prank error

[bharat1912]

Hi Panaroo is a great extension to the suite of pangenome tools. I like the idea of outputs that are compatible with other tools eg Roary.

I have a problem with panaroo. Specifically, prank errors out when aligning core genes but this does not happen when mafft is selected.

I have installed panaroo using conda and have updated conda.

Below is the error output.

Assistance appreciated. Thanks Bharat

generating core genome MSAs... 100%|███████████████████████████████████████████████████████████████████████████████████████████████| 1097/1097 [03:28<00:00, 5.25it/s] 3%|██▊ | 32/1097 [00:13<00:18, 57.84it/s]Traceback (most recent call last): File "/home/bharat/opt/anaconda3/envs/panaroo/bin/panaroo", line 10, in sys.exit(main()) File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/panaroo/main.py", line 479, in main args.core, len(args.input_files)) File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/panaroo/generate_output.py", line 297, in generate_core_genome_alignment threads, aligner) File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/panaroo/generate_alignments.py", line 159, in multi_align_sequences delayed(align_sequences)(x, outdir, aligner) for x in tqdm(commands)) File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/joblib/parallel.py", line 1054, in call self.retrieve() File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/joblib/parallel.py", line 933, in retrieve self._output.extend(job.get(timeout=self.timeout)) File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/multiprocessing/pool.py", line 657, in get raise self._value File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, *kwds)) File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/joblib/_parallel_backends.py", line 595, in call return self.func(args, **kwargs) File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/joblib/parallel.py", line 263, in call for func, args, kwargs in self.items] File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/joblib/parallel.py", line 263, in for func, args, kwargs in self.items] File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/panaroo/generate_alignments.py", line 148, in align_sequences stdout, stderr = command[0]() File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/Bio/Application/init.py", line 574, in call raise ApplicationError(return_code, str(self), stdout_str, stderr_str) Bio.Application.ApplicationError: Non-zero return code 139 from 'prank -d=/media/bharat/volume1/Analysis_Final/panaroo_2/tmpp9g1jzcv/ndoA.fasta -o=ndoA -f=8 -codon', message 'Segmentation fault (core dumped)' 4%|████

[gtonkinhill]

Hi Bharat,

Thanks for flagging this. It's a bit hard to work out why Prank has failed without seeing the MSA. Would you be able to attach the one that is causing the error? It should be at /media/bharat/volume1/Analysis_Final/panaroo_2/tmpp9g1jzcv/ndoA.fasta

[bharat1912]

Thanks for your response.

