-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M15
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/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:
-86
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Mar 11 22:02:41 EDT 2019
Running on node : scc-tl4
Current directory : /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/04_TopHat_Paired_End
Current job ID : 3518979
Current job name : Step_04_G168_G169_M15
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/3518979.1.linga

Loading required modules...


Here is the Left_List:
G168_G169_M15_R1.fastq.gz


Here is the Right_List:
G168_G169_M15_R2.fastq.gz


List files in the scratch directory:

total 5.8G
drwx------   4 kkarri waxmanlab 4.0K Mar 11 22:03 .
drwxrwxrwt. 15 root   root       40K Mar 11 22:02 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 11 22:03 Bowtie2Index
-rw-r--r--   1 kkarri waxmanlab 2.8G Mar 11 22:02 G168_G169_M15_R1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 3.0G Mar 11 22:02 G168_G169_M15_R2.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  72M Mar 11 22:03 RefSeq_GeneBody.gtf
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 11 22:03 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/3518979.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r -86 --mate-std-dev 150 Bowtie2Index/genome G168_G169_M15_R1.fastq.gz G168_G169_M15_R2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 5.8G
drwx------   4 kkarri waxmanlab 4.0K Mar 12 02:10 .
drwxrwxrwt. 15 root   root       40K Mar 12 01:56 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 11 22:03 Bowtie2Index
-rw-r--r--   1 kkarri waxmanlab 2.8G Mar 11 22:02 G168_G169_M15_R1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 3.0G Mar 11 22:02 G168_G169_M15_R2.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  72M Mar 11 22:03 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri waxmanlab    9 Mar 12 02:10 numunique_hits.txt
drwxr-xr-x   3 kkarri waxmanlab 4.0K Mar 12 02:46 tophat2
==========================================================
Finished on : Tue Mar 12 02:46:47 EDT 2019
4 hours, 44 minutes and 6 seconds elapsed.
==========================================================