-----------------------
Start of variable list:
-----------------------
Sample_ID:
G166_M6
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/00_Setup_Pipeline
Bowtie2Index_DIR:
/projectnb/wax-es/aramp10/Bowtie2
GTF_Files_DIR:
/restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
STRANDEDNESS:
fr-firststrand
DISTANCE_BT_READ_PAIR:
80
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Apr 22 20:11:18 EDT 2019
Running on node : scc-ka8
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/04_TopHat_Paired_End
Current job ID : 5525167
Current job name : Step_04_G166_M6
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5525167.1.linga

Loading required modules...


Here is the Left_List:
G166_M6.R1.fastq.gz


Here is the Right_List:
G166_M6.R2.fastq.gz


List files in the scratch directory:

total 364M
drwx------   4 kkarri waxmanlab 4.0K Apr 22 20:11 .
drwxrwxrwt. 54 root   root       72K Apr 22 20:11 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 22 20:11 Bowtie2Index
-rw-r-----   1 kkarri waxmanlab 141M Apr 22 20:11 G166_M6.R1.fastq.gz
-rw-r-----   1 kkarri waxmanlab 151M Apr 22 20:11 G166_M6.R2.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  72M Apr 22 20:11 RefSeq_GeneBody.gtf
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 22 20:11 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/5525167.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r 80 --mate-std-dev 150 Bowtie2Index/genome G166_M6.R1.fastq.gz G166_M6.R2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 364M
drwx------   4 kkarri waxmanlab 4.0K Apr 22 21:19 .
drwxrwxrwt. 55 root   root       72K Apr 22 21:10 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 22 20:11 Bowtie2Index
-rw-r-----   1 kkarri waxmanlab 141M Apr 22 20:11 G166_M6.R1.fastq.gz
-rw-r-----   1 kkarri waxmanlab 151M Apr 22 20:11 G166_M6.R2.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  72M Apr 22 20:11 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri waxmanlab    8 Apr 22 21:19 numunique_hits.txt
drwxr-xr-x   3 kkarri waxmanlab 4.0K Apr 22 21:22 tophat2
==========================================================
Finished on : Mon Apr 22 21:22:08 EDT 2019
1 hours, 10 minutes and 50 seconds elapsed.
==========================================================