error occurred after setting the "yahs -l" parameter

[xychen233]

Hi yahs developers. I have encountered an issue and would like to seek for your help. YaHS can only handle up to 45,000 contigs. So I set the "yahs -l" parameter
/yahs-main/yahs -l 3500 $contigsFasta aligned.bed
Then the command successfully generated the yahs result file.
But when I run /yahs-main/juicer pre -a -o output yahs.out.bin yahs.out_scaffolds_final.agp $contigsFasta.fai
Some errors occurred, and this is the error log.
[I::main_pre] make juicer pre input from BIN file yahs.out.bin [E::make_juicer_pre_file_from_bin] Not a valid BIN file or BIN file header does not match sequence dictionary: 3 [E::make_juicer_pre_file_from_bin] Make sure no contig length threshold (YaHS option '-l') applied for the BIN file [E::make_juicer_pre_file_from_bin] Consider using a BAM or BED file instead
Can I ask how to resolve this issue? Did I misuse the “yahs -l” parameter? Do I need to filter the contigs to less than 45,000 and then perform the alignment again?

[c-zhou]

Hello @xychen233,

You can try to run juicer pre command with the BED file aligned.bed instead of the yahs.out.bin. The BIN file maintains a dictionary of the input sequences which caused the inconsistency.

Best,
Chenxi