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Need shift 1 command (have more than 9 arguments):
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-----------------------
Start of variable list:
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Sample_ID:
G123_M11
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New/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/G123_New/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Dec  7 19:06:11 EST 2018
Running on node : scc-tk1
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 27232
Current job name : Step_08a_G123_M11
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/27232.1.linga

Loading required modules...


List files in scratch directory:

total 1.1G
drwx------   2 kkarri waxmanlab 4.0K Dec  7 19:06 .
drwxrwxrwt. 19 root   root       36K Dec  7 19:06 ..
-rw-r--r--   1 kkarri waxmanlab    0 Dec  7 19:06 G123_M11_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.1G Dec  7 19:06 G123_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  72M Dec  7 19:06 RefSeq_GeneBody.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view G123_M11'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > G123_M11_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 2.5G
drwx------   2 kkarri waxmanlab 4.0K Dec  7 19:15 .
drwxrwxrwt. 20 root   root       36K Dec  7 19:33 ..
-rw-r--r--   1 kkarri waxmanlab 242K Dec  7 19:34 G123_M11_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.1G Dec  7 19:06 G123_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.5G Dec  7 19:15 G123_M11_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  72M Dec  7 19:06 RefSeq_GeneBody.gtf
==========================================================
Finished on : Fri Dec  7 19:34:39 EST 2018
0 hours, 28 minutes and 28 seconds elapsed.
==========================================================