-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M22
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_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 : Wed Aug 30 13:54:25 EDT 2017
Running on node : scc-ca5
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/04_TopHat_Paired_End
Current job ID : 469154
Current job name : Step_04_G160_M22
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/469154.1.c

Loading required modules...


Here is the Left_List:
G160-M22-Index2_CGATGT-_ACB0DPANXX_L004_001.R1.fastq.gz


Here is the Right_List:
G160-M22-Index2_CGATGT-_ACB0DPANXX_L004_001.R2.fastq.gz


List files in the scratch directory:

total 2.3G
drwxr-xr-x   4 kkarri pulmseq 4.0K Aug 30 13:54 .
drwxrwxrwt. 15 root   root    4.0K Aug 30 13:54 ..
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 13:54 Bowtie2Index
-rwx------   1 kkarri pulmseq 1.1G Aug 30 13:54 G160-M22-Index2_CGATGT-_ACB0DPANXX_L004_001.R1.fastq.gz
-rwx------   1 kkarri pulmseq 1.1G Aug 30 13:54 G160-M22-Index2_CGATGT-_ACB0DPANXX_L004_001.R2.fastq.gz
-rw-r--r--   1 kkarri pulmseq  72M Aug 30 13:54 RefSeq_GeneBody.gtf
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 13:54 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/469154.1.c/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r -41 --mate-std-dev 150 Bowtie2Index/genome G160-M22-Index2_CGATGT-_ACB0DPANXX_L004_001.R1.fastq.gz G160-M22-Index2_CGATGT-_ACB0DPANXX_L004_001.R2.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
drwxr-xr-x   4 kkarri pulmseq 4.0K Aug 30 15:28 .
drwxrwxrwt. 15 root   root    4.0K Aug 30 13:54 ..
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 13:54 Bowtie2Index
-rwx------   1 kkarri pulmseq 1.1G Aug 30 13:54 G160-M22-Index2_CGATGT-_ACB0DPANXX_L004_001.R1.fastq.gz
-rwx------   1 kkarri pulmseq 1.1G Aug 30 13:54 G160-M22-Index2_CGATGT-_ACB0DPANXX_L004_001.R2.fastq.gz
-rw-r--r--   1 kkarri pulmseq  72M Aug 30 13:54 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri pulmseq    9 Aug 30 15:28 numunique_hits.txt
drwxr-xr-x   3 kkarri pulmseq 4.0K Aug 30 15:47 tophat2
==========================================================
Finished on : Wed Aug 30 15:47:54 EDT 2017
1 hours, 53 minutes and 29 seconds elapsed.
==========================================================