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constraint tree #200

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hjt1129 opened this issue Oct 23, 2024 · 12 comments
Closed

constraint tree #200

hjt1129 opened this issue Oct 23, 2024 · 12 comments

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@hjt1129
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hjt1129 commented Oct 23, 2024

hi,
I run the raxml-ng using SNP data, when i used four individuals (S1,S2,S3,S4) from one population as outgroup, they did not formed in one lineage. I used "--tree-constraint" to specify a constraint tree for these four individuals, the file content is "(S1,S2,S3,S4);", however, i comes the error "Segmentation fault (core dumped)". What's wrong with this? how can i take this four individuals into one lineage.
The executive command is "raxml-ng --all --msa ./074GSC_12535_no39_tab.min4.min4.phy --outgroup S40 S41 S43 --model TVM+G4+ASC_LEWIS --tree pars{10} --bs-trees 1000 --tree-constraint constraint.tree"
@amkozlov
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Please post your .raxml.log file as well as input data, and I will have a look.

@hjt1129
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hjt1129 commented Oct 24, 2024 via email

@amkozlov
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1 please try the latest version: https://github.com/amkozlov/raxml-ng/releases/tag/1.2.2
2. outgroup taxa names must be separated by comma, e.g. --outgroup S40,S41,S43
3. if it still doesn't work, please attach 074GSC_12535_no39_tab.min4.min4.phy and constraint.mld files, and I'll have a look

@hjt1129
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hjt1129 commented Oct 24, 2024 via email

@amkozlov
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unfortunately I don't see the attachments

@domivika
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Hello,

I've run into a similar issue as the author of the post. I get the "Segmentation fault (core dumped)" error when running the command with 2 threads:
raxml-ng --redo --msa results/fasta/family/67-of-79/aligned.fa --outgroup AAHYM041-16,AANIC173-10,AASFB349-10 --model GTR+G --tree-constraint results/fasta/family/67-of-79/remapped.tre --search --threads 2

and when running with 1 thread:
raxml-ng --redo --msa results/fasta/family/67-of-79/aligned.fa --outgroup AAHYM041-16,AANIC173-10,AASFB349-10 --model GTR+G --tree-constraint results/fasta/family/67-of-79/remapped.tre --search --threads 1
I get the following error:
free(): invalid pointer
Aborted (core dumped)

Please see the attached zip file for logs, trees, and other relevant files

Thank you!
raxml_files.zip

@amkozlov
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Hi Dominika,

thanks for reporting.

Your MSA has only 4 sequences, and your constraint tree has only 3 taxa. This means that only one topology is possible under the topological constraint.

Sure, raxml-ng should still process this trivial situation without failure, and I will fix it in the next version.
But for the time being, maybe you could just detect and handle such edge cases in your pipeline?

@domivika
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domivika commented Nov 11, 2024 •
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Hello,

Thanks for your reply. In my pipeline, I simply skip files with insufficient number of aligned sequences (<4) for now. Also, if there is an error regarding the complex constraint tree like this:

[00:00:00] Loaded comprehensive constraint tree with 5 taxa
ERROR: You provided a comprehensive, fully-resolved tree as a topological constraint.
Since this is almost certainly not what you intended, RAxML-NG will now exit...

I simply copy the input tree to the output one for the sake of testing.

I think the problem lays somewhere else here. This is my snakemake rule for raxml tool:

rule run_raxml:
    input:
        alignment="results/fasta/family/{scatteritem}/aligned.fa",
        tree="results/fasta/family/{scatteritem}/remapped.tre"
    output:
        tree="results/fasta/family/{scatteritem}/aligned.fa.raxml.bestTree"
    params:
        model=config['model'],
        num_outgroups=config['outgroups']
    log: "logs/run_raxml/run_raxml-{scatteritem}.log"
    conda: "envs/raxml.yml"
    shell:
        """
        # Check the number of taxa in the alignment
        TAXON_COUNT=$(grep -c '>' {input.alignment})

        # Ensure there are at least 4 taxa
        if [ "$TAXON_COUNT" -lt 4 ]; then
            echo "Skipping RAxML-NG: alignment has only $TAXON_COUNT taxa, which is insufficient." > {log}
            echo "No tree generated due to insufficient taxa." > {output.tree}
            exit 0
        fi

        # Extract the outgroup names from the alignment file
        OG=$(grep '>' {input.alignment} | tail -{params.num_outgroups} | sed -e 's/>//' | tr '\n' ',')

        # Define a function to run RAxML-NG with error handling
        run_raxml () {{
            raxml-ng \
                --redo \
                --msa {input.alignment} \
                --outgroup $OG \
                --model {params.model} \
                --tree-constraint {input.tree} \
                --threads $1 \
                --search > {log} 2>&1
        }}

        # Check if the constraint tree file exists
        if [ -s {input.tree} ]; then
            run_raxml 20

            # Handle errors based on log output
            if grep -q "core oversubscription" {log}; then
                echo "Oversubscription detected; rerunning with fewer threads." >> {log}
                run_raxml 10
            elif grep -q "core dumped" {log}; then
                echo "Core dump detected, retrying with single-thread mode." >> {log}
                run_raxml 1
            elif grep -q "ERROR: You provided a comprehensive" {log}; then
                echo "Comprehensive constraint detected; copying input tree to output." >> {log}
                cp {input.tree} {output.tree}
            fi
        else
            # Run without constraint if not available
            raxml-ng \
                --redo \
                --msa {input.alignment} \
                --outgroup $OG \
                --model {params.model} \
                --threads 20 \
                --search > {log} 2>&1
        fi
        """

and I keep getting this core dumped error (only for few fasta files):

    environment: line 16: 4153872 Aborted                 (core dumped) raxml-ng --redo --msa results/fasta/family/67-of-79/aligned.fa --outgroup $OG --model GTR+G --tree-constraint results/fasta/family/67-of-79/remapped.tre --threads $1 --search > logs/run_raxml/run_raxml-67-of-79.log 2>&1

I tried digging into this issue, and apparently the program is trying to access the memory it doesn't have access to? I'm a bit confused, example: relevant reddit thread

Do you have any idea what is going on?

Thanks!
Dominika

@domivika
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Hi,

It seems like the issue is also similar to #152

@amkozlov
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Well, as I said, the original problem that leads to the core dump has to be fixed inside raxml-ng.

But as a quick workaround, I suggest you simply disable tree constraint (and probably also outgroup) if alignment has 4 taxa, since it makes little sense.

Maybe you could even skip 4-taxa MSAs altogether. Please note that there are only 2 possible alternative tree topologies with 4 taxa.

@domivika
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Okay, I understand! Will do as you suggest.
Thanks a lot for your quick answer. I'm looking forward to the next version!

Dominika

amkozlov added a commit that referenced this issue Nov 21, 2024
@amkozlov
check that constraint tree has at least 4 taxa and print a clear erro…
ecdf971 
…r message otherwise (#200, #202)
@amkozlov
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Fixed in the dev branch.

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@amkozlov @hjt1129 @domivika