Segmentation fault for taxor search

[Iamcluless]

Hello,

I'm not sure if this is an issue with Taxor, but when I try to run taxor search it fails with a segmentation fault. The following output is produced:

checking input ... done!
use syncmer model
Segmentation fault

This is the command:
taxor search --index-file ${database} --query-file ${reads}/${sample}*.fastq.gz --output-file ${sample}.search.txt --error-rate 0.1 --threads ${cores}

This is on a Linux HPC.

Any ideas?

Thank you!

Andrew Wood

[JensUweUlrich]

Dear @Iamcluless,

thanks for your question. Taxor is not able to resolve the ${reads}/${sample}*.fastq.gz from the command line. Here, you need to create a comma-separated string of all sample files first as workaround (e.g. sample1.fastq.gz,sample2.fastq.gz,sampl3.fast.gz). Then you use this string as parameter value for the --query-file parameter.

Best,
Jens

[Iamcluless]

Ah, thank you! I really appreciate the help.

Andrew

[angelovangel]

Hi,
I get the same error, using the downloaded hixf database (refseq-abfv-k22-s12.hixf) and normal ONT/PacBio fastq files.