-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M6
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/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:
-41
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sat Jul 14 20:20:19 EDT 2018
Running on node : scc-ka5
Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/04_TopHat_Paired_End
Current job ID : 6936771
Current job name : Step_04_G167_M6
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6936771.1.linga

Loading required modules...


Here is the Left_List:
6_S28_R1_001.fastq.gz


Here is the Right_List:
6_S28_R2_001.fastq.gz


List files in the scratch directory:

total 2.3G
drwx------   4 kkarri waxmanlab 4.0K Jul 14 20:21 .
drwxrwxrwt. 68 root   root      128K Jul 14 20:20 ..
-rwxr-xr-x   1 kkarri waxmanlab 1.1G Jul 14 20:20 6_S28_R1_001.fastq.gz
-rwxr-xr-x   1 kkarri waxmanlab 1.2G Jul 14 20:20 6_S28_R2_001.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 20:20 Bowtie2Index
-rw-r--r--   1 kkarri waxmanlab  72M Jul 14 20:21 RefSeq_GeneBody.gtf
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 20:21 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/6936771.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r -41 --mate-std-dev 150 Bowtie2Index/genome 6_S28_R1_001.fastq.gz 6_S28_R2_001.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 2.3G
drwx------   4 kkarri waxmanlab 4.0K Jul 15 10:31 .
drwxrwxrwt. 69 root   root      128K Jul 14 21:48 ..
-rwxr-xr-x   1 kkarri waxmanlab 1.1G Jul 14 20:20 6_S28_R1_001.fastq.gz
-rwxr-xr-x   1 kkarri waxmanlab 1.2G Jul 14 20:20 6_S28_R2_001.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 14 20:20 Bowtie2Index
-rw-r--r--   1 kkarri waxmanlab  72M Jul 14 20:21 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri waxmanlab    8 Jul 15 10:31 numunique_hits.txt
drwxr-xr-x   3 kkarri waxmanlab 4.0K Jul 15 10:48 tophat2
==========================================================
Finished on : Sun Jul 15 10:48:28 EDT 2018
14 hours, 28 minutes and 9 seconds elapsed.
==========================================================