-----------------------
Start of variable list:
-----------------------
Sample_ID:
PB_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-tl1
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/04_TopHat_Paired_End
Current job ID : 9351458
Current job name : Step_04_PB_M1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9351458.1.linga

Loading required modules...


Here is the Left_List (updated):
SRR1177961_R1.fastq.gz


Here is the Right_List (updated):
SRR1177961_R2.fastq.gz


List files in the scratch directory:

total 3.4G
drwxr-xr-x   4 kkarri montilab-p 4.0K Jun 16 10:19 .
drwxrwxrwt. 10 root   root        20K Jun 16 10:18 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 16 10:19 Bowtie2Index
-rwx------   1 kkarri montilab-p  41M Jun 16 10:19 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri montilab-p 1.7G Jun 16 10:18 SRR1177961_R1.fastq.gz
-rw-r--r--   1 kkarri montilab-p 1.7G Jun 16 10:18 SRR1177961_R2.fastq.gz
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 16 10:19 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/9351458.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-unstranded -r -41 --mate-std-dev 150 Bowtie2Index/genome SRR1177961_R1.fastq.gz SRR1177961_R2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 3.4G
drwxr-xr-x   4 kkarri montilab-p 4.0K Jun 16 12:03 .
drwxrwxrwt. 10 root   root        20K Jun 16 12:19 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 16 10:19 Bowtie2Index
-rwx------   1 kkarri montilab-p  41M Jun 16 10:19 RefSeq_GeneBody.gtf
-rw-r--r--   1 kkarri montilab-p 1.7G Jun 16 10:18 SRR1177961_R1.fastq.gz
-rw-r--r--   1 kkarri montilab-p 1.7G Jun 16 10:18 SRR1177961_R2.fastq.gz
-rw-r--r--   1 kkarri montilab-p    9 Jun 16 12:03 numunique_hits.txt
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun 16 12:24 tophat2
==========================================================
Finished on : Fri Jun 16 12:24:29 EDT 2017
2 hours, 6 minutes and 21 seconds elapsed.
==========================================================