-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
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Sample_ID:
G167_M11
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:
Intron_Only_Regions.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Jul 18 13:43:15 EDT 2018
Running on node : scc-kb8
Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 6966632
Current job name : Step_08a_G167_M11
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6966632.1.linga

Loading required modules...


List files in scratch directory:

total 933M
drwx------    2 kkarri waxmanlab 4.0K Jul 18 13:43 .
drwxrwxrwt. 101 root   root      112K Jul 18 13:43 ..
-rw-r--r--    1 kkarri waxmanlab    0 Jul 18 13:43 G167_M11_HTSeq.out
-rw-r--r--    1 kkarri waxmanlab 916M Jul 18 13:43 G167_M11_primary_unique.bam
-rw-r--r--    1 kkarri waxmanlab  18M Jul 18 13:43 Intron_Only_Regions.gtf

Starting to run my commands


Starting samtools and htseq-count


Starting splice read filter


Ending splice read filter

samtools view G167_M11'_sorted'.bam | htseq-count --stranded=reverse --type=Intronic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Intron_Only_Regions.gtf  > G167_M11_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 19G
drwx------   2 kkarri waxmanlab 4.0K Jul 18 13:59 .
drwxrwxrwt. 99 root   root      112K Jul 18 13:59 ..
-rw-r--r--   1 kkarri waxmanlab  38K Jul 18 13:59 G167_M11_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 420M Jul 18 13:51 G167_M11_primary_no_splice.bam
-rw-r--r--   1 kkarri waxmanlab 916M Jul 18 13:43 G167_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 816M Jul 18 13:59 G167_M11_sorted.bam
-rw-r--r--   1 kkarri waxmanlab    0 Jul 18 13:59 HTSeq_Extra_Lines.txt
-rw-r--r--   1 kkarri waxmanlab  858 Jul 18 13:44 Header.txt
-rw-r--r--   1 kkarri waxmanlab  18M Jul 18 13:43 Intron_Only_Regions.gtf
-rwxr-xr-x   1 kkarri waxmanlab  38K Jul 18 13:59 RefSeq_Genes_Zero_Count.txt
-rw-r--r--   1 kkarri waxmanlab 8.5G Jul 18 13:46 temp1.sam
-rw-r--r--   1 kkarri waxmanlab 3.9G Jul 18 13:47 temp2.sam
-rw-r--r--   1 kkarri waxmanlab 3.9G Jul 18 13:47 temp3.sam
==========================================================
Finished on : Wed Jul 18 13:59:55 EDT 2018
0 hours, 16 minutes and 40 seconds elapsed.
==========================================================