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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:
G168_G169_M18
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/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/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/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 : Mon Apr 15 21:45:04 EDT 2019
Running on node : scc-wg4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 5226038
Current job name : Step_08a_G168_G169_M18
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5226038.1.w

Loading required modules...


List files in scratch directory:

total 1.7G
drwx------   2 kkarri waxmanlab 4.0K Apr 15 21:54 .
drwxrwxrwt. 24 root   root       60K Apr 15 21:53 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 15 21:54 G168_G169_M18_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.6G Apr 15 21:54 G168_G169_M18_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  72M Apr 15 21:54 RefSeq_GeneBody.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view G168_G169_M18'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - RefSeq_GeneBody.gtf  > G168_G169_M18_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 4.8G
drwx------   2 kkarri waxmanlab 4.0K Apr 15 22:09 .
drwxrwxrwt. 23 root   root       60K Apr 15 22:36 ..
-rw-r--r--   1 kkarri waxmanlab 243K Apr 15 22:36 G168_G169_M18_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.6G Apr 15 21:54 G168_G169_M18_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.1G Apr 15 22:09 G168_G169_M18_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  72M Apr 15 21:54 RefSeq_GeneBody.gtf
==========================================================
Finished on : Mon Apr 15 22:36:41 EDT 2019
0 hours, 51 minutes and 37 seconds elapsed.
==========================================================