A copy of the nodA.fasta file below

A_flavithermus_GAB_PacBio;0_0_2813 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTGGGATCTGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAGCGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTTGGTCTTATTGATTTTTAA Ali_Anoxybacillus_caldiproteolyticus_DSM_15730_NZ_JACDUT010000001;1_10_87 TTGATTGTTAAACGTGGCGACGTTTATTTTGCGGACCTTTCCCCGGTAGTTGGCTCAGAG CAAGGAGGCGTTCGTCCGGTATTAGTCATTCAAAATGACATCGGAAATCGCTTTAGTCCG ACGGTCATCGTGGCGGCGATTACGGCGCAAATCCAAAAAGCGAAGCTACCAACACATGTT GAAATCGATGCAAAGCGCTACGGATTTGAACGAGATTCCGTCATTCTTTTAGAACAAATT CGTACAATTGATAAGCAGCGACTAACGGATAAAATTACTCATCTAGATGACGAAATGATG GATAAAGTGGACGAAGCATTACAAATTAGTCTAGGTCTGATTGACTTTTAA Amp_Anoxybacillus_amylolyticus_DSM_15939_NZ_CP015438;2_2_60 TTGATTGTCAAACGTGGCGACGTTTATTTTGCGGATCTTTCCCCTGTCGTTGGCTCGGAA CAAGGAGGCGTTCGTCCGGTATTGGTCATTCAAAATGACATCGGAAACAGGTTTAGCCCG ACGGTCATTGTGGCGGCGATTACAGCCCAAATCCAAAAAGCGAAGCTGCCGACGCATGTC GAAATTGACGCAAAACGCTACGGGTTTGAGCGAGATTCCGTCATTCTTTTAGAGCAAATT CGGACGATTGACAAACAGCGGCTAACGGATAAAATTACTCACCTAGACGATGAAATGATG GATAAAGTAGACGAAGCACTGCAAATTAGCTTAGGACTTATCGATTTTTAA Amp_Anoxybacillus_tepidamans_DSM_16325_NZ_JACHEP010000001;3_24_37 TTGATTGTTAAACGTGGCGACGTTTATTTTGCGGACCTTTCCCCGGTCGTTGGCTCAGAG CAAGGTGGAGTTCGTCCGGTATTAGTCATTCAAAATGACATTGGAAATCGATTTAGCCCG ACTGTCATTGTGGCGGCGATTACGGCCCAAATCCAAAAGGCAAAGCTGCCGACACATGTA GAAATTGATGCGAAACGCTACGGATTTGAGCGCGATTCTGTCATTCTTTTAGAGCAAATT CGGACGATTGACAAACAGCGGCTAACGGACAAGATTACGCATTTAGATGATGAAATGATG GATAAAGTAGACGAAGCACTGCAAATCAGCTTAGGACTTATCGACTTTTAA Amp_Anoxybacillus_voinovskiensis_DSM_17075_NZ_JACIDE010000001;4_30_28 TTGATTGTCAAACGTGGCGACGTTTATTTTGCGGATCTTTCCCCTGTCGTTGGCTCAGAA CAAGGAGGCGTTCGTCCGGTATTAGTCATTCAAAATGACATCGGAAATCGGTTTAGCCCG ACGGTCATTGTGGCGGCGATTACAGCCCAAATCCAAAAAGCGAAGCTGCCGACGCATGTC GAAATTGATGCAAAACGCTACGGGTTTGAGCGCGATTCCGTCATTCTTTTAGAGCAAATT CGGACGATTGACAAACAGCGGCTAACGGATAAAATTACTCACTTAGACGATGAAATGATG GATAAAGTAGACGAAGCACTGCAAATTAGTTTAGGACTTATCGACTTTTAA Anoxybacillus_103_NZ_MQAD01000001;5_20_51 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTCAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_ayderensis_MT-Cab_NZ_NDEZ01000001;6_29_31 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCTGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATTCAAAAAGCGAAGTTGCCCACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATCGATAAACAGCGTCTGACAGATAAGATTACCCATCTAGATGACGAAATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTTGGTCTTATTGATTTTTAA Anoxybacillus_ayderensis_NZ_JXTG01000001;7_22_20 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCTGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATTCAAAAAGCGAAGTTGCCCACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATCGATAAACAGCGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTTGGTCTTATTGATTTTTAA Anoxybacillus_ayderensis_SK3-4;8_58_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCTGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATTCAAAAAGCGAAGTTGCCCACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATCGATAAACAGCGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTTGGTCTTATTGATTTTTAA Anoxybacillus_BCO1_JRLC01000001;9_54_9 GTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCAACCGTCATTGTTGCTGCC