Question: Bwa Failing To Index?
gravatar for Joshua Orvis
5.5 years ago by
Joshua Orvis100
Joshua Orvis100 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
bwa alignment • 2.6k views
ADD COMMENTlink modified 2.4 years ago by 5140796850 • written 5.5 years ago by Joshua Orvis100
gravatar for Jennifer Hillman Jackson
5.5 years ago by
United States
Jennifer Hillman Jackson25k 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: If you need follow-up help, you will want to post a brand new question as a brand new thread on the mailing list. That list is for local install questions and will get you the most feedback from the development community. Take care, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training
ADD COMMENTlink written 5.5 years ago by Jennifer Hillman Jackson25k

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

ADD REPLYlink written 3.6 years ago by Student-T0
gravatar for 514079685
2.4 years ago by
5140796850 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 COMMENTlink written 2.4 years ago by 5140796850
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour