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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:
KI3
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 05:09:08 EDT 2019
Running on node : scc-kb7
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 5782393
Current job name : Step_08a_KI3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5782393.1.linga

Loading required modules...


List files in scratch directory:

total 370M
drwx------   2 kkarri waxmanlab 4.0K Apr 30 05:16 .
drwxrwxrwt. 62 root   root      168K Apr 30 05:15 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 30 05:16 KI3_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 290M Apr 30 05:15 KI3_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M Apr 30 05:15 genes.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view KI3'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - genes.gtf  > KI3_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 824M
drwx------   2 kkarri waxmanlab 4.0K Apr 30 05:20 .
drwxrwxrwt. 47 root   root      168K Apr 30 05:36 ..
-rw-r--r--   1 kkarri waxmanlab 230K Apr 30 05:37 KI3_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 290M Apr 30 05:15 KI3_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 454M Apr 30 05:20 KI3_sorted.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M Apr 30 05:15 genes.gtf
==========================================================
Finished on : Tue Apr 30 05:37:12 EDT 2019
0 hours, 28 minutes and 4 seconds elapsed.
==========================================================