run-bwamem from BWAKIT does not work

Question

[laura.zalba]

Hi, everyone!

I am currently performing HLA typing analysis using the bwakit-0.7.17 for Linux Mint 20. The problem comes when running the "run-bwamem" file, when we obtain empty output files. We have even tried to perform it through Miniconda by typing the next:

$ bin/run-bwamem -o out -H -R"@A01056:45:HJ2KFDSXY" hs38DH.fa read_1.fq read_2.fq

and then we obtain:

bin/seqtk mergepe read_1.fq read_2.fq \
  | bin/bwa mem -p -R'@A01056:45:HJ2KFDSXY' hs38DH.fa - 2> out.log.bwamem \
  | bin/samtools view -1 - > out.aln.bam;

I don't know what it might be happening, but it is nerve-racking! Maybe, we lack of some dependencies. I would be really pleased if someone could figure it out the problem.

Thank you all in advanced!

Regards,

Laura

[Pierre Lindenbaum]

what are the error messages ? is there anything in out.log.bwamem ? your read group definition is WRONG. what is this option '-1' of samtools view ? samtools view doesn't generate a BAM file here.

Answer 1

[dinosaurur]

If anyone else encounters the issue where there's no output after executing the given instructions, I'd like to clarify a specific detail.

In the example provided by bwakit:

#mapping
bwa.kit/run-bwamem -o out -H hs38DH.fa read1.fq read2.fq | sh

Please note that the ' | sh' part at the end is crucial. You must include it to pipe the code to the 'sh' shell, as I learned from chatGPT. This ensures that the code is executed correctly.