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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_M8
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:
genes.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Dec 18 18:53:46 EST 2018
Running on node : scc-tl4
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 365183
Current job name : Step_08a_G123_M8
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/365183.1.linga

Loading required modules...


List files in scratch directory:

total 1.4G
drwx------   2 kkarri waxmanlab 4.0K Dec 18 18:54 .
drwxrwxrwt. 12 root   root       40K Dec 18 18:53 ..
-rw-r--r--   1 kkarri waxmanlab    0 Dec 18 18:54 G123_M8_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.3G Dec 18 18:53 G123_M8_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M Dec 18 18:54 genes.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view G123_M8'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - genes.gtf  > G123_M8_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 3.1G
drwx------   2 kkarri waxmanlab 4.0K Dec 18 19:05 .
drwxrwxrwt. 12 root   root       40K Dec 18 19:11 ..
-rw-r--r--   1 kkarri waxmanlab 239K Dec 18 19:29 G123_M8_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.3G Dec 18 18:53 G123_M8_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.8G Dec 18 19:05 G123_M8_sorted.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M Dec 18 18:54 genes.gtf
==========================================================
Finished on : Tue Dec 18 19:29:50 EST 2018
0 hours, 36 minutes and 4 seconds elapsed.
==========================================================