-----------------------
Start of variable list:
-----------------------
Sample_ID:
O2-MAA000907-3_11_M-1-1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/00_Setup_Pipeline
Bowtie2Index_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/Bowtie2
GTF_Files_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/GTF_Files
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
STRANDEDNESS:
fr-unstranded
DISTANCE_BT_READ_PAIR:
-41
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sat Oct 13 16:25:59 EDT 2018
Running on node : scc-ca1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/04_TopHat_Paired_End
Current job ID : 8793355
Current job name : Step_04_O2-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8793355.1.c

Loading required modules...


Here is the Left_List:
SRR6576689_1.fastq.gz


Here is the Right_List:
SRR6576689_2.fastq.gz


List files in the scratch directory:

total 86M
drwx------   4 kkarri waxmanlab 4.0K Oct 13 16:26 .
drwxrwxrwt. 14 root   root      4.0K Oct 13 16:25 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 13 16:26 Bowtie2Index
-rw-r--r--   1 kkarri waxmanlab  72M Oct 13 16:26 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri waxmanlab 6.4M Oct 13 16:25 SRR6576689_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 7.0M Oct 13 16:25 SRR6576689_2.fastq.gz
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 13 16:26 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/8793355.1.c/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-unstranded -r -41 --mate-std-dev 150 Bowtie2Index/genome SRR6576689_1.fastq.gz SRR6576689_2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 86M
drwx------   4 kkarri waxmanlab 4.0K Oct 13 16:41 .
drwxrwxrwt. 14 root   root      4.0K Oct 13 16:25 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 13 16:26 Bowtie2Index
-rw-r--r--   1 kkarri waxmanlab  72M Oct 13 16:26 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri waxmanlab 6.4M Oct 13 16:25 SRR6576689_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 7.0M Oct 13 16:25 SRR6576689_2.fastq.gz
-rw-r--r--   1 kkarri waxmanlab    7 Oct 13 16:41 numunique_hits.txt
drwxr-xr-x   3 kkarri waxmanlab 4.0K Oct 13 16:41 tophat2
==========================================================
Finished on : Sat Oct 13 16:41:33 EDT 2018
0 hours, 15 minutes and 34 seconds elapsed.
==========================================================