[2021-12-20 19:52:07] INFO: ## Assigning sequences with TreeSAPP ## [2021-12-20 19:52:07] INFO: Arguments used: -i McrAFastq/BO45_S2_L001_R1_001.fastq -o McrA_output --refpkg_dir RefPkgs/Methanogenesis/McrA/IMG_Archaeal_MAGs_update/final_outputs -v -n 4 --overwrite [2021-12-20 19:52:07] DEBUG: Sequences appear to be 'dna'. [2021-12-20 19:52:07] DEBUG: Continuing with stage 'orf-call' [2021-12-20 19:52:07] DEBUG: Gathering reference package files... [2021-12-20 19:52:07] DEBUG: done. [2021-12-20 19:52:07] DEBUG: Writing split fasta to file '/Users/melodymale/McrA_output/intermediates/orf-call/BO45_S2_L001_R1_001.1.fasta'. [2021-12-20 19:52:11] DEBUG: Writing split fasta to file '/Users/melodymale/McrA_output/intermediates/orf-call/BO45_S2_L001_R1_001.2.fasta'. [2021-12-20 19:52:16] DEBUG: Writing split fasta to file '/Users/melodymale/McrA_output/intermediates/orf-call/BO45_S2_L001_R1_001.3.fasta'. [2021-12-20 19:52:20] DEBUG: Writing split fasta to file '/Users/melodymale/McrA_output/intermediates/orf-call/BO45_S2_L001_R1_001.4.fasta'. [2021-12-20 19:52:25] DEBUG: Writing split fasta to file '/Users/melodymale/McrA_output/intermediates/orf-call/BO45_S2_L001_R1_001.5.fasta'. [2021-12-20 19:52:25] DEBUG: McrAFastq/BO45_S2_L001_R1_001.fastq completed fq2fa in 18.52400279045105s. [2021-12-20 20:38:45] INFO: Concatenating and formatting coding sequences... [2021-12-20 20:39:26] DEBUG: /Users/melodymale/McrA_output/intermediates/orf-call/BO45_S2_L001_R1_001_ORFs.faa.tmp read by pyfastx in 28.52 seconds. [2021-12-20 20:40:24] DEBUG: /Users/melodymale/McrA_output/intermediates/orf-call/BO45_S2_L001_R1_001_ORFs.fna.tmp read by pyfastx in 57.99 seconds. [2021-12-20 20:40:26] INFO: done. [2021-12-20 20:40:26] DEBUG: Prodigal time required: 0.0:48.0:19.29 [2021-12-20 20:40:26] INFO: Reading and formatting /Users/melodymale/McrA_output/intermediates/orf-call/BO45_S2_L001_R1_001_ORFs.faa... [2021-12-20 20:40:53] DEBUG: /Users/melodymale/McrA_output/intermediates/orf-call/BO45_S2_L001_R1_001_ORFs.faa read by pyfastx in 27.09 seconds. [2021-12-20 20:41:17] INFO: done. [2021-12-20 20:41:17] INFO: TreeSAPP will analyze the 9572757 sequences found in input. [2021-12-20 20:41:17] INFO: Searching for marker proteins in ORFs using hmmsearch. [2021-12-20 20:41:21] INFO: Parsing HMMER domain tables for high-quality matches... [2021-12-20 20:41:21] INFO: done. [2021-12-20 20:41:21] DEBUG: Initial alignments: 83 Alignments discarded: 0 Fragmented alignments: 0 Inversions detected: 0 Alignments scaffolded: 0 Multi-alignments: 0 Sequences identified: 83 Number of markers identified: McrA 83 [2021-12-20 20:41:21] INFO: Loading homologous sequences identified... [2021-12-20 20:41:43] DEBUG: 9572674 sequences were excluded after synchronizing FASTA. [2021-12-20 20:41:47] INFO: done. [2021-12-20 20:41:47] DEBUG: Instantiating the PQuery instances... [2021-12-20 20:41:47] DEBUG: done. [2021-12-20 20:41:47] INFO: Extracting and grouping the quality-controlled sequences... [2021-12-20 20:41:47] INFO: done. [2021-12-20 20:41:47] DEBUG: Number of query sequences in each marker's group: McrA 0 7 McrA 1 10 McrA 2 3 McrA 3 9 McrA 4 9 McrA 5 11 McrA 6 3 McrA 7 2 McrA 8 1 McrA 9 3 McrA 10 6 McrA 11 3 McrA 12 2 McrA 13 3 McrA 14 2 McrA 15 3 McrA 16 2 McrA 17 1 McrA 18 1 McrA 19 1 McrA 20 1 [2021-12-20 20:41:47] INFO: Writing the grouped sequences to FASTA files... [2021-12-20 20:41:47] INFO: done. [2021-12-20 20:41:47] DEBUG: hmmalign time required: 0.0:0.0:0.61 [2021-12-20 20:41:48] DEBUG: Read 437 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group0.mfa'. [2021-12-20 20:41:48] DEBUG: Read 440 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group1.mfa'. [2021-12-20 20:41:48] DEBUG: Read 436 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group10.mfa'. [2021-12-20 20:41:48] DEBUG: Read 433 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group11.mfa'. [2021-12-20 20:41:48] DEBUG: Read 432 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group12.mfa'. [2021-12-20 20:41:48] DEBUG: Read 433 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group13.mfa'. [2021-12-20 20:41:48] DEBUG: Read 432 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group14.mfa'. [2021-12-20 20:41:48] DEBUG: Read 433 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group15.mfa'. [2021-12-20 20:41:48] DEBUG: Read 432 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group16.mfa'. [2021-12-20 20:41:48] DEBUG: Read 431 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group17.mfa'. [2021-12-20 20:41:48] DEBUG: Read 431 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group18.mfa'. [2021-12-20 20:41:48] DEBUG: Read 431 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group19.mfa'. [2021-12-20 20:41:48] DEBUG: Read 433 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group2.mfa'. [2021-12-20 20:41:48] DEBUG: Read 431 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group20.mfa'. [2021-12-20 20:41:48] DEBUG: Read 439 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group3.mfa'. [2021-12-20 20:41:48] DEBUG: Read 439 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group4.mfa'. [2021-12-20 20:41:48] DEBUG: Read 441 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group5.mfa'. [2021-12-20 20:41:48] DEBUG: Read 433 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group6.mfa'. [2021-12-20 20:41:48] DEBUG: Read 432 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group7.mfa'. [2021-12-20 20:41:48] DEBUG: Read 431 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group8.mfa'. [2021-12-20 20:41:48] DEBUG: Read 433 headers from FASTA file '/Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group9.mfa'. [2021-12-20 20:41:48] ERROR: /opt/homebrew/Caskroom/miniconda/base/envs/treesapp_cenv/bin/epa-ng did not complete successfully! Command used: /opt/homebrew/Caskroom/miniconda/base/envs/treesapp_cenv/bin/epa-ng -s /Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group0_references.mfa -t /Users/melodymale/McrA_output/intermediates/McrA_RefPkg/0423.1619159847/McrA.nwk -q /Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group0_queries.mfa --model /Users/melodymale/McrA_output/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/melodymale/McrA_output/intermediates/place/ -T 4 > /Users/melodymale/McrA_output/intermediates/place/McrA_hmm_purified_group0_EPA.txt Output: /bin/sh: line 1: 53035 Segmentation fault: 11 /opt/homebrew/Caskroom/miniconda/base/envs/treesapp_cenv/bin/epa-ng -s /Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group0_references.mfa -t /Users/melodymale/McrA_output/intermediates/McrA_RefPkg/0423.1619159847/McrA.nwk -q /Users/melodymale/McrA_output/intermediates/align/McrA_hmm_purified_group0_queries.mfa --model /Users/melodymale/McrA_output/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/melodymale/McrA_output/intermediates/place/ -T 4 > /Users/melodymale/McrA_output/intermediates/place/McrA_hmm_purified_group0_EPA.txt