-----------------------
Need shift 1 command (have more than 9 arguments):
-----------------------
-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M2
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New/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_New/Scripts/08a_Extract_Counts_HTSeq
ANNOTATION_FILE:
Intron_Only_Regions.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Dec  7 19:06:09 EST 2018
Running on node : scc-tm2
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/08a_Extract_Counts_HTSeq
Current job ID : 27195
Current job name : Step_08a_G123_M2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/27195.1.linga

Loading required modules...


List files in scratch directory:

total 1.2G
drwx------   2 kkarri waxmanlab 4.0K Dec  7 19:06 .
drwxrwxrwt. 13 root   root      116K Dec  7 19:06 ..
-rw-r--r--   1 kkarri waxmanlab    0 Dec  7 19:06 G123_M2_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.2G Dec  7 19:06 G123_M2_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  18M Dec  7 19:06 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_M2'_sorted'.bam | htseq-count --stranded=reverse --type=Intronic_Only --idattr=gene_id --order=name --mode=intersection-nonempty - Intron_Only_Regions.gtf  > G123_M2_HTSeq.out

Ending samtools and htseq-count


List files in scratch

total 24G
drwx------   2 kkarri waxmanlab 4.0K Dec  7 19:39 .
drwxrwxrwt. 12 root   root      116K Dec  7 19:37 ..
-rw-r--r--   1 kkarri waxmanlab 240K Dec  7 19:39 G123_M2_HTSeq.out
-rw-r--r--   1 kkarri waxmanlab 1.1G Dec  7 19:13 G123_M2_primary_no_splice.bam
-rw-r--r--   1 kkarri waxmanlab 1.2G Dec  7 19:06 G123_M2_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.5G Dec  7 19:21 G123_M2_sorted.bam
-rw-r--r--   1 kkarri waxmanlab   98 Dec  7 19:39 HTSeq_Extra_Lines.txt
-rw-r--r--   1 kkarri waxmanlab  922 Dec  7 19:07 Header.txt
-rw-r--r--   1 kkarri waxmanlab  18M Dec  7 19:06 Intron_Only_Regions.gtf
-rwxr-xr-x   1 kkarri waxmanlab  38K Dec  7 19:39 RefSeq_Genes_Zero_Count.txt
-rw-r--r--   1 kkarri waxmanlab 7.1G Dec  7 19:08 temp1.sam
-rw-r--r--   1 kkarri waxmanlab 6.4G Dec  7 19:09 temp2.sam
-rw-r--r--   1 kkarri waxmanlab 6.4G Dec  7 19:09 temp3.sam
==========================================================
Finished on : Fri Dec  7 19:39:42 EST 2018
0 hours, 33 minutes and 33 seconds elapsed.
==========================================================