-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
C_IP3
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:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Jun 15 06:27:16 EDT 2017
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 9332951
Current job name : Step_08a_C_IP3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9332951.1.linga

Loading required modules...


List files in scratch directory:

total 2.1G
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 06:27 .
drwxrwxrwt. 68 root   root       164K Jun 15 06:27 ..
-rw-r--r--   1 kkarri montilab-p    0 Jun 15 06:27 C_IP3_HTSeq.out
-rw-r--r--   1 kkarri montilab-p 2.1G Jun 15 06:27 C_IP3_primary_unique.bam
-rwx------   1 kkarri montilab-p  41M Jun 15 06:27 RefSeq_GeneBody.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view C_IP3'_sorted'.bam | htseq-count --stranded=no --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > C_IP3_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 5.3G
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 06:51 .
drwxrwxrwt. 61 root   root       164K Jun 15 07:50 ..
-rw-r--r--   1 kkarri montilab-p 165K Jun 15 07:51 C_IP3_HTSeq.out
-rw-r--r--   1 kkarri montilab-p 2.1G Jun 15 06:27 C_IP3_primary_unique.bam
-rw-r--r--   1 kkarri montilab-p 3.2G Jun 15 06:51 C_IP3_sorted.bam
-rwx------   1 kkarri montilab-p  41M Jun 15 06:27 RefSeq_GeneBody.gtf
==========================================================
Finished on : Thu Jun 15 07:51:09 EDT 2017
1 hours, 23 minutes and 53 seconds elapsed.
==========================================================