ATTACTGCGCAAATTCAAAAAGCGAAGTTGCCCACACATGTTGAAATCGACGCAAAGCGC TACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATTCGGACGATCGATAAACAG CGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATGGATAAAGTAGATGAAGCG TTGCAAATTAGTCTTGGTCTTATTGATTTTTAA Anoxybacillus_CHMUD_NZ_SDLG01000100;10_13_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTCAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTCTAA Anoxybacillus_EFIL_NZ_SDLH01000099;11_2_55 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTTGGTCTTATTGATTTTTAA Anoxybacillus_eryuanensis_DSM23212;12_17_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGAAGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_52-1A_NZ_CP021838;13_0_2302 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_AF14_NZ_LUFB01000038;14_5_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_AF16_NZ_LUCQ01000090;15_92_24 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_AK1_NZ_APCD01000001;16_22_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGATATCGGGAACCGTTTCAGTCCG ACCGTCATTGTTGCTGCCATTACTGCGCAAATTCAAAAAGCCAAGCTGCCTACACATGTT GAAATCGATGCAAAGCGCTACGGATTTGAGCGGGACTCTGTCATTTTGCTTGAACAAATT CGAACGATTGATAAACAACGTCTGACAGATAAGATTACCCATTTAGATGACGAGATGATG GATAAAGTTGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_DSM_2641;17_0_320 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTCATTGATTTTTAA Anoxybacillus_flavithermus_FHS-PPAM212_NZ_SBBW01000001;18_97_1 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_KU2-6_11_NZ_PEDM01000010;19_12_44 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTCAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATCGATAAACAGCGTCTGACAGATAAGATTACCCATCTAGATGAAGAGATGATG GATAAAGTAGATGAAGCGCTGCAAATTAGTCTTGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_NBRC_109594_NZ_BARH01000090;20_28_49 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTCAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_sub_yunnanensis_E13_KN127218;21_12_37 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGAAGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_TNO-09.006_chrAF6_NZ_KB205935;22_0_181 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WK1_NC_011567;23_0_202 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTCATTGATTTTTAA Anoxybacillus_flavithermus_WS5279_NZ_JABJUR010000100;24_144_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5281_NZ_JABJUS010000100;25_107_1 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5284_NZ_JABJUZ010000100;26_154_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5285_NZ_JABJUT010000100;27_92_20 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5286_NZ_JABJUU010000100;28_145_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5287_NZ_JABJUV010000100;29_174_8 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5290_NZ_JABJUW010000100;30_177_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5291_NZ_JABJUX010000100;31_143_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5292_NZ_JABJUY010000100;32_145_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5364_NZ_JABJVA010000100;33_110_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5446_NZ_JABJVB010000100;34_146_1 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5448_NZ_JABJVC010000099;35_153_1 