spaln error in BRAKER

[cfz1998]

When I run the example data. I get a error.

ERROR in file /home/chaofan/software/BRAKER/scripts/startAlign.pl at line 763 failed to execute: /home/chaofan/miniconda3/envs/EDTA/bin/spaln -Q7 -O0 /home/chaofan/software/BRAKER/example/test3/braker/tmp_spaln/genomeX4.fa proteins_addstop.fa > /home/chaofan/software/BRAKER/example/test3/braker/align_spaln/X4.spaln.aln 2>/home/chaofan/software/BRAKER/example/test3/braker/align_spaln/X4.spaln.stderr!

The cmdline is: braker.pl --cores=32 --genome=../genome.fa --species=test --softmasking --prot_seq=../proteins.fa --bam=../RNAseq.bam --prg=spaln

spaln version: SPALN version 2.4.0 <191118>

But when I run "spaln -Q3 -O0 genomeX4.fa proteins_addstop.fa ", it's normal! Why? (if -Q[num] num < 3) = normal.
-Q# 0:DP; 1-3:HSP-Search; 4-7; Block-Search (3)

And the content in the file[braker/align_spaln/X1.spaln.stderr] is : Gd:0 No:0 My:256 MS:0 Mb:18241 Tw:0 Tl:500141 0.00 100.00 0.00 : Block table may be destroyed !

[cfz1998]

Thank you for your reply! BEST! Chaofan Zhang

[fayjustin]

@cfz1998 Did you find a solution? I have nearly the same problem: works with Q3 but not Q7. spaln readme states: 4<=N<=7: Genome mapping and alignment. The genomic sequence must be formatted beforehand. So, it appears that the genome isn't formatted.

[KatharinaHoff]

Please use ProtHint instead of other aligners.

fayjustin @.***> schrieb am Mi. 1. Juni 2022 um 04:36:

@cfz1998 https://github.com/cfz1998 Did you find a solution? I have nearly the same problem: works with Q3 but not Q7. spaln readme states: 4<=N<=7: Genome mapping and alignment. The genomic sequence must be formatted beforehand. So, it appears that the genome isn't formatted.

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[fayjustin]

Thanks, I will. I was able to get spaln to run with Q7 on its own, just not using the perl script.