-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
PB_M3
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_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/Water_Saline/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sat Jun 17 05:06:48 EDT 2017
Running on node : scc-ka5
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 9395004
Current job name : Step_08a_PB_M3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9395004.1.linga

Loading required modules...


List files in scratch directory:

total 2.5G
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 17 05:07 .
drwxrwxrwt. 88 root   root        72K Jun 17 05:07 ..
-rw-r--r--   1 kkarri montilab-p    0 Jun 17 05:07 PB_M3_HTSeq.out
-rw-r--r--   1 kkarri montilab-p 2.4G Jun 17 05:07 PB_M3_primary_unique.bam
-rwx------   1 kkarri montilab-p  41M Jun 17 05:07 RefSeq_GeneBody.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view PB_M3'_sorted'.bam | htseq-count --stranded=no --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > PB_M3_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 6.2G
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 17 05:33 .
drwxrwxrwt. 83 root   root        72K Jun 17 06:35 ..
-rw-r--r--   1 kkarri montilab-p 166K Jun 17 06:38 PB_M3_HTSeq.out
-rw-r--r--   1 kkarri montilab-p 2.4G Jun 17 05:07 PB_M3_primary_unique.bam
-rw-r--r--   1 kkarri montilab-p 3.7G Jun 17 05:33 PB_M3_sorted.bam
-rwx------   1 kkarri montilab-p  41M Jun 17 05:07 RefSeq_GeneBody.gtf
==========================================================
Finished on : Sat Jun 17 06:38:28 EDT 2017
1 hours, 31 minutes and 40 seconds elapsed.
==========================================================