-----------------------
Start of variable list:
-----------------------
Sample_ID:
WT2
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/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:
94
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Apr 29 16:39:34 EDT 2019
Running on node : scc-ca3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/04_TopHat_Paired_End
Current job ID : 5765328
Current job name : Step_04_WT2
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5765328.1.c

Loading required modules...


Here is the Left_List:
SRR5345533_1.fastq.gz


Here is the Right_List:
SRR5345533_2.fastq.gz


List files in the scratch directory:

total 365M
drwx------   4 kkarri waxmanlab 4.0K Apr 29 16:40 .
drwxrwxrwt. 11 root   root      4.0K Apr 29 16:39 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 29 16:39 Bowtie2Index
-rw-r--r--   1 kkarri waxmanlab  72M Apr 29 16:39 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri waxmanlab 145M Apr 29 16:39 SRR5345533_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 150M Apr 29 16:39 SRR5345533_2.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 29 16:40 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/5765328.1.c/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r 94 --mate-std-dev 150 Bowtie2Index/genome SRR5345533_1.fastq.gz SRR5345533_2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 365M
drwx------   4 kkarri waxmanlab 4.0K Apr 29 17:03 .
drwxrwxrwt. 11 root   root      4.0K Apr 29 16:39 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 29 16:39 Bowtie2Index
-rw-r--r--   1 kkarri waxmanlab  72M Apr 29 16:39 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri waxmanlab 145M Apr 29 16:39 SRR5345533_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 150M Apr 29 16:39 SRR5345533_2.fastq.gz
-rw-r--r--   1 kkarri waxmanlab    8 Apr 29 17:03 numunique_hits.txt
drwxr-xr-x   3 kkarri waxmanlab 4.0K Apr 29 17:07 tophat2
==========================================================
Finished on : Mon Apr 29 17:07:13 EDT 2019
0 hours, 27 minutes and 39 seconds elapsed.
==========================================================