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5449_NZ_JABJVD010000100;36_149_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5490_NZ_JABJVE010000100;37_173_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5491_NZ_JABJVF010000100;38_160_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5492_NZ_JABJVG010000100;39_3_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5493_NZ_JABJVH010000100;40_4_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5494_NZ_JABJVI010000100;41_113_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5495_NZ_JABJVJ010000100;42_98_1 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5496_NZ_JABJVK010000100;43_117_1 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_flavithermus_WS5497_NZ_JABJVL010000100;44_114_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTTAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAGGCGCTACGGATTTGAACGGGACTCTGTCATTTTACTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGATGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_gonensis_DT3-1_NZ_ANMT01000001;45_22_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCTGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAGCGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_gonensis_G2_NZ_JRZG01000001;46_0_190 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTGGGATCTGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAGCGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_kamchatkensis_DSM_14988_NZ_JACDUV010000001;47_11_41 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCTGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATTCAAAAAGCGAAGTTGCCCACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATCGATAAACAGCGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTTGGTCTTATTGATTTTTAA Anoxybacillus_kamchatkensis_G10_NZ_CP025535;48_0_1110 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCTGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAGCGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_kamchatkensis_PD13_NZ_NQLB01000001;49_10_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCTGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAGCGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_KU2-6_11_NZ_JPZN01000001;50_36_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTCAGTCCA ACCGTCATCGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATCGATAAACAGCGTCTGACAGATAAGATTACCCATCTAGATGAAGAGATGATG GATAAAGTAGATGAAGCGCTGCAAATTAGTCTTGGTCTTATTGATTTTTAA Anoxybacillus_MB8_NZ_RXXX01000100;51_35_24 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_mongoliensis_DSM_19169_NZ_JACHEQ010000001;52_14_51 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTCTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATCGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGATGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATG GATAAAGTAGATGAAGCGCTGCAAATTAGTCTTGGTCTTATTGATTTTTAA Anoxybacillus_mongoliensis_MB4_NZ_MRZM01000010;53_34_9 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCTGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATTCAAAAAGCGAAGTTGCCCACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATCGATAAACAGCGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTTGGTCTTATTGATTTTTAA