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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_M5
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:
Intron_Only_Regions.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
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==========================================================
Starting on : Mon Apr 15 21:35:25 EDT 2019
Running on node : scc-wh2
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 : 5225979
Current job name : Step_08a_G168_G169_M5
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5225979.1.w

Loading required modules...


List files in scratch directory:

total 1.9G
drwx------   2 kkarri waxmanlab 4.0K Apr 15 21:47 .
drwxrwxrwt. 21 root   root       72K Apr 15 21:46 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 15 21:47 G168_G169_M5_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.9G Apr 15 21:45 G168_G169_M5_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  18M Apr 15 21:45 Intron_Only_Regions.gtf

Starting to run my commands


Starting samtools and htseq-count


Starting splice read filter


Ending splice read filter

samtools view G168_G169_M5'_sorted'.bam | htseq-count --stranded=reverse --type=Intronic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Intron_Only_Regions.gtf  > G168_G169_M5_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 39G
drwx------   2 kkarri waxmanlab  4.0K Apr 15 22:18 .
drwxrwxrwt. 19 root   root        72K Apr 15 22:16 ..
-rw-r--r--   1 kkarri waxmanlab  233K Apr 15 22:18 G168_G169_M5_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1013M Apr 15 21:55 G168_G169_M5_primary_no_splice.bam
-rw-r--r--   1 kkarri waxmanlab  1.9G Apr 15 21:45 G168_G169_M5_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  1.9G Apr 15 22:04 G168_G169_M5_sorted.bam
-rw-r--r--   1 kkarri waxmanlab    99 Apr 15 22:18 HTSeq_Extra_Lines.txt
-rw-r--r--   1 kkarri waxmanlab   890 Apr 15 21:49 Header.txt
-rw-r--r--   1 kkarri waxmanlab   18M Apr 15 21:45 Intron_Only_Regions.gtf
-rwxr-xr-x   1 kkarri waxmanlab   38K Apr 15 22:18 RefSeq_Genes_Zero_Count.txt
-rw-r--r--   1 kkarri waxmanlab   17G Apr 15 21:51 temp1.sam
-rw-r--r--   1 kkarri waxmanlab  8.7G Apr 15 21:51 temp2.sam
-rw-r--r--   1 kkarri waxmanlab  8.7G Apr 15 21:52 temp3.sam
==========================================================
Finished on : Mon Apr 15 22:18:12 EDT 2019
0 hours, 42 minutes and 47 seconds elapsed.
==========================================================