-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M13
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 : Sun May 13 12:12:50 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/04_TopHat_Single_End
Current job ID : 6184251
Current job name : Step_04_LZ_M13
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6184251.1.linga

Loading required modules...


Here is the Left_List:
LZ_M13.fastq.gz


List files in the scratch directory:

total 1000M
drwx------   4 kkarri waxmanlab 4.0K May 13 12:13 .
drwxrwxrwt. 40 root   root      116K May 13 12:12 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 13 12:13 Bowtie2Index
-rw-r--r--   1 kkarri waxmanlab 929M May 13 12:12 LZ_M13.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  72M May 13 12:13 RefSeq_GeneBody.gtf
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 13 12:13 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/6184251.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand Bowtie2Index/genome LZ_M13.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 1000M
drwx------   4 kkarri waxmanlab 4.0K May 13 13:42 .
drwxrwxrwt. 38 root   root      116K May 13 13:33 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 13 12:13 Bowtie2Index
-rw-r--r--   1 kkarri waxmanlab 929M May 13 12:12 LZ_M13.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  72M May 13 12:13 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri waxmanlab    9 May 13 13:42 numunique_hits.txt
drwxr-xr-x   3 kkarri waxmanlab 4.0K May 13 13:50 tophat2
==========================================================
Finished on : Sun May 13 13:51:01 EDT 2018
1 hours, 38 minutes and 11 seconds elapsed.
==========================================================