Getting error when running treesapp assign

[melodymale]

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]

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]

@cmorganl Thank you for replying

How can I send the file to you?

Best regards

[cmorganl]

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 [email protected].

[cmorganl]

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]

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]

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]

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]

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]

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

Happy Holidays!!

[melodymale]

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