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hallamlab / TreeSAPP

A Python package for gene-centric taxonomic and functional classification using phylogenetic placement
GNU General Public License v3.0
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Getting error when running treesapp assign #89

Open melodymale opened 2 years ago

melodymale commented 2 years ago

I'm getting error when running this command treesapp assign -i /Users/melody/graftM/1_RAWDATA/BO45_S2_L001_R1_001.fastq --refpkg_dir /Users/melody/TreeSAPP/RefPkgs/Methanogenesis/McrA/IMG_Archaeal_MAGs_update/final_outputs -o /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG -v -n 8

but it's working when running with treesapp assign -i /Users/melody/graftM/1_RAWDATA/BO45_S2_L001_R1_001.fastq -t McrA -o /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG -v -n 8

This is some error.

[2021-12-13 15:55:29] DEBUG: Read 433 headers from FASTA file '/Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/align/McrA_hmm_purified_group9.mfa'

[2021-12-13 15:55:35] ERROR: /Users/melody/opt/miniconda3/envs/treesapp_cenv/bin/epa-ng did not complete successfully! Command used:
/Users/melody/opt/miniconda3/envs/treesapp_cenv/bin/epa-ng -s /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/align/McrA_hmm_purified_group1_references.mfa -t /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/McrA_RefPkg/0423.1619159847/McrA.nwk -q /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/align/McrA_hmm_purified_group1_queries.mfa --model /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/McrA_RefPkg/0423.1619159847/McrA_epa.model --no-pre-mask --dyn-heur 0.9 --preserve-rooting on --filter-min-lwr 0.01 --outdir /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/place/ -T 8 > /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/place/McrA_hmm_purified_group1_EPA.txt
Output:
/bin/sh: line 1: 35640 Segmentation fault: 11  /Users/melody/opt/miniconda3/envs/treesapp_cenv/bin/epa-ng -s /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/align/McrA_hmm_purified_group1_references.mfa -t /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/McrA_RefPkg/0423.1619159847/McrA.nwk -q /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/align/McrA_hmm_purified_group1_queries.mfa --model /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/McrA_RefPkg/0423.1619159847/McrA_epa.model --no-pre-mask --dyn-heur 0.9 --preserve-rooting on --filter-min-lwr 0.01 --outdir /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/place/ -T 8 > /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/place/McrA_hmm_purified_group1_EPA.txt
cmorganl commented 2 years ago

Hi, thanks for reporting this issue. As you demonstrated, there might be a problem with the McrA reference package provided in RefPkgs. I tested it with some sequences and it doesn't look obviously broken so there must be some combination of factors in play.

Could you please send me the file /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/search/McrA_hmm_purified.faa?

melodymale commented 2 years ago

@cmorganl Thank you for replying

How can I send the file to you?

Best regards

cmorganl commented 2 years ago

You could either attach it to this thread by changing the extension from .faa to .txt and following these instructions (preferred), or by emailing me at c.morganlang@gmail.com.

cmorganl commented 2 years ago

I was unable to reproduce the issue with the file you sent. Can you please tell me the computer's operating system and amount of RAM? Please send me the following files that triggered the segmentation fault in EPA:

/Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/align/McrA_hmm_purified_group1_references.mfa
/Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/McrA_RefPkg/0423.1619159847/McrA.nwk
/Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/align/McrA_hmm_purified_group1_queries.mfa
/Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/McrA_RefPkg/0423.1619159847/McrA_epa.model
melodymale commented 2 years ago

I ran on 

Mac M1
Ram 16GB 
OSX 12.0.1 (Monterey)

McrA_hmm_purified_group1_references.txt McrA.txt McrA_hmm_purified_group1_queries.txt McrA_epa.txt

cmorganl commented 2 years ago

Thanks!

Unfortunately, EPA-NG ran successfully with those files on my system. Could you send the output of treesapp info? I want to make sure we're using the same version of EPA-NG. I'm assuming you installed it with conda?

Could you also send the TreeSAPP (/Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/TreeSAPP_classify_log.txt) and EPA-NG log (/Users/melody/TreeSAPP/TreeSAPP_McrA_IMG/intermediates/place/McrA_hmm_purified_group1_EPA.txt) files for the run that failed?

melodymale commented 2 years ago

Thanks for replying

This result come from treesapp_info

TreeSAPP version 0.11.3.
Python package dependency versions:
    biopython: 1.79
    ete3: 3.1.2
    joblib: 1.0.0
    numpy: 1.21.4
    packaging: 21.3
    pyfastx: 0.8.4
    pygtrie: 2.4.2
    samsum: 0.1.4
    scikit-learn: 0.23.1
    scipy: 1.7.3
    seaborn: 0.11.2
    tqdm: 4.62.3
Software versions used:
    BMGE.jar    1.12
    FastTree    2.1.10
    epa-ng      v0.3.8
    hmmalign    3.3.2
    hmmbuild    3.3.2
    hmmsearch   3.3.2
    mafft       v7.490
    mmseqs      13.45111
    prodigal    V2.6.3
    raxml-ng
TreeSAPP has finished successfully.

TreeSAPP_classify_log.txt McrA_hmm_purified_group0_EPA.txt

Sorry for making confusion, actually I change the user's folder name to melody. At first, the output comes from my friend macbook but the result after first comment come from my macbook melodymale folder name

cmorganl commented 2 years ago

I'm still not able to reproduce the error with the exact same software versions. Could you please send me the McrA reference package that is causing EPA-NG to fail?

I'll probably need to test this on a Mac virtual machine. I hope to have an answer after the holidays.

melodymale commented 2 years ago

I clone the package from here https://github.com/hallamlab/RefPkgs/tree/master/Methanogenesis/McrA/IMG_Archaeal_MAGs_update/final_outputs

Happy Holidays!!

melodymale commented 2 years ago

@cmorganl Sorry for interrupting. Do you have any progress?