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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:
G170_M19
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/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:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
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End of variable list
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==========================================================
Starting on : Thu Sep  5 16:04:52 EDT 2019
Running on node : scc-kb2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 9162079
Current job name : Step_08a_G170_M19
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9162079.1.linga

Loading required modules...


List files in scratch directory:

total 2.0G
drwx------   2 kkarri waxmanlab 4.0K Sep  5 16:39 .
drwxrwxrwt. 28 root   root      4.0K Sep  5 16:03 ..
-rw-r--r--   1 kkarri waxmanlab    0 Sep  5 16:39 G170_M19_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.9G Sep  5 16:39 G170_M19_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  72M Sep  5 16:39 RefSeq_GeneBody.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view G170_M19'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > G170_M19_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 5.8G
drwx------   2 kkarri waxmanlab 4.0K Sep  5 17:13 .
drwxrwxrwt. 23 root   root      4.0K Sep  5 18:41 ..
-rw-r--r--   1 kkarri waxmanlab 249K Sep  5 18:43 G170_M19_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.9G Sep  5 16:39 G170_M19_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.8G Sep  5 17:13 G170_M19_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  72M Sep  5 16:39 RefSeq_GeneBody.gtf
==========================================================
Finished on : Thu Sep  5 18:43:03 EDT 2019
2 hours, 38 minutes and 11 seconds elapsed.
==========================================================