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Question: Problem BWA in Galaxy Tool
0
gravatar for kunaphas.kon
3.6 years ago by
kunaphas.kon • 0
Thailand
kunaphas.kon • 0 wrote:

Hello everyone

I'm a new guy in galaxy tool

I try to run BWA tool that I install it from  Galaxy main tool shed.

but I got this error after run

Generating BWA index with is algorithm
[bwa_index] Pack FASTA... 40.74 sec
[bwa_index] Construct BWT for the packed sequence...
Aborted
[bwt_restore_sa] fail to open file 'localref.fa.sa' : No such file or directory

What thing I have to do to solve this problem

Note

 

 
bwa galaxy • 2.6k views
ADD COMMENT • link •
modified 3.4 years ago • written 3.6 years ago by kunaphas.kon • 0
1
gravatar for Jennifer Hillman Jackson
3.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Have you created the indexes for BWA already? For the reference genome selected? If you need to load the ref genome and create indexes, the Tool Shed has tools to do this - see the section "Data Managers".

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

thank you for answering me ,I'm curies if there any possible to create index from ref outside galaxy and upload those files into galaxy.After that, I can use it with BWA rather than using tool bwa index builder in Toolshed.

Sincerely yours,

Note

 

ADD REPLY • link written 3.5 years ago by kunaphas.kon • 0
1

Hi Note, This section of the Galaxy wiki explains how to create indexes line command. http://wiki.galaxyproject.org/Admin/DataPreparation Best, Jen, Galaxy team

 

ADD REPLY • link written 3.5 years ago by Jennifer Hillman Jackson ♦ 25k

I follow your link and I got error below 

E::bwa_idx_load] fail to locate the index files

 

 

ADD REPLY • link written 3.4 years ago by kunaphas.kon • 0
0
gravatar for kunaphas.kon
3.4 years ago by
kunaphas.kon • 0
Thailand
kunaphas.kon • 0 wrote:


Hi Jennifer

I just installed  Map with BWA (Version 0.7.5) This new version BWA (0.7.5) use 'mem' algorithm for mapping, dosen't need 'aln', 'samse', 'sampe' and picard AddOrReplace anymore. (Galaxy Tool Version 0.7.5) from tool shed

but when I run it , it  show error below 

Could not determine BWA version  The cmd is bwa mem -t 1 /var/www/galaxy/ref/human_g1k_v37.fa /var/www/galaxy/database/files/000/dataset_202.dat /var/www/galaxy/database/files/000/dataset_201.dat > /var/www/galaxy/database/files/000/dataset_374.dat Traceb

what I have done wrong , please help me

thank you 

Note
ADD COMMENT • link written 3.4 years ago by kunaphas.kon • 0
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