proali error within phg: line 22: 4021905 Floating point exception"${EXE}_sse4.1" "$@

[eead-csic-compbio]

Hi @baoxingsong @lynnjo,
I am running phg version 2.2.59.108, installed from conda, which in turn calls anchorwave. The exact command I am running is:

phg align-assemblies \
    --gff reference/GCA_904849725.1_MorexV3_HC.gff \
    --reference-file reference/GCA_904849725.1_MorexV3.fa  \
    --assemblies assemblies/assemblies_list.txt \
    --total-threads 20 \
    --in-parallel 2 \
    -o alignment_files

This job will produce SAM files:

-rw-r--r-- 1 contrera contrera   64415761 Mar 15 13:36 Barke.sam
-rw-r--r-- 1 contrera contrera   64359462 Mar 15 13:37 HOR13942.sam

And then it calls anchorware as follows:

[DefaultDispatcher-worker-2] INFO net.maizegenetics.phgv2.cli.AlignAssemblies 2024-03-15 13:37:37,331: runAnchorwaveProali proali Command for HOR13942: conda run -n phgv2-conda anchorwave proali -i reference/GCA_904849725.1_MorexV3_HC.gff -r reference/GCA_904849725.1_MorexV3.fa -as alignment_files/ref.cds.fasta -a alignment_files/HOR13942.sam -ar alignment_files/GCA_904849725.1_MorexV3.sam -s assemblies/HOR13942.gz -n alignment_files/HOR13942_GCA_904849725.1_MorexV3.anchorspro -R 1 -Q 1 -t 5 -o alignment_files/HOR13942.maf
[DefaultDispatcher-worker-2] ERROR net.maizegenetics.phgv2.cli.AlignAssemblies 2024-03-15 13:37:46,704: proali for assembly assemblies/HOR13942.gz run via ProcessBuilder returned error code 136

I then called anchorwave directly as follows:

(phgv2-conda) $ anchorwave proali -i reference/GCA_904849725.1_MorexV3_HC.gff -r reference/GCA_904849725.1_MorexV3.fa -as alignment_files/ref.cds.fasta -a alignment_files/HOR13942.sam -ar alignment_files/GCA_904849725.1_MorexV3.sam -s assemblies/HOR13942.gz -n alignment_files/HOR13942_GCA_904849725.1_MorexV3.anchorspro -R 1 -Q 1 -t 4 -o alignment_files/HOR13942.maf

And this is what I get in the terminal:

SSE4.1 is enabled
anaconda3/envs/phgv2-conda/bin/anchorwave: line 22: 4021905 Floating point exception"${EXE}_sse4.1" "$@

To rule out this was a conda issue I cloned and compiled the latest anchorwave from GitHub and got:

SSE4.1 is enabled
Floating point exception

I also tried with a different GFF file but also failed. I have gone through the issues and the only one related might be #47 , in case you have the chance to check it I have put a 2.5GB tar file with exactly those input files here (removed)

Thanks for your feedback,
Bruno

[baoxingsong]

Due to the internet problem, I am having a problem with downloading the files. But I am wondering if you could uncompress "assemblies/HOR13942.gz" and try again, please?

[eead-csic-compbio]

You were right, it seems uncompressing the assembly files solves that error. It is running now, hopefully it will complete now, thanks!