3_sorted.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M Apr 30 05:35 genes.gtf
==========================================================
Finished on : Tue Apr 30 06:01:43 EDT 2019
0 hours, 32 minutes and 1 seconds elapsed.
==========================================================