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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_M7
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/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_Env/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Dec 18 18:53:47 EST 2018
Running on node : scc-ka6
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 365178
Current job name : Step_08a_G123_M7
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/365178.1.linga

Loading required modules...


List files in scratch directory:

total 1.4G
drwx------   2 kkarri waxmanlab 4.0K Dec 18 18:58 .
drwxrwxrwt. 36 root   root       92K Dec 18 18:53 ..
-rw-r--r--   1 kkarri waxmanlab    0 Dec 18 18:58 G123_M7_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.4G Dec 18 18:57 G123_M7_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  72M Dec 18 18:57 RefSeq_GeneBody.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view G123_M7'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > G123_M7_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 3.3G
drwx------   2 kkarri waxmanlab 4.0K Dec 18 19:17 .
drwxrwxrwt. 26 root   root       92K Dec 18 20:14 ..
-rw-r--r--   1 kkarri waxmanlab 245K Dec 18 20:16 G123_M7_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.4G Dec 18 18:57 G123_M7_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.9G Dec 18 19:17 G123_M7_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  72M Dec 18 18:57 RefSeq_GeneBody.gtf
==========================================================
Finished on : Tue Dec 18 20:16:10 EST 2018
1 hours, 22 minutes and 23 seconds elapsed.
==========================================================