"Buffer to small for input line lengths"

[vyx-lucy-kaplun]

Hi, I am running longphase with ONT long reads data and getting an error "Buffer to small for input line lengths". How can I fix that?

[twolinin]

Hi @vyx-lucy-kaplun

Can you please provide the command you used and the size of the file you input, so that we can identify the cause of the issue?

This issue may be caused by the buffer size being too small during the parsing of *.gz files. One simple solution is to decompress the file and use it as input. We need to adjust the parsing of compressed files accordingly. If possible, you can also provide the file you are using for us to test.

thanks

[vyx-lucy-kaplun]

@twolinin Thank you for the speedy reply!

The command I am using is longphase_linux-x64 phase -s nano_snp.vcf.gz --sv-file nano_sv_cutesv.vcf.gz -b nano.sorted.bam -r hg38.no_alt.fa -t 12 -o longphase_combined.phased. --ont

File sizes are: 92M nano_snp.vcf.gz 29M nano_sv_cutesv.vcf.gz 192G nano.sorted.bam

Unfortunately, I cannot share the files due to some security guidelines.

Thank you again!

[twolinin]

Hi, @vyx-lucy-kaplun

This issue may be caused by one of the lines in the vcf.gz file exceeding the default buffer size of 1M. This problem will be addressed in the next version update. For now, you can try uncompressing the file and running longphase again as a temporary solution.

Thanks.

[vyx-lucy-kaplun]

@twolinin Thank you!