Freebayes error message

Question

[ocortes]

Hi all,

I am running freebayes with 42 .bam files and after several minutes running the instruction I got an error message:

[E::bgzf_read] Read block operation failed with error -1 after 23 of 32 bytes  
terminate called after throwing an instance of 'std::runtime_error'  
  what():  sam_read1 return status: -3 file: Bov14.final.bam  
Aborted (core dumped)

Can anyone help me to solve this error?

Thanks in advance.

[ATpoint]

See also Freebayes error message and maybe try your luck opening another Github issue. Many are unanswered but you might be lucky. Be sure to provide full code and a reproducible minimal dataset for the developer.

[ocortes]

Thanks¡ Done.

Anyway I really appreciated if anyone more can tell me other possible solution .

[Mehmet]

how many memory did you use? Mostly, core dumped error points lack of enough memory. Another possible reason for this error could be interrupted files. you may try to increase memory and check your bam files.

[ocortes]

Thanks for your reply.

I have checked the bam files using: ValidateSamFile and the 42 files are correct I got the following message for the 42 files. ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. No errors found

I am trying to increase the memory to run freebayes usinf the comand -mem and also -Xmx:

freebayes -mem 15 -f rf.fa file1.bam ...to...file42.bam >output.vcf or freebayes -Xmx15 -f rf.fa file1.bam...to...file42.bam >output.vcf

but I get the following message could not parse min-mapping-quality

So I thought that I had a problem with my bam files but I have checked it and aparently are ok.

Previosuly to run freebayes I have mapped the files using bwa mem and after that I have used the instructions SortSam, MarkDuplicates an AddOrReplaceReadGroups (picard) then I run freebayes with the 42 files and I got all the problems that I have explained.

Thanks for any suggestion!