-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M11
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/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 : Tue Dec 18 14:25:36 EST 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/04_TopHat_Paired_End
Current job ID : 359406
Current job name : Step_04_G123_M11
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/359406.1.linga

Loading required modules...


Here is the Left_List:
G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R1.fastq.gz


Here is the Right_List:
G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R2.fastq.gz


List files in the scratch directory:

total 1.4G
drwx------   4 kkarri waxmanlab 4.0K Dec 18 14:29 .
drwxrwxrwt. 33 root   root      180K Dec 18 14:25 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 18 14:27 Bowtie2Index
-rw-r-----   1 kkarri waxmanlab 641M Dec 18 14:26 G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R1.fastq.gz
-rw-r-----   1 kkarri waxmanlab 664M Dec 18 14:26 G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R2.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  72M Dec 18 14:29 RefSeq_GeneBody.gtf
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 18 14:29 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/359406.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r 130 --mate-std-dev 150 Bowtie2Index/genome G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R1.fastq.gz G123-pool-GGCTAC_GGCTAC_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 1.4G
drwx------   4 kkarri waxmanlab 4.0K Dec 18 16:17 .
drwxrwxrwt. 31 root   root      180K Dec 18 15:54 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec 18 14:27 Bowtie2Index
-rw-r-----   1 kkarri waxmanlab 641M Dec 18 14:26 G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R1.fastq.gz
-rw-r-----   1 kkarri waxmanlab 664M Dec 18 14:26 G123-pool-GGCTAC_GGCTAC_BC8TK0ANXX_L008_001.R2.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  72M Dec 18 14:29 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri waxmanlab    9 Dec 18 16:17 numunique_hits.txt
drwxr-xr-x   3 kkarri waxmanlab 4.0K Dec 18 16:36 tophat2
==========================================================
Finished on : Tue Dec 18 16:36:10 EST 2018
2 hours, 10 minutes and 34 seconds elapsed.
==========================================================