-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
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Sample_ID:
G160_M11
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_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/G160_Samples/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
Intron_Only_Regions.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Aug 30 20:41:49 EDT 2017
Running on node : scc-kb5
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 473945
Current job name : Step_08a_G160_M11
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/473945.1.linga

Loading required modules...


List files in scratch directory:

total 1.1G
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 20:41 .
drwxrwxrwt. 60 root   root    268K Aug 30 20:41 ..
-rw-r--r--   1 kkarri pulmseq    0 Aug 30 20:41 G160_M11_HTSeq.out
-rw-r--r--   1 kkarri pulmseq 1.1G Aug 30 20:41 G160_M11_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq  18M Aug 30 20:41 Intron_Only_Regions.gtf

Starting to run my commands


Starting samtools and htseq-count


Starting splice read filter


Ending splice read filter

samtools view G160_M11'_sorted'.bam | htseq-count --stranded=reverse --type=Intronic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Intron_Only_Regions.gtf  > G160_M11_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 24G
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 22:05 .
drwxrwxrwt. 61 root   root    268K Aug 30 22:02 ..
-rw-r--r--   1 kkarri pulmseq 240K Aug 30 22:05 G160_M11_HTSeq.out
-rw-r--r--   1 kkarri pulmseq 1.1G Aug 30 20:53 G160_M11_primary_no_splice.bam
-rw-r--r--   1 kkarri pulmseq 1.1G Aug 30 20:41 G160_M11_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq 1.4G Aug 30 21:10 G160_M11_sorted.bam
-rw-r--r--   1 kkarri pulmseq   98 Aug 30 22:05 HTSeq_Extra_Lines.txt
-rw-r--r--   1 kkarri pulmseq  921 Aug 30 20:43 Header.txt
-rw-r--r--   1 kkarri pulmseq  18M Aug 30 20:41 Intron_Only_Regions.gtf
-rwxr-xr-x   1 kkarri pulmseq  38K Aug 30 22:05 RefSeq_Genes_Zero_Count.txt
-rw-r--r--   1 kkarri pulmseq 7.1G Aug 30 20:45 temp1.sam
-rw-r--r--   1 kkarri pulmseq 6.7G Aug 30 20:46 temp2.sam
-rw-r--r--   1 kkarri pulmseq 6.7G Aug 30 20:46 temp3.sam
==========================================================
Finished on : Wed Aug 30 22:05:59 EDT 2017
1 hours, 24 minutes and 10 seconds elapsed.
==========================================================