Question: BWA mem error: [bwt_restore_sa] SA-BWT inconsistency: seq_len is not the same. Abort!
0
gravatar for kdeere
4.1 years ago by
kdeere0
United States
kdeere0 wrote:

I have already mapped my data with STAMPY/ However, I'm trying to map with BWA in order to use GATK. I am running BWA 0.7.12 on a linux cluster.

I first built my reference index:

bwa index reference.fa

Then I tried to run the alignment:

bwa mem -M - reference.fa single_end_read_file.fq > test_aligned_reads.sam

And receive the following error:

[bwt_restore_sa] SA-BWT inconsistency: seq_len is not the same. Abort!

I'm not quite sure what to do as BWA created the indices it says don't work together. Any suggestions would be helpful. Thanks.

software error • 3.4k views
ADD COMMENTlink modified 8 weeks ago by RamRS21k • written 4.1 years ago by kdeere0
0
gravatar for Pierre Lindenbaum
4.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

there is something wrong in your bwa index :

https://github.com/lh3/bwa/blob/af606fc31a76eb02d3ef88c3056f53b4c915a743/bwt.c#L433

you should re-run

bwa index reference.fa && echo "OK. Done."
ADD COMMENTlink modified 8 weeks ago by RamRS21k • written 4.1 years ago by Pierre Lindenbaum120k

Hi Pierre,

I'm facing the same issue but I can't figure out a way to fix this. I have re-run the bwa index in all the possible ways but is not working. Surprisingly for is that I have done this many other times with other sequencing data. Any other idea Pierre?

Thanks Alejandro

ADD REPLYlink written 3.0 years ago by ariverosw0
0
gravatar for kdeere
4.1 years ago by
kdeere0
United States
kdeere0 wrote:

I've rerun with the suggestion:

bwa index reference.fa && echo "OK. Done."

Output:

[bwa_index] Pack FASTA... 11.30 sec
[bwa_index] Reverse the packed sequence... 3.07 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 280.36 seconds elapse.
[bwa_index] Construct BWT for the reverse packed sequence...
[bwa_index] 279.26 seconds elapse.
[bwa_index] Update BWT... 3.47 sec
[bwa_index] Update reverse BWT... 3.42 sec
[bwa_index] Construct SA from BWT and Occ... 97.42 sec
[bwa_index] Construct SA from reverse BWT and Occ... 97.71 sec
OK. Done.

Then I tried to rerun my mapping again and got the same error:

bwa mem -M - reference.fa single_end_read_file.fq > test_aligned_reads.sam

Output:

[bwt_restore_sa] SA-BWT inconsistency: seq_len is not the same. Abort!
/var/spool/slurmd/job4200029/slurm_script: line 14: 34491 Aborted
ADD COMMENTlink modified 8 weeks ago by RamRS21k • written 4.1 years ago by kdeere0

Did you were able to fix this issue. I'm now having the same problem.

Thanks!

Alejandro

ADD REPLYlink modified 8 weeks ago by RamRS21k • written 3.0 years ago by ariverosw0
0
gravatar for Rashedul Islam
8 weeks ago by
Canada
Rashedul Islam300 wrote:

I had the same issue. Solved by creating the reference index using the same version of bwa that I used for alignment (bwa mem). Before I was using the reference index created by the older version of bwa and I was getting the above mentioned error while running bwa mem.

ADD COMMENTlink written 8 weeks ago by Rashedul Islam300
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