NOVOALIGN

[GoogleCodeExporter]

Hi Sam,

a conceptual  question as I have never used Novoalign before. WHat is the Index 
file name? Because The moidule is validated ok, but I have these errors:

-NOVO INDEX

===Pipeline Errors===
Error encountered while trying to execute 
/projects1/Alignment/Novoalign/novoindex.sh 
/projects1/test_pipeline/NEW_ORGANIZATION/Aligners/NOVOALIGN/SE indexfile 
/projects1/Reference_genomes/hg18_ensembl/gatk-canonical/gatk-hg18_ensembl.fa 
instance 1      

-NOVO ALIGN

# novoalign (V2.07.13 - Build Jul 18 2011 @ 09:03:08 - A short read aligner 
with qualities.
# (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd.
# novoalign.lic file not found.
# Licensed for evaluation, educational, and not-for-profit use only.
#  novoalign -d indexfile -f 
/projects2/USC/canonical-test-data/hg18_ensembl-bwa/mini-bam/s_1_1_sequence.150k
.txt 
/projects2/USC/canonical-test-data/hg18_ensembl-bwa/mini-bam/s_1_2_sequence.150k
.txt -F ILMFQ -o SAM 
# Starting at Fri Sep  9 14:52:03 2011
# Interpreting input files as Illumina FASTQ, Casava Pipeline 1.3 to 1.7.
Bad file descriptor
Error opening file indexfile

I attach the pipe I have mosified to use if from my local client.

Fed      

Original issue reported on code.google.com by federica...@gmail.com on 9 Sep 2011 at 10:01

Attachments:

• Novoalign_UCI.pipe

[GoogleCodeExporter]

Honestly I have no idea what the problem was with this. I tried the workflow 
you attached and got the same error. Then I modified the script to run in 
debugging mode (-x flag) and now it seems to be working.

Original comment by shobe...@gmail.com on 14 Sep 2011 at 8:36

[GoogleCodeExporter]

This workflow doesn't take very long to run (~30min) but the program isn't 
exiting when it's done. In the error stream, it will tell you when it's 
finished (ex: "Done at Wed Sep 14 13:38:33 2011"). You can go to the "Output 
Files" tab to see the results. I'm looking into this. 

Sam

Original comment by shobe...@gmail.com on 14 Sep 2011 at 11:57

[GoogleCodeExporter]

Ok, I donno if may be of any help but I am running it also on fgene3 ...from 
your message I understand that nothing has changed in the .pipe, but you have 
only modified the script so I am using tha same pipe I have attached you in the 
first post of the issue.

fed

Original comment by federica...@gmail.com on 15 Sep 2011 at 5:33

[GoogleCodeExporter]

Perfect!!! It ran both in SE and PE super fast..I have put in in the server 
library already.

Tks!

fed

Original comment by federica...@gmail.com on 15 Sep 2011 at 6:03