-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
MM_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-ka1
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 9394998
Current job name : Step_08a_MM_M3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9394998.1.linga

Loading required modules...


List files in scratch directory:

total 2.5G
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 17 05:06 .
drwxrwxrwt. 202 root   root       124K Jun 17 05:06 ..
-rw-r--r--    1 kkarri montilab-p    0 Jun 17 05:06 MM_M3_HTSeq.out
-rw-r--r--    1 kkarri montilab-p 2.5G Jun 17 05:06 MM_M3_primary_unique.bam
-rwx------    1 kkarri montilab-p  41M Jun 17 05:06 RefSeq_GeneBody.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view MM_M3'_sorted'.bam | htseq-count --stranded=no --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > MM_M3_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 6.3G
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 17 05:35 .
drwxrwxrwt. 199 root   root       124K Jun 17 06:31 ..
-rw-r--r--    1 kkarri montilab-p 166K Jun 17 06:42 MM_M3_HTSeq.out
-rw-r--r--    1 kkarri montilab-p 2.5G Jun 17 05:06 MM_M3_primary_unique.bam
-rw-r--r--    1 kkarri montilab-p 3.8G Jun 17 05:34 MM_M3_sorted.bam
-rwx------    1 kkarri montilab-p  41M Jun 17 05:06 RefSeq_GeneBody.gtf
==========================================================
Finished on : Sat Jun 17 06:42:18 EDT 2017
1 hours, 35 minutes and 30 seconds elapsed.
==========================================================