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Alignment using bwa-mem2

Hello

I need help in aligning the sequence with reference using bwa-mem2. I used the following code:

bwa-mem2 mem -t 8 gch38.fa DE98NGSUKBD117612_1_1.fq DE98NGSUKBD117612_1_2.fq > d3_align.sam

I got the following error:

ERROR! Unable to open the file: gch38.fa.bwt.2bit.64

There is no gch38.fa.bwt.2bit.64 file. I have the following the reference indexes:

gch38.fa  gch38.fa.0123  gch38.fa.amb  gch38.fa.ann  gch38.fa.pac

What is the gch38.fa.bwt.2bit.64 file?

Thank you

Priya

alignment bwa-mem2
• 11,670 views • link
written by priya.bmg • priya.bmg

Did you re-make your own indexes? bwa-mem indexes are not compatible with bwa-mem2.

• 0 views • link
written by GenoMax GenoMax

This is the command used to build indexes:

 bwa-mem2 index gch38.fa
• 0 views • link
written by priya.bmg • priya.bmg

If you have no 2bit.64 files then your index was not properly made. It is not enough just to run commands. You should also look at the logs/error files that are generated as a part of the process.

• 0 views • link
written by GenoMax GenoMax

I am using bwa-mem2/2.2.1-foss-2018b to build reference indexes.Is this version has bug?.

• 0 views • link
written by priya.bmg • priya.bmg

Unlikely. Probably you job got killed due to memory (or whatever) shortage.

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written by ATpoint ATpoint

Yes the job got killed. Thanks. I am running in server and still the process got killed.

• 0 views • link
written by priya.bmg • priya.bmg

How much memory is available?

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written by ATpoint ATpoint

How much memory is available?

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written by ATpoint ATpoint

1 answer

Should be enough. Be sure that if you are using a job scheduler you actually allocated this memory (in SLURM that would be the --mem argument).

• 0 views • link
written by ATpoint ATpoint

Thank you, I have specified the memory in slurm script and running it again

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written by priya.bmg • priya.bmg

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