-----------------------
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
Bowtie2Index_DIR:
/projectnb/wax-es/aramp10/Bowtie2
GTF_Files_DIR:
/unprotected/projects/waxmanlab/routines/GTF_Files
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
STRANDEDNESS:
fr-firststrand
DISTANCE_BT_READ_PAIR:
130
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Dec  7 14:38:39 EST 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/04_TopHat_Paired_End
Current job ID : 24800
Current job name : Step_04_G123_M2
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/24800.1.linga

Loading required modules...


Here is the Left_List:
G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R1.fastq.gz


Here is the Right_List:
G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R2.fastq.gz


List files in the scratch directory:

total 1.6G
drwx------   4 kkarri waxmanlab 4.0K Dec  7 14:39 .
drwxrwxrwt. 62 root   root       84K Dec  7 14:38 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec  7 14:38 Bowtie2Index
-rw-r-----   1 kkarri waxmanlab 722M Dec  7 14:38 G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R1.fastq.gz
-rw-r-----   1 kkarri waxmanlab 748M Dec  7 14:38 G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R2.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  72M Dec  7 14:39 RefSeq_GeneBody.gtf
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec  7 14:39 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/24800.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r 130 --mate-std-dev 150 Bowtie2Index/genome G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R1.fastq.gz G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 1.6G
drwx------   4 kkarri waxmanlab 4.0K Dec  7 17:07 .
drwxrwxrwt. 64 root   root       84K Dec  7 17:32 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec  7 14:38 Bowtie2Index
-rw-r-----   1 kkarri waxmanlab 722M Dec  7 14:38 G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R1.fastq.gz
-rw-r-----   1 kkarri waxmanlab 748M Dec  7 14:38 G123-pool-CGATGT_CGATGT_BC8TK0ANXX_L008_001.R2.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  72M Dec  7 14:39 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri waxmanlab    9 Dec  7 17:07 numunique_hits.txt
drwxr-xr-x   3 kkarri waxmanlab 4.0K Dec  7 17:32 tophat2
==========================================================
Finished on : Fri Dec  7 17:32:17 EST 2018
2 hours, 53 minutes and 38 seconds elapsed.
==========================================================