Anoxybacillus_pushchinoensis_K1_NZ_FOJQ01000117;54_58_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTACTTGTTATTCAAAATGATATCGGGAACCGTTTCAGTCCG ACCGTCATTGTTGCTGCCATTACTGCGCAAATTCAAAAAGCCAAGCTGCCCACACATGTC GAAATCGATGCAAAGCGCTACGGATTTGAGCGGGACTCTGTCATTTTGCTTGAACAAATT CGAACGATTGATAAACAACGTCTGACAGATAAGATTACCCATTTAGATGACGAGATGATG GATAAGGTTGATGAAGCGTTGCAAATCAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_salavatile_DSM22626;55_17_2 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGAAGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTCGGTCTTATTGATTTTTAA Anoxybacillus_suryakundensis_DSM_27374_NZ_LIOK01000001;56_21_26 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGAAGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTTGGTCTTATTGATTTTTAA Anoxybacillus_tengchongensis_DSM_23211_NZ_JACHES010000001;57_14_41 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCAGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATCCAAAAAGCGAAGTTGCCTACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTTGGTCTTATTGATTTTTAA Anoxybacillus_thermarum_AF_04_NZ_JXTH01000001;58_5_52 TTGATTGTCAAACGTGGTGACGTGTATTTTGCCGATCTTTCTCCAGTAGTTGGATCTGAG CAAGGGGGCGTGCGCCCTGTGCTTGTTATTCAAAATGACATTGGGAACCGTTTCAGTCCA ACCGTCATTGTTGCTGCCATTACTGCGCAAATTCAAAAAGCGAAGTTGCCCACACATGTT GAAATCGACGCAAAGCGCTACGGATTTGAACGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATCGATAAACAGCGTCTGACAGATAAGATTACCCATCTAGATGACGAGATGATG GATAAAGTAGATGAAGCGTTGCAAATTAGTCTTGGTCTTATTGATTTTTAA Cal_A_geothermalis_GAB_PacBio;59_0_2303 TTGATTGTTAAGCGTGGCGACGTTTATTTCGCGGACCTTTCCCCGGTAGTTGGTTCGGAG CAAGGAGGCGTGCGTCCGGTATTAGTTATTCAAAACGACATCGGAAATCGGTTTAGTCCA ACAGTTATTGTGGCAGCTATAACAGCGCAGATCCAGAAAGCCAAATTGCCCACCCACGTG GAAATTGATGCGAAACGGTATGGATTTGAACGAGATTCCGTCATTCTTTTAGAGCAAATT CGTACGATTGACAAACAAAGGCTCACGGACAAGATTACGCACTTAGATGACGAAATGATG GATAAAGTAGATGAGGCGCTCCAAATCAGTCTAGGGCTCATTGATTTTTAA Cal_Anoxybacillus_B2M1_NZ_CP015435;60_0_2318 TTGATTGTTAAGCGTGGCGACGTTTATTTCGCGGACCTTTCCCCGGTAGTTGGTTCGGAG CAAGGAGGCGTGCGTCCGGTATTAGTTATTCAAAACGACATCGGAAATCGGTTTAGTCCA ACAGTTATTGTGGCAGCTATAACAGCGCAGATCCAGAAAGCCAAATTGCCCACCCACGTG GAAATTGATGCGAAACGGTATGGATTTGAACGAGATTCCGTCATTCTTTTAGAGCAAATT CGTACGATTGACAAACAAAGGCTCACGGACAAGATTACGCACTTAGATGACGAAATGATG GATAAAGTAGATGAGGCGCTCCAAATCAGTCTAGGGCTCATTGATTTTTAA Cal_Anoxybacillus_B7M1_NZ_CP015436;61_0_2951 TTGATTGTTAAGCGTGGCGACGTTTATTTCGCGGACCTTTCCCCGGTAGTTGGTTCGGAG CAAGGAGGCGTGCGTCCGGTATTAGTTATTCAAAACGACATCGGAAATCGGTTTAGTCCA ACAGTTATTGTGGCAGCTATAACAGCGCAGATCCAGAAAGCCAAATTGCCCACCCACGTG GAAATTGATGCGAAACGGTATGGATTTGAACGAGATTCCGTCATTCTTTTAGAGCAAATT CGTACGATTGACAAACAAAGGCTCACGGACAAGATTACGCACTTAGATGACGAAATGATG GATAAAGTAGATGAGGCGCTCCAAATCAGTCTAGGGCTCATTGATTTTTAA Cal_Anoxybacillus_P3H1B_NZ_LPUG01000001;62_14_84 TTGATTGTTAAGCGTGGCGACGTTTATTTCGCGGACCTTTCCCCGGTAGTTGGTTCGGAG CAAGGAGGCGTGCGTCCGGTATTAGTTATTCAAAACGACATCGGAAATCGGTTTAGTCCA ACAGTTATTGTGGCAGCTATAACAGCGCAGATCCAGAAAGCCAAATTGCCCACCCACGTG GAAATTGATGCGAAACGGTATGGATTTGAACGAGATTCCGTCATTCTTTTAGAGCAAATT CGTACGATTGACAAACAAAGGCTCACGGACAAGATTACGCACTTAGATGACGAAATGATG GATAAAGTAGATGAGGCGCTCCAAATCAGTCTAGGGCTCATTGATTTTTAA Cal_Anoxybacillus_PDR2_NZ_CP047158;63_0_298 TTGATTGTTAAGCGTGGCGACGTTTATTTCGCGGACCTTTCCCCGGTAGTTGGTTCGGAG