-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
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Sample_ID:
LZ_M16
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/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/liver_zonation/infusion/Scripts/07a_Extract_Counts_HTSeq
ANNOTATION_FILE:
Intron_Only_Regions.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri May 11 15:11:23 EDT 2018
Running on node : scc-wl2
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/07a_Extract_Counts_HTSeq
Current job ID : 6178467
Current job name : Step_07a_LZ_M16
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6178467.1.w

Loading required modules...


List files in scratch directory:

total 303M
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 15:11 .
drwxrwxrwt. 38 root   root      4.0K May 11 15:11 ..
-rw-r--r--   1 kkarri waxmanlab  18M May 11 15:11 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab    0 May 11 15:11 LZ_M16_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 286M May 11 15:11 LZ_M16_primary_unique.bam

Starting to run my commands


Starting samtools and htseq-count


Starting splice read filter


Ending splice read filter

samtools view LZ_M16'_sorted'.bam | htseq-count --stranded=reverse --type=Intronic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Intron_Only_Regions.gtf  > LZ_M16_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 7.1G
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 15:22 .
drwxrwxrwt. 37 root   root      4.0K May 11 15:19 ..
-rw-r--r--   1 kkarri waxmanlab   97 May 11 15:22 HTSeq_Extra_Lines.txt
-rw-r--r--   1 kkarri waxmanlab  799 May 11 15:11 Header.txt
-rw-r--r--   1 kkarri waxmanlab  18M May 11 15:11 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab 231K May 11 15:22 LZ_M16_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 251M May 11 15:13 LZ_M16_primary_no_splice.bam
-rw-r--r--   1 kkarri waxmanlab 286M May 11 15:11 LZ_M16_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 408M May 11 15:15 LZ_M16_sorted.bam
-rwxr-xr-x   1 kkarri waxmanlab  38K May 11 15:22 RefSeq_Genes_Zero_Count.txt
-rw-r--r--   1 kkarri waxmanlab 2.3G May 11 15:12 temp1.sam
-rw-r--r--   1 kkarri waxmanlab 2.0G May 11 15:12 temp2.sam
-rw-r--r--   1 kkarri waxmanlab 2.0G May 11 15:12 temp3.sam
==========================================================
Finished on : Fri May 11 15:22:17 EDT 2018
0 hours, 10 minutes and 54 seconds elapsed.
==========================================================