-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M4
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 20:42:06 EDT 2017
Running on node : scc-kb5
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 473965
Current job name : Step_08a_G160_M4
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/473965.1.linga

Loading required modules...


List files in scratch directory:

total 666M
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 20:42 .
drwxrwxrwt. 66 root   root    268K Aug 30 20:42 ..
-rw-r--r--   1 kkarri pulmseq    0 Aug 30 20:42 G160_M4_HTSeq.out
-rw-r--r--   1 kkarri pulmseq 649M Aug 30 20:42 G160_M4_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq  18M Aug 30 20:42 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_M4'_sorted'.bam | htseq-count --stranded=reverse --type=Intronic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Intron_Only_Regions.gtf  > G160_M4_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 20G
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 21:54 .
drwxrwxrwt. 65 root   root    268K Aug 30 21:53 ..
-rw-r--r--   1 kkarri pulmseq 225K Aug 30 21:54 G160_M4_HTSeq.out
-rw-r--r--   1 kkarri pulmseq 632M Aug 30 20:50 G160_M4_primary_no_splice.bam
-rw-r--r--   1 kkarri pulmseq 649M Aug 30 20:42 G160_M4_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq 1.1G Aug 30 21:03 G160_M4_sorted.bam
-rw-r--r--   1 kkarri pulmseq   98 Aug 30 21:54 HTSeq_Extra_Lines.txt
-rw-r--r--   1 kkarri pulmseq  918 Aug 30 20:43 Header.txt
-rw-r--r--   1 kkarri pulmseq  18M Aug 30 20:42 Intron_Only_Regions.gtf
-rwxr-xr-x   1 kkarri pulmseq  38K Aug 30 21:54 RefSeq_Genes_Zero_Count.txt
-rw-r--r--   1 kkarri pulmseq 5.9G Aug 30 20:44 temp1.sam
-rw-r--r--   1 kkarri pulmseq 5.8G Aug 30 20:45 temp2.sam
-rw-r--r--   1 kkarri pulmseq 5.8G Aug 30 20:45 temp3.sam
==========================================================
Finished on : Wed Aug 30 21:54:53 EDT 2017
1 hours, 12 minutes and 47 seconds elapsed.
==========================================================