CAAGGAGGCGTGCGTCCGGTATTAGTTATTCAAAACGACATCGGAAATCGGTTTAGTCCA ACAGTTATTGTGGCAGCTATAACAGCGCAGATCCAGAAAGCCAAATTGCCCACCCACGTG GAAATTGATGCGAAACGGTATGGATTTGAACGAGATTCCGTCATTCTTTTAGAGCAAATT CGTACGATTGACAAACAAAGGCTCACGGACAAGATTACGCACTTAGATGACGAAATGATG GATAAAGTAGATGAGGCGCTCCAAATCAGTCTAGGGCTCATTGATTTTTAA Cal_Anoxybacillus_rupiensis_DSM_17127_NZ_JACIDF010000001;64_10_97 TTGATTGTTAAGCGTGGCGACGTTTATTTCGCGGACCTTTCCCCGGTAGTTGGTTCGGAG CAAGGAGGCGTGCGTCCGGTATTAGTTATTCAAAACGACATCGGAAATCGGTTTAGTCCA ACAGTTATTGTGGCAGCTATAACAGCGCAGATCCAGAAAGCCAAATTGCCCACCCACGTG GAAATTGATGCGAAACGGTATGGATTTGAACGAGATTCCGTCATTCTTTTAGAGCAAATT CGTACGATTGACAAACAAAGGCTCACGGACAAGATTACGCACTTAGATGACGAAATGATG GATAAAGTAGATGAGGCGCTCCAAATCAGTCTAGGGCTCATTGATTTTTAA Cal_Anoxybacillus_tepidamans_PS2_NZ_JHVN01000001;65_20_2 TTGATTGTGAAGCGTGGCGACGTTTATTTTGCGGATCTTTCCCCAGTAGTTGGCTCTGAA CAGGGAGGCGTTCGCCCGGTATTAGTGATTCAAAACGATATCGGGAATCGCTTTAGTCCG ACGGTCATTGTGGCGGCGATTACGGCGCAAATCCAGAAAGCAAAGTTGCCGACGCATGTG GAAATTGATGCGAAACGCTATGGATTTGAACGGGACTCCGTCATTCTTTTAGAACAAATT CGGACGATTGACAAACAACGGCTAACAGACAAGATTACGCATTTAGATGACGAAATGATG GATAAAGTGGATGAGGCACTTCAAATTAGCCTAGGACTCATTGACTTTTAA Cal_Anoxybacillus_UARK-01_NZ_NASY01000001;66_48_23 TTGATTGTTAAGCGTGGCGACGTTTATTTCGCGGACCTTTCCCCGGTAGTTGGTTCGGAG CAAGGAGGCGTGCGTCCGGTATTAGTTATTCAAAACGACATCGGAAATCGGTTTAGTCCA ACAGTTATTGTGGCAGCTATAACAGCGCAGATCCAGAAAGCCAAATTGCCCACCCACGTG GAAATTGATGCGAAACGGTATGGATTTGAACGAGATTCCGTCATTCTTTTAGAGCAAATT CGTACGATTGACAAACAAAGGCTCACGGACAAGATTACGCACTTAGATGACGAAATGATG GATAAAGTAGATGAGGCGCTCCAAATCAGTCTAGGGCTCATTGATTTTTAA Cal_A_rupensis_GAB_PacBio;67_0_2426 TTGATTGTTAAGCGTGGCGACGTTTATTTCGCGGACCTTTCCCCGGTAGTTGGTTCGGAG CAAGGAGGCGTGCGTCCGGTATTAGTTATTCAAAACGACATCGGAAATCGGTTTAGTCCA ACAGTTATTGTGGCAGCTATAACAGCGCAGATCCAGAAAGCCAAATTGCCCACCCACGTG GAAATTGATGCGAAACGGTATGGATTTGAACGAGATTCCGTCATTCTTTTAGAGCAAATT CGTACGATTGACAAACAAAGGCTCACGGACAAGATTACGCACTTAGATGACGAAATGATG GATAAAGTAGATGAGGCGCTCCAAATCAGTCTAGGGCTCATTGATTTTTAA Tal_Anoxybacillus_calidus_DSM_25220_NZ_JACDUU010000001;68_10_2 TTGATTGTCAAGCGTGGCGACGTGTATTTTGCAGACCTTTCCCCGGTAGTTGGCTCAGAG CAAGGAGGCGTTCGTCCGGTATTAGTTATTCAGAATGATATTGGAAACCGTTTTAGTCCT ACTGTAATAGTGGCGGCTATTACCGCGCAAATCCAAAAAGCGAAATTGCCAACGCACGTG GAAATTGATGCGAAACGCTACGGATTTGAGCGGGATTCCGTTATCCTTCTGGAACAAATA CGGACGATTGATAAACAACGCTTAACAGATAAGATTACTCATCTCGATGATGAGATGATG GATAAAGTGGATGAAGCTCTTCAAATCAGCCTAGGACTCATTGATTTTTAA Tal_Anoxybacillus_vitaminiphilus_CGMCC_1.8979_NZ_QLMH01000001;69_18_46 TTGATTGTCAAGCGTGGCGACGTGTATTTTGCAGACCTTTCCCCGGTAGTTGGCTCAGAG CAAGGAGGCGTTCGTCCGGTATTAGTCATTCAGAATGACATTGGGAACCGCTTTAGTCCT ACTGTAATAGTGGCGGCTATTACCGCACAAATCCAAAAAGCGAAGTTGCCAACGCACGTG GAAATTGATGCGAAGCGCTACGGATTTGAGCGTGATTCCGTTATCCTTTTGGAACAAATA CGGACGATTGATAAACAACGCTTAACAGATAAGATTACCCATCTCGATGATGAGATGATG GATAAAGTGGATGAAGCCCTTCAAATCAGCTTAGGACTCATTGATTTTTAA Thermolongibacillus_altinsuensis_DSM_24979_NZ_SLUL01000001;70_17_2 TTGATTGTCAAACGTGGCGATGTTTATTTTGCGGATCTTTCTCCAGTAGTTGGTTCAGAA CAAGGAGGCATTCGCCCTGTATTAGTCATCCAAAATGACATTGGGAACCGCTTCAGTCCC ACCGTCATTGTTGCTGCCATCACTGCTCAAATTCAAAAAGCGAAATTGCCGACACATGTT GAAATCGATGCGAAGCGTTATGGGTTTGAGCGGGACTCTGTCATTTTGCTTGAACAAATT CGGACGATTGATAAACAACGTCTGACAGATAAGATTACCCATCTGGATGATGAAATGATG GATAAAGTGGATGAAGCGTTACAAATTAGCCTAGGTCTTATTGACTTTTAA

