-----------------------
Start of variable list:
-----------------------
Sample_ID:
C_IP5
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/00_Setup_Pipeline
Bowtie2Index_DIR:
/restricted/projectnb/waxmanlab/kkarri/Bowtie2
GTF_Files_DIR:
/restricted/projectnb/waxmanlab/kkarri/GTF_Files1
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
STRANDEDNESS:
fr-unstranded
DISTANCE_BT_READ_PAIR:
-41
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Jun 14 21:33:22 EDT 2017
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/04_TopHat_Paired_End
Current job ID : 9328372
Current job name : Step_04_C_IP5
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9328372.1.linga

Loading required modules...


Here is the Left_List (updated):
SRR1178070_R1.fastq.gz


Here is the Right_List (updated):
SRR1178070_R2.fastq.gz


List files in the scratch directory:

total 8.0G
drwxr-xr-x    4 kkarri montilab-p 4.0K Jun 14 21:34 .
drwxrwxrwt. 191 root   root       108K Jun 14 21:33 ..
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 14 21:34 Bowtie2Index
-rwx------    1 kkarri montilab-p  41M Jun 14 21:34 RefSeq_GeneBody.gtf
-rw-r--r--    1 kkarri montilab-p 3.9G Jun 14 21:33 SRR1178070_R1.fastq.gz
-rw-r--r--    1 kkarri montilab-p 4.1G Jun 14 21:34 SRR1178070_R2.fastq.gz
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 14 21:34 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/9328372.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-unstranded -r -41 --mate-std-dev 150 Bowtie2Index/genome SRR1178070_R1.fastq.gz SRR1178070_R2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 8.0G
drwxr-xr-x    4 kkarri montilab-p 4.0K Jun 15 04:34 .
drwxrwxrwt. 190 root   root       108K Jun 15 06:13 ..
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 14 21:34 Bowtie2Index
-rwx------    1 kkarri montilab-p  41M Jun 14 21:34 RefSeq_GeneBody.gtf
-rw-r--r--    1 kkarri montilab-p 3.9G Jun 14 21:33 SRR1178070_R1.fastq.gz
-rw-r--r--    1 kkarri montilab-p 4.1G Jun 14 21:34 SRR1178070_R2.fastq.gz
-rw-r--r--    1 kkarri montilab-p    9 Jun 15 04:34 numunique_hits.txt
drwxr-xr-x    3 kkarri montilab-p 4.0K Jun 15 06:09 tophat2
==========================================================
Finished on : Thu Jun 15 06:13:06 EDT 2017
8 hours, 39 minutes and 44 seconds elapsed.
==========================================================