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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_M22
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:
genes.gtf
FEATURE_TYPE:
exon
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End of variable list
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==========================================================
Starting on : Mon Apr 15 21:45:40 EDT 2019
Running on node : scc-wl4
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 : 5226055
Current job name : Step_08a_G168_G169_M22
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5226055.1.w

Loading required modules...


List files in scratch directory:

total 1.9G
drwx------   2 kkarri waxmanlab 4.0K Apr 15 21:58 .
drwxrwxrwt. 29 root   root       12K Apr 15 21:55 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 15 21:58 G168_G169_M22_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.8G Apr 15 21:58 G168_G169_M22_primary_unique.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M Apr 15 21:58 genes.gtf

Starting to run my commands


Starting samtools and htseq-count

samtools view G168_G169_M22'_sorted'.bam | htseq-count --stranded=reverse --type=exon --idattr=gene_id --order=name --mode=intersection-nonempty - genes.gtf  > G168_G169_M22_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 5.4G
drwx------   2 kkarri waxmanlab 4.0K Apr 15 22:16 .
drwxrwxrwt. 30 root   root       12K Apr 15 22:46 ..
-rw-r--r--   1 kkarri waxmanlab 239K Apr 15 22:46 G168_G169_M22_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.8G Apr 15 21:58 G168_G169_M22_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 3.5G Apr 15 22:16 G168_G169_M22_sorted.bam
-rwxr-xr-x   1 kkarri waxmanlab  81M Apr 15 21:58 genes.gtf
==========================================================
Finished on : Mon Apr 15 22:46:47 EDT 2019
1 hours, 1 minutes and 7 seconds elapsed.
==========================================================