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balabanmetin / uDance

BSD 3-Clause "New" or "Revised" License
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stitch fails: AttributeError: 'list' object has no attribute 'root' #11

Closed Ufungi closed 1 month ago

Ufungi commented 1 month ago

Hello, I commented out rules except genetreeinfer, refine, and stitch in udance.smk file, because I only wanted to refine the phylogenetically placed tree using backbone alignment, tree, and jplace file. However, run fails at the stitch step. Below is the re-run of my previous run, which skipped the decomposing step.

(udance) genome@limsfep-zen-32c:/data/genome/run/snyoo/programs/uDance$ snakemake -c 16 --configfile config.yaml --snakefile udance.smk all localrules directive specifies rules that are not present in the Snakefile: trimcollect copybb

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 16 Rules claiming more threads will be scaled down. Job stats: job count

all 1 stitch 1 total 2

/data/genome/run/snyoo/programs/uDance/Fungi/udance.log already exists.Moving it to /data/genome/run/snyoo/programs/uDance/Fungi/udance.log.bak Select jobs to execute...

[Sun May 12 16:20:07 2024] rule stitch: input: Fungi/output/udance/137/astral_output.incremental.nwk, Fungi/output/udance/137/astral_output.updates.nwk, Fungi/output/udance/174/astral_output.incremental.nwk, Fungi/output/udance/174/astral_output.updates.nwk, Fungi/output/udance/84/astral_output.incremental.nwk, Fungi/output/udance/84/astral_output.updates.nwk, Fungi/output/udance/138/astral_output.incremental.nwk, Fungi/output/udance/138/astral_output.updates.nwk, Fungi/output/udance/177/astral_output.incremental.nwk, Fungi/output/udance/177/astral_output.updates.nwk, Fungi/output/udance/26/astral_output.incremental.nwk, Fungi/output/udance/26/astral_output.updates.nwk, Fungi/output/udance/7/astral_output.incremental.nwk, Fungi/output/udance/7/astral_output.updates.nwk, Fungi/output/udance/103/astral_output.incremental.nwk, Fungi/output/udance/103/astral_output.updates.nwk, Fungi/output/udance/121/astral_output.incremental.nwk, Fungi/output/udance/121/astral_output.updates.nwk, 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Fungi/output/udance/87/astral_output.updates.nwk, Fungi/output/udance/66/astral_output.incremental.nwk, Fungi/output/udance/66/astral_output.updates.nwk, Fungi/output/udance/80/astral_output.incremental.nwk, Fungi/output/udance/80/astral_output.updates.nwk, Fungi/output/udance/144/astral_output.incremental.nwk, Fungi/output/udance/144/astral_output.updates.nwk, Fungi/output/udance/73/astral_output.incremental.nwk, Fungi/output/udance/73/astral_output.updates.nwk, Fungi/output/udance/15/astral_output.incremental.nwk, Fungi/output/udance/15/astral_output.updates.nwk, Fungi/output/udance/1/astral_output.incremental.nwk, Fungi/output/udance/1/astral_output.updates.nwk, Fungi/output/udance/114/astral_output.incremental.nwk, Fungi/output/udance/114/astral_output.updates.nwk, Fungi/output/udance/181/astral_output.incremental.nwk, Fungi/output/udance/181/astral_output.updates.nwk, Fungi/output/udance/91/astral_output.incremental.nwk, Fungi/output/udance/91/astral_output.updates.nwk, Fungi/output/udance/95/astral_output.incremental.nwk, Fungi/output/udance/95/astral_output.updates.nwk, Fungi/output/udance/0/astral_output.incremental.nwk, Fungi/output/udance/0/astral_output.updates.nwk, Fungi/output/udance/128/astral_output.incremental.nwk, Fungi/output/udance/128/astral_output.updates.nwk, Fungi/output/udance/141/astral_output.incremental.nwk, Fungi/output/udance/141/astral_output.updates.nwk, Fungi/output/udance/24/astral_output.incremental.nwk, Fungi/output/udance/24/astral_output.updates.nwk, Fungi/output/udance/149/astral_output.incremental.nwk, Fungi/output/udance/149/astral_output.updates.nwk, Fungi/output/udance/86/astral_output.incremental.nwk, Fungi/output/udance/86/astral_output.updates.nwk, Fungi/output/udance/33/astral_output.incremental.nwk, Fungi/output/udance/33/astral_output.updates.nwk, Fungi/output/udance/78/astral_output.incremental.nwk, Fungi/output/udance/78/astral_output.updates.nwk, Fungi/output/udance/190/astral_output.incremental.nwk, Fungi/output/udance/190/astral_output.updates.nwk, Fungi/output/udance/88/astral_output.incremental.nwk, Fungi/output/udance/88/astral_output.updates.nwk, Fungi/output/udance/165/astral_output.incremental.nwk, Fungi/output/udance/165/astral_output.updates.nwk output: Fungi/output/udance.incremental.nwk, Fungi/output/udance.updates.nwk jobid: 1 benchmark: Fungi/output/benchmarks/stitch.txt reason: Missing output files: Fungi/output/udance.updates.nwk, Fungi/output/udance.incremental.nwk resources: tmpdir=/tmp

[Sun May 12 16:20:08 2024] Error in rule stitch: jobid: 1 input: Fungi/output/udance/137/astral_output.incremental.nwk, Fungi/output/udance/137/astral_output.updates.nwk, Fungi/output/udance/174/astral_output.incremental.nwk, Fungi/output/udance/174/astral_output.updates.nwk, Fungi/output/udance/84/astral_output.incremental.nwk, Fungi/output/udance/84/astral_output.updates.nwk, Fungi/output/udance/138/astral_output.incremental.nwk, Fungi/output/udance/138/astral_output.updates.nwk, Fungi/output/udance/177/astral_output.incremental.nwk, Fungi/output/udance/177/astral_output.updates.nwk, Fungi/output/udance/26/astral_output.incremental.nwk, Fungi/output/udance/26/astral_output.updates.nwk, Fungi/output/udance/7/astral_output.incremental.nwk, Fungi/output/udance/7/astral_output.updates.nwk, Fungi/output/udance/103/astral_output.incremental.nwk, Fungi/output/udance/103/astral_output.updates.nwk, Fungi/output/udance/121/astral_output.incremental.nwk, 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Fungi/output/udance/142/astral_output.incremental.nwk, Fungi/output/udance/142/astral_output.updates.nwk, Fungi/output/udance/53/astral_output.incremental.nwk, Fungi/output/udance/53/astral_output.updates.nwk, Fungi/output/udance/166/astral_output.incremental.nwk, Fungi/output/udance/166/astral_output.updates.nwk, Fungi/output/udance/3/astral_output.incremental.nwk, Fungi/output/udance/3/astral_output.updates.nwk, Fungi/output/udance/118/astral_output.incremental.nwk, Fungi/output/udance/118/astral_output.updates.nwk, Fungi/output/udance/134/astral_output.incremental.nwk, Fungi/output/udance/134/astral_output.updates.nwk, Fungi/output/udance/160/astral_output.incremental.nwk, Fungi/output/udance/160/astral_output.updates.nwk, Fungi/output/udance/49/astral_output.incremental.nwk, Fungi/output/udance/49/astral_output.updates.nwk, Fungi/output/udance/129/astral_output.incremental.nwk, Fungi/output/udance/129/astral_output.updates.nwk, Fungi/output/udance/189/astral_output.incremental.nwk, Fungi/output/udance/189/astral_output.updates.nwk, Fungi/output/udance/179/astral_output.incremental.nwk, Fungi/output/udance/179/astral_output.updates.nwk, Fungi/output/udance/62/astral_output.incremental.nwk, Fungi/output/udance/62/astral_output.updates.nwk, Fungi/output/udance/104/astral_output.incremental.nwk, Fungi/output/udance/104/astral_output.updates.nwk, Fungi/output/udance/113/astral_output.incremental.nwk, Fungi/output/udance/113/astral_output.updates.nwk, Fungi/output/udance/94/astral_output.incremental.nwk, Fungi/output/udance/94/astral_output.updates.nwk, Fungi/output/udance/31/astral_output.incremental.nwk, Fungi/output/udance/31/astral_output.updates.nwk, Fungi/output/udance/54/astral_output.incremental.nwk, Fungi/output/udance/54/astral_output.updates.nwk, Fungi/output/udance/36/astral_output.incremental.nwk, Fungi/output/udance/36/astral_output.updates.nwk, Fungi/output/udance/9/astral_output.incremental.nwk, Fungi/output/udance/9/astral_output.updates.nwk, Fungi/output/udance/146/astral_output.incremental.nwk, Fungi/output/udance/146/astral_output.updates.nwk, Fungi/output/udance/43/astral_output.incremental.nwk, Fungi/output/udance/43/astral_output.updates.nwk, Fungi/output/udance/85/astral_output.incremental.nwk, Fungi/output/udance/85/astral_output.updates.nwk, Fungi/output/udance/164/astral_output.incremental.nwk, Fungi/output/udance/164/astral_output.updates.nwk, Fungi/output/udance/32/astral_output.incremental.nwk, Fungi/output/udance/32/astral_output.updates.nwk, Fungi/output/udance/169/astral_output.incremental.nwk, Fungi/output/udance/169/astral_output.updates.nwk, Fungi/output/udance/168/astral_output.incremental.nwk, Fungi/output/udance/168/astral_output.updates.nwk, Fungi/output/udance/82/astral_output.incremental.nwk, Fungi/output/udance/82/astral_output.updates.nwk, Fungi/output/udance/41/astral_output.incremental.nwk, Fungi/output/udance/41/astral_output.updates.nwk, Fungi/output/udance/167/astral_output.incremental.nwk, Fungi/output/udance/167/astral_output.updates.nwk, Fungi/output/udance/87/astral_output.incremental.nwk, Fungi/output/udance/87/astral_output.updates.nwk, Fungi/output/udance/66/astral_output.incremental.nwk, Fungi/output/udance/66/astral_output.updates.nwk, Fungi/output/udance/80/astral_output.incremental.nwk, Fungi/output/udance/80/astral_output.updates.nwk, Fungi/output/udance/144/astral_output.incremental.nwk, Fungi/output/udance/144/astral_output.updates.nwk, Fungi/output/udance/73/astral_output.incremental.nwk, Fungi/output/udance/73/astral_output.updates.nwk, Fungi/output/udance/15/astral_output.incremental.nwk, Fungi/output/udance/15/astral_output.updates.nwk, Fungi/output/udance/1/astral_output.incremental.nwk, Fungi/output/udance/1/astral_output.updates.nwk, Fungi/output/udance/114/astral_output.incremental.nwk, Fungi/output/udance/114/astral_output.updates.nwk, Fungi/output/udance/181/astral_output.incremental.nwk, Fungi/output/udance/181/astral_output.updates.nwk, Fungi/output/udance/91/astral_output.incremental.nwk, Fungi/output/udance/91/astral_output.updates.nwk, Fungi/output/udance/95/astral_output.incremental.nwk, Fungi/output/udance/95/astral_output.updates.nwk, Fungi/output/udance/0/astral_output.incremental.nwk, Fungi/output/udance/0/astral_output.updates.nwk, Fungi/output/udance/128/astral_output.incremental.nwk, Fungi/output/udance/128/astral_output.updates.nwk, Fungi/output/udance/141/astral_output.incremental.nwk, Fungi/output/udance/141/astral_output.updates.nwk, Fungi/output/udance/24/astral_output.incremental.nwk, Fungi/output/udance/24/astral_output.updates.nwk, Fungi/output/udance/149/astral_output.incremental.nwk, Fungi/output/udance/149/astral_output.updates.nwk, Fungi/output/udance/86/astral_output.incremental.nwk, Fungi/output/udance/86/astral_output.updates.nwk, Fungi/output/udance/33/astral_output.incremental.nwk, Fungi/output/udance/33/astral_output.updates.nwk, Fungi/output/udance/78/astral_output.incremental.nwk, Fungi/output/udance/78/astral_output.updates.nwk, Fungi/output/udance/190/astral_output.incremental.nwk, Fungi/output/udance/190/astral_output.updates.nwk, Fungi/output/udance/88/astral_output.incremental.nwk, Fungi/output/udance/88/astral_output.updates.nwk, Fungi/output/udance/165/astral_output.incremental.nwk, Fungi/output/udance/165/astral_output.updates.nwk output: Fungi/output/udance.incremental.nwk, Fungi/output/udance.updates.nwk shell:

       (
        if [[ "False" == "False" ]] ; then
            python run_udance.py stitch -o Fungi/output/udance
        else
            python run_udance.py stitch -o Fungi/output/udance -b
        fi
        cp Fungi/output/udance/udance.*.nwk Fungi/output
       ) >> /data/genome/run/snyoo/programs/uDance/Fungi/udance.log 2>&1

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Execution failed. Logfile of the execution: /data/genome/run/snyoo/programs/uDance/Fungi/udance.log Complete log: .snakemake/log/2024-05-12T162006.990760.snakemake.log

Would it be a problem of Tree.reroot() function in the treeswift package? (version of mine is 1.1.42) If so, How can I fix it? Thank you in advance for your help.

udance.log udance.smk.txt config.yaml.txt