Bwa Failing To Index?

Question: Bwa Failing To Index?

5.5 years ago by

Joshua Orvis • 100 wrote:

I just installed a new instance of Galaxy and bwa_wrappers from the main toolshed. I then uploaded a reference genome along with two FASTQ files in order to run "Map with BWA for Illumina". When I run it, I get this error: The alignment failed. Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwt_restore_bwt] fail to open file '/export/galaxy-dist/database/files/000/dataset_1.dat.bwt'. Abort! Aborted I've used the same tool on other Galaxy instances and it always auto-indexes the reference genome here before continuing. What's going wrong? (I made sure bwa was in the user's PATH that is running run.sh)

bwa alignment • 2.6k views

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modified 2.4 years ago by 514079685 • 0 • written 5.5 years ago by Joshua Orvis • 100

5.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Joshua, It may be that the local instance is running out of memory and the custom reference genome approach is the wrong one for your configuration. Instead, try installing the reference database as a built-in index. Instructions are here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup If you need follow-up help, you will want to post a brand new question as a brand new thread on the galaxy-dev@bx.psu.edu mailing list. That list is for local install questions and will get you the most feedback from the development community. http://wiki.galaxyproject.org/MailingLists Take care, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD COMMENT • link written 5.5 years ago by Jennifer Hillman Jackson ♦ 25k

I don't think so. My reference file is a very small data-set but I got the same problem.

ADD REPLY • link written 3.6 years ago by Student-T • 0

2.4 years ago by

514079685 • 0

China

514079685 • 0 wrote:

you can rebuild the index of hg19.fa use "bwa index hg19.fa" . then the problem may be solved . i also have this problem and solve it by this way.

ADD COMMENT • link written 2.4 years ago by 514079685 • 0

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