-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
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Sample_ID:
KI1
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:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Apr 30 05:09:25 EDT 2019
Running on node : scc-ka8
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 5782376
Current job name : Step_08a_KI1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5782376.1.linga

Loading required modules...


List files in scratch directory:

total 355M
drwx------   2 kkarri waxmanlab 4.0K Apr 30 05:21 .
drwxrwxrwt. 70 root   root       72K Apr 30 05:16 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 30 05:21 KI1_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 284M Apr 30 05:13 KI1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  72M Apr 30 05:13 RefSeq_GeneBody.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view KI1'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > KI1_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 801M
drwx------   2 kkarri waxmanlab 4.0K Apr 30 05:27 .
drwxrwxrwt. 62 root   root       72K Apr 30 05:43 ..
-rw-r--r--   1 kkarri waxmanlab 236K Apr 30 05:44 KI1_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 284M Apr 30 05:13 KI1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 446M Apr 30 05:27 KI1_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  72M Apr 30 05:13 RefSeq_GeneBody.gtf
==========================================================
Finished on : Tue Apr 30 05:44:26 EDT 2019
0 hours, 35 minutes and 1 seconds elapsed.
==========================================================