-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M16
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 15:18:32 EST 2018
Running on node : scc-ca8
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/04_TopHat_Paired_End
Current job ID : 24814
Current job name : Step_04_G123_M16
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/24814.1.c

Loading required modules...


Here is the Left_List:
G123-pool-GTGAAA_GTGAAA_BC8TK0ANXX_L008_001.R1.fastq.gz


Here is the Right_List:
G123-pool-GTGAAA_GTGAAA_BC8TK0ANXX_L008_001.R2.fastq.gz


List files in the scratch directory:

total 2.2G
drwx------  4 kkarri waxmanlab 4.0K Dec  7 15:18 .
drwxrwxrwt. 8 root   root      4.0K Dec  7 15:18 ..
drwxr-xr-x  2 kkarri waxmanlab 4.0K Dec  7 15:18 Bowtie2Index
-rw-r-----  1 kkarri waxmanlab 1.1G Dec  7 15:18 G123-pool-GTGAAA_GTGAAA_BC8TK0ANXX_L008_001.R1.fastq.gz
-rw-r-----  1 kkarri waxmanlab 1.1G Dec  7 15:18 G123-pool-GTGAAA_GTGAAA_BC8TK0ANXX_L008_001.R2.fastq.gz
-rw-r--r--  1 kkarri waxmanlab  72M Dec  7 15:18 RefSeq_GeneBody.gtf
drwxr-xr-x  2 kkarri waxmanlab 4.0K Dec  7 15:18 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/24814.1.c/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r 130 --mate-std-dev 150 Bowtie2Index/genome G123-pool-GTGAAA_GTGAAA_BC8TK0ANXX_L008_001.R1.fastq.gz G123-pool-GTGAAA_GTGAAA_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 2.2G
drwx------  4 kkarri waxmanlab 4.0K Dec  7 16:34 .
drwxrwxrwt. 8 root   root      4.0K Dec  7 15:18 ..
drwxr-xr-x  2 kkarri waxmanlab 4.0K Dec  7 15:18 Bowtie2Index
-rw-r-----  1 kkarri waxmanlab 1.1G Dec  7 15:18 G123-pool-GTGAAA_GTGAAA_BC8TK0ANXX_L008_001.R1.fastq.gz
-rw-r-----  1 kkarri waxmanlab 1.1G Dec  7 15:18 G123-pool-GTGAAA_GTGAAA_BC8TK0ANXX_L008_001.R2.fastq.gz
-rw-r--r--  1 kkarri waxmanlab  72M Dec  7 15:18 RefSeq_GeneBody.gtf
-rw-r--r--  1 kkarri waxmanlab    9 Dec  7 16:34 numunique_hits.txt
drwxr-xr-x  3 kkarri waxmanlab 4.0K Dec  7 16:53 tophat2
==========================================================
Finished on : Fri Dec  7 16:53:09 EST 2018
1 hours, 34 minutes and 37 seconds elapsed.
==========================================================