-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M2
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/unprotected/projects/waxmanlab/routines/GTF_Files
MODE:
intersection-nonempty
STRANDEDNESS_HTSeq:
reverse
FEATURE_ID:
gene_id
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
genes.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Jul 18 13:42:51 EDT 2018
Running on node : scc-tl1
Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 6966598
Current job name : Step_08a_G167_M2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6966598.1.linga

Loading required modules...


List files in scratch directory:

total 987M
drwx------   2 kkarri waxmanlab 4.0K Jul 18 13:42 .
drwxrwxrwt. 28 root   root       20K Jul 18 13:42 ..
-rw-r--r--   1 kkarri waxmanlab    0 Jul 18 13:42 G167_M2_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 907M Jul 18 13:42 G167_M2_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M Jul 18 13:42 genes.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view G167_M2'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - genes.gtf  > G167_M2_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 2.7G
drwx------   2 kkarri waxmanlab 4.0K Jul 18 13:52 .
drwxrwxrwt. 33 root   root       20K Jul 18 13:51 ..
-rw-r--r--   1 kkarri waxmanlab    0 Jul 18 13:52 G167_M2_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 907M Jul 18 13:42 G167_M2_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.8G Jul 18 13:52 G167_M2_sorted.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M Jul 18 13:42 genes.gtf
==========================================================
Finished on : Wed Jul 18 13:52:37 EDT 2018
0 hours, 9 minutes and 46 seconds elapsed.
==========================================================