-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
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Sample_ID:
G166_M7
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 05:01:49 EDT 2019
Running on node : scc-kb8
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 5533321
Current job name : Step_08a_G166_M7
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5533321.1.linga

Loading required modules...


List files in scratch directory:

total 1.3G
drwx------   2 kkarri waxmanlab 4.0K Apr 23 05:03 .
drwxrwxrwt. 21 root   root      112K Apr 23 05:02 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 23 05:03 G166_M7_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.3G Apr 23 05:03 G166_M7_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  72M Apr 23 05:03 RefSeq_GeneBody.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view G166_M7'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > G166_M7_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 3.9G
drwx------   2 kkarri waxmanlab 4.0K Apr 23 05:31 .
drwxrwxrwt. 11 root   root      112K Apr 23 07:01 ..
-rw-r--r--   1 kkarri waxmanlab 244K Apr 23 07:11 G166_M7_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.3G Apr 23 05:03 G166_M7_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 2.6G Apr 23 05:31 G166_M7_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  72M Apr 23 05:03 RefSeq_GeneBody.gtf
==========================================================
Finished on : Tue Apr 23 07:11:55 EDT 2019
2 hours, 10 minutes and 6 seconds elapsed.
==========================================================