-----------------------
Start of variable list:
-----------------------
Sample_ID:
C_M1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_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 : Fri Jun 16 10:18:08 EDT 2017
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/04_TopHat_Paired_End
Current job ID : 9351451
Current job name : Step_04_C_M1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9351451.1.linga

Loading required modules...


Here is the Left_List (updated):
SRR1178062_R1.fastq.gz


Here is the Right_List (updated):
SRR1178062_R2.fastq.gz


List files in the scratch directory:

total 12G
drwxr-xr-x   4 kkarri montilab-p 4.0K Jun 16 10:20 .
drwxrwxrwt. 70 root   root        92K Jun 16 10:18 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 16 10:20 Bowtie2Index
-rwx------   1 kkarri montilab-p  41M Jun 16 10:20 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri montilab-p 5.6G Jun 16 10:19 SRR1178062_R1.fastq.gz
-rw-r--r--   1 kkarri montilab-p 5.7G Jun 16 10:20 SRR1178062_R2.fastq.gz
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 16 10:20 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/9351451.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-unstranded -r -41 --mate-std-dev 150 Bowtie2Index/genome SRR1178062_R1.fastq.gz SRR1178062_R2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 12G
drwxr-xr-x   4 kkarri montilab-p 4.0K Jun 16 21:49 .
drwxrwxrwt. 68 root   root        92K Jun 16 23:00 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 16 10:20 Bowtie2Index
-rwx------   1 kkarri montilab-p  41M Jun 16 10:20 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri montilab-p 5.6G Jun 16 10:19 SRR1178062_R1.fastq.gz
-rw-r--r--   1 kkarri montilab-p 5.7G Jun 16 10:20 SRR1178062_R2.fastq.gz
-rw-r--r--   1 kkarri montilab-p    9 Jun 16 21:49 numunique_hits.txt
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun 16 23:49 tophat2
==========================================================
Finished on : Fri Jun 16 23:50:28 EDT 2017
13 hours, 32 minutes and 20 seconds elapsed.
==========================================================