[gtonkinhill]

Hi Bharat,

I am afraid I can not reproduce the issue. What version of Prank do you have installed? Are you able to run the Prank command separately as

prank -d=nodeA.fasta -o=ndoA -f=8 -codon

I am wondering if this is an issue with the number of processes being used leading to a memory problem. It might help to reduce the number of cpu cores being used by panaroo.

[bharat1912]

Hi gerry, Thanks for your feedback.

1. I reran panaroo with the following parameters. It is a Dell workstation with 2Core, 64G memory. $panaroo -i /media/bharat/volume1/Analysis_Final/Roary/Roary_of_Anoxybacillus_according_to_ANI_clusters/All_Anoxybacillus_clusters/*.gff -o /media/bharat/volume1/Analysis_Final/panaroo_3 --clean-mode moderate --remove-invalid-genes -a core --aligner prank -t 8

2. It again failed to run prank. The prank version is v.170427. (Minimal usage: 'prank sequence_file')

3. The Error message is: 100%|██████████████████████████████████████████████████████████████████| 730/730 [04:20<00:00, 2.80it/s] 3%|██▏ | 24/730 [05:03<3:05:39, 15.78s/it]Traceback (most recent call last): File "/home/bharat/opt/anaconda3/envs/panaroo/bin/panaroo", line 10, in sys.exit(main()) File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/panaroo/main.py", line 485, in main args.core, len(args.input_files)) File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/panaroo/generate_output.py", line 297, in generate_core_genome_alignment threads, aligner) File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/panaroo/generate_alignments.py", line 159, in multi_align_sequences delayed(align_sequences)(x, outdir, aligner) for x in tqdm(commands)) File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/joblib/parallel.py", line 1054, in call self.retrieve() File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/joblib/parallel.py", line 933, in retrieve self._output.extend(job.get(timeout=self.timeout)) File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/multiprocessing/pool.py", line 657, in get raise self._value File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, *kwds)) File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/joblib/_parallel_backends.py", line 595, in call return self.func(args, **kwargs) File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/joblib/parallel.py", line 263, in call for func, args, kwargs in self.items] File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/joblib/parallel.py", line 263, in for func, args, kwargs in self.items] File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/panaroo/generate_alignments.py", line 148, in align_sequences stdout, stderr = command[0]() File "/home/bharat/opt/anaconda3/envs/panaroo/lib/python3.7/site-packages/Bio/Application/init.py", line 574, in call raise ApplicationError(return_code, str(self), stdout_str, stderr_str) Bio.Application.ApplicationError: Non-zero return code 134 from 'prank -d=/media/bharat/volume1/Analysis_Final/panaroo_3/tmp6cblxav7/rpmI.fasta -o=rpmI -f=8 -codon', message "terminate called after throwing an instance of 'std::out_of_range'" 4%|██▊

