-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M9
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/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:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
Intron_Only_Regions.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Dec 18 18:53:47 EST 2018
Running on node : scc-ka6
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 365185
Current job name : Step_08a_G123_M9
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/365185.1.linga

Loading required modules...


List files in scratch directory:

total 1.3G
drwx------   2 kkarri waxmanlab 4.0K Dec 18 18:58 .
drwxrwxrwt. 36 root   root       92K Dec 18 18:53 ..
-rw-r--r--   1 kkarri waxmanlab    0 Dec 18 18:58 G123_M9_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.3G Dec 18 18:57 G123_M9_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  18M Dec 18 18:57 Intron_Only_Regions.gtf

Starting to run my commands


Starting samtools and htseq-count


Starting splice read filter


Ending splice read filter

samtools view G123_M9'_sorted'.bam | htseq-count --stranded=reverse --type=Intronic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Intron_Only_Regions.gtf  > G123_M9_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 26G
drwx------   2 kkarri waxmanlab 4.0K Dec 18 20:12 .
drwxrwxrwt. 29 root   root       92K Dec 18 20:10 ..
-rw-r--r--   1 kkarri waxmanlab 240K Dec 18 20:12 G123_M9_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.2G Dec 18 19:08 G123_M9_primary_no_splice.bam
-rw-r--r--   1 kkarri waxmanlab 1.3G Dec 18 18:57 G123_M9_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.6G Dec 18 19:24 G123_M9_sorted.bam
-rw-r--r--   1 kkarri waxmanlab   98 Dec 18 20:12 HTSeq_Extra_Lines.txt
-rw-r--r--   1 kkarri waxmanlab  951 Dec 18 18:59 Header.txt
-rw-r--r--   1 kkarri waxmanlab  18M Dec 18 18:57 Intron_Only_Regions.gtf
-rwxr-xr-x   1 kkarri waxmanlab  38K Dec 18 20:12 RefSeq_Genes_Zero_Count.txt
-rw-r--r--   1 kkarri waxmanlab 7.8G Dec 18 19:01 temp1.sam
-rw-r--r--   1 kkarri waxmanlab 7.1G Dec 18 19:02 temp2.sam
-rw-r--r--   1 kkarri waxmanlab 7.1G Dec 18 19:02 temp3.sam
==========================================================
Finished on : Tue Dec 18 20:12:17 EST 2018
1 hours, 18 minutes and 30 seconds elapsed.
==========================================================