-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M27
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/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
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri May 11 13:37:24 EDT 2018
Running on node : scc-pf2
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/04_TopHat_Single_End
Current job ID : 6177261
Current job name : Step_04_LZ_M27
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6177261.1.p8

Loading required modules...


Here is the Left_List:
LZ_M27.fastq.gz


List files in the scratch directory:

total 898M
drwx------   4 kkarri waxmanlab 4.0K May 11 13:37 .
drwxrwxrwt. 21 root   root      4.0K May 11 13:37 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 13:37 Bowtie2Index
-rw-r--r--   1 kkarri waxmanlab 827M May 11 13:37 LZ_M27.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  72M May 11 13:37 RefSeq_GeneBody.gtf
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 13:37 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/6177261.1.p8/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand Bowtie2Index/genome LZ_M27.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 898M
drwx------   4 kkarri waxmanlab 4.0K May 11 14:09 .
drwxrwxrwt. 21 root   root      4.0K May 11 13:37 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 13:37 Bowtie2Index
-rw-r--r--   1 kkarri waxmanlab 827M May 11 13:37 LZ_M27.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  72M May 11 13:37 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri waxmanlab    9 May 11 14:09 numunique_hits.txt
drwxr-xr-x   3 kkarri waxmanlab 4.0K May 11 14:14 tophat2
==========================================================
Finished on : Fri May 11 14:14:58 EDT 2018
0 hours, 37 minutes and 34 seconds elapsed.
==========================================================