4. The data file where prank failed is -- rpmI.fasta

   A_flavithermus_GAB_PacBio;0_0_1913 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTTGCAAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Ali_Anoxybacillus_caldiproteolyticus_DSM_15730_NZ_JACDUT010000001;1_0_503 ATGCCAAAAATGAAAACTCATCGAGGCTCTGCTAAGCGTTTCAAAAAAACTGGTACTGGT AAGCTAAAACGTTCTCATGCGTTTACTAGCCACTTATTCGCAAACAAAACGCAAAAACAA AAACGTAAACTTCGCAAAGCGACATTAGTATCTTCTGGTGATTTCAAACGCATTCGTCAA ATGCTTGATAACTTAAAATAA Amp_Anoxybacillus_amylolyticus_DSM_15939_NZ_CP015438;2_1_53 ATGCCAAAAATGAAAACACATAAAGGCTCTGCAAAGCGTTTTAAAAAGACGGGCACTGGG AAATTAAAACGTTCTCATGCATTTACTAGCCATTTATTCGCTAACAAAACACAGAAACAA AAACGCAAACTTCGCAAAGCAACGCTTGTATCTTCTGGCGACTTCAAACGCATTCGTCAA TTGCTTGACAACGTAAAATAA Amp_Anoxybacillus_tepidamans_DSM_16325_NZ_JACHEP010000001;3_5_107 ATGCCAAAAATGAAAACACATAAAGGCTCTGCAAAGCGTTTTAAAAAGACGGGCACTGGT AAGTTAAAACGTTCTCATGCATTTACTAGCCATTTATTCGCAAACAAAACGCAAAAACAA AAACGAAAACTTCGTAAAGCAACGCTTGTATCTTCTGGAGACTTCAAACGCATTCGTCAA TTGCTTGACAACGTAAAATAA Amp_Anoxybacillus_voinovskiensis_DSM_17075_NZ_JACIDE010000001;4_18_13 ATGCCAAAAATGAAAACACATAAAGGCTCTGCAAAGCGTTTTAAAAAGACGGGCACTGGG AAATTAAAACGTTCTCATGCATTTACTAGCCATTTATTCGCCAACAAAACACAAAAACAA AAACGCAAACTTCGCAAAGCAACGCTTGTATCTTCTGGCGACTTCAAACGCATTCGTCAA TTGCTTGACAACGTAAAATAA Anoxybacillus_103_NZ_MQAD01000001;5_4_135 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCAAATAAAACACAAAAACAA AAACGTAAACTTCGCAAAGCAACACTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_ayderensis_MT-Cab_NZ_NDEZ01000001;6_6_65 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCAAACAAAACGCAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTCGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_ayderensis_NZ_JXTG01000001;7_3_160 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCAAACAAAACGCAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTCGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_ayderensis_SK3-4;8_2_48 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTTGCAAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_BCO1_JRLC01000001;9_15_9 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTTGCAAACAAAACACAAAAACAA AAAGCGTAA Anoxybacillus_CHMUD_NZ_SDLG01000100;10_0_64 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCAAATAAAACACAAAAACAA AAACGTAAACTTCGCAAAGCAACACTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_EFIL_NZ_SDLH01000099;11_15_160 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCAAACAAAACGCAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTCGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_52-1A_NZ_CP021838;13_0_2722 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_AF14_NZ_LUFB01000038;14_95_13 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_AF16_NZ_LUCQ01000090;15_86_23 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_AK1_NZ_APCD01000001;16_13_26 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGCAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGACAACGTAAAATAA Anoxybacillus_flavithermus_DSM_2641;17_0_1185 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCAAATAAAACACAAAAACAA AAACGTAAACTTCGCAAAGCAACACTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_FHS-PPAM212_NZ_SBBW01000001;18_15_19 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_KU2-6_11_NZ_PEDM01000010;19_64_96 ATGCCAAAGATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCGTTCACTAGCCACTTATTCGCAAACAAAACACAAAAACAA AAACGTAAACTTCGTAAAGCAACACTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_NBRC_109594_NZ_BARH01000090;20_17_11 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCAAATAAAACACAAAAACAA AAGCGTAAACTTCGCAAAGCAACACTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_sub_yunnanensis_E13_KN127218;21_1_728 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCAAACAAAACGCAAAAACAA AAACGTAAACTTCGTAAAGCAACACTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_TNO-09.006_chrAF6_NZ_KB205935;22_0_581 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WK1_NC_011567;23_0_535 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCGTTCACTAGCCACTTATTCGCAAATAAAACACAAAAACAA AAGCGTAAACTTCGCAAAGCAACACTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5279_NZ_JABJUR010000100;24_45_25 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5281_NZ_JABJUS010000100;25_40_172 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5284_NZ_JABJUZ010000100;26_83_7 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5285_NZ_JABJUT010000100;27_94_20 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5286_NZ_JABJUU010000100;28_80_121 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5287_NZ_JABJUV010000100;29_144_20 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5290_NZ_JABJUW010000100;30_52_25 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5291_NZ_JABJUX010000100;31_9_25 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5292_NZ_JABJUY010000100;32_67_13 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5364_NZ_JABJVA010000100;33_50_174 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5446_NZ_JABJVB010000100;34_53_25 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5448_NZ_JABJVC010000099;35_61_28 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5449_NZ_JABJVD010000100;36_48_19 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5490_NZ_JABJVE010000100;37_79_19 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5491_NZ_JABJVF010000100;38_84_12 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5492_NZ_JABJVG010000100;39_53_19 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5493_NZ_JABJVH010000100;40_74_19 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5494_NZ_JABJVI010000100;41_55_174 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5495_NZ_JABJVJ010000100;42_45_26 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5496_NZ_JABJVK010000100;43_54_26 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_flavithermus_WS5497_NZ_JABJVL010000100;44_56_174 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_gonensis_DT3-1_NZ_ANMT01000001;45_12_171 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTTGCAAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_gonensis_G2_NZ_JRZG01000001;46_0_2289 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTTGCAAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_kamchatkensis_DSM_14988_NZ_JACDUV010000001;47_3_160 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCAAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTCGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_kamchatkensis_G10_NZ_CP025535;48_0_2000 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTTGCAAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_kamchatkensis_PD13_NZ_NQLB01000001;49_5_197 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTTGCAAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_KU2-6_11_NZ_JPZN01000001;50_91_2 ATGCCAAAGATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCGTTCACTAGCCACTTATTCGCAAACAAAACACAAAAACAA AAACGTAAACTTCGTAAAGCAACACTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_MB8_NZ_RXXX01000100;51_39_2 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTTGCAAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_mongoliensis_DSM_19169_NZ_JACHEQ010000001;52_3_159 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGC CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCAAACAAAACACAAAAGCAA AAACGTAAACTTCGCAAAGCAACACTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_mongoliensis_MB4_NZ_MRZM01000010;53_81_31 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGCAAAGCAACGCTTGTATCAAAAGGCGACTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_pushchinoensis_K1_NZ_FOJQ01000117;54_33_42 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACTGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCTAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_salavatile_DSM22626;55_7_21 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGC CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCAAACAAAACACAAAAACAA AAACGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_suryakundensis_DSM_27374_NZ_LIOK01000001;56_0_83 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCAAACAAAACGCAAAAACAA AAACGTAAACTTCGTAAAGCAACACTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_tengchongensis_DSM_23211_NZ_JACHES010000001;57_7_106 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTCGCAAACAAAACACAAAAACAA AAACGTAAACTTCGTAAAGCAACACTTGTATCAAAAGGCGATTTCAAACGTATTCGTCAA TTGTTAGATAACGTAAAATAA Anoxybacillus_thermarum_AF_04_NZ_JXTH01000001;58_59_11 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCGAAGCGTTTCAAAAAGACAGGAACAGGT CAATTAAAACGTTCACACGCATTCACTAGCCACTTATTTGCAAACAAAACACAAAAACAA AAGCGTAAACTTCGTAAAGCAACGCTTGTATCAAAAGGCGATTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA Cal_A_geothermalis_GAB_PacBio;59_0_3317 ATGCCAAAAATGAAAACTCACAGAGGCTCTGCAAAGCGTTTTAAAAAGACGGGTACTGGT AAATTGAAGCGTTCTCATGCGTTTACTAGCCACTTGTTTGCTAATAAAACTCAAAAGCAA AAACