-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
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Sample_ID:
G166_M8
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files
MODE:
intersection-nonempty
STRANDEDNESS_HTSeq:
reverse
FEATURE_ID:
gene_id
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Apr 23 05:01:16 EDT 2019
Running on node : scc-ka4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 5533325
Current job name : Step_08a_G166_M8
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5533325.1.linga

Loading required modules...


List files in scratch directory:

total 955M
drwx------   2 kkarri waxmanlab 4.0K Apr 23 05:01 .
drwxrwxrwt. 55 root   root       84K Apr 23 05:01 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 23 05:01 G166_M8_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 884M Apr 23 05:01 G166_M8_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  72M Apr 23 05:01 RefSeq_GeneBody.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view G166_M8'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > G166_M8_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 2.4G
drwx------   2 kkarri waxmanlab 4.0K Apr 23 05:15 .
drwxrwxrwt. 43 root   root       84K Apr 23 06:03 ..
-rw-r--r--   1 kkarri waxmanlab 240K Apr 23 06:07 G166_M8_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 884M Apr 23 05:01 G166_M8_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.4G Apr 23 05:15 G166_M8_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  72M Apr 23 05:01 RefSeq_GeneBody.gtf
==========================================================
Finished on : Tue Apr 23 06:07:49 EDT 2019
1 hours, 6 minutes and 33 seconds elapsed.
==========================================================