-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
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Sample_ID:
G170_M8
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:
Exon_Only_Regions.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Sep  5 16:03:57 EDT 2019
Running on node : scc-ka1
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 9162033
Current job name : Step_08a_G170_M8
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9162033.1.linga

Loading required modules...


List files in scratch directory:

total 2.7G
drwx------   2 kkarri waxmanlab 4.0K Sep  5 16:38 .
drwxrwxrwt. 47 root   root      4.0K Sep  5 16:36 ..
-rw-r--r--   1 kkarri waxmanlab  19M Sep  5 16:33 Exon_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab    0 Sep  5 16:38 G170_M8_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 2.7G Sep  5 16:33 G170_M8_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  18M Sep  5 16:33 Intron_Only_Regions.gtf

Starting to run my commands


Starting samtools and htseq-count


Starting Intron_Only_Regions read overlap filter


Ending Intron_Only_Regions read overlap filter

samtools view G170_M8'_sorted'.bam | htseq-count --stranded=reverse --type=Exonic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Exon_Only_Regions.gtf  > G170_M8_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 6.3G
drwx------   2 kkarri waxmanlab 4.0K Sep  5 17:10 .
drwxrwxrwt. 45 root   root      4.0K Sep  5 17:41 ..
-rw-r--r--   1 kkarri waxmanlab  19M Sep  5 16:33 Exon_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab 246K Sep  5 17:49 G170_M8_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.2G Sep  5 16:51 G170_M8_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri waxmanlab 2.7G Sep  5 16:33 G170_M8_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 2.4G Sep  5 17:10 G170_M8_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  18M Sep  5 16:33 Intron_Only_Regions.gtf
==========================================================
Finished on : Thu Sep  5 17:49:07 EDT 2019
1 hours, 45 minutes and 10 seconds elapsed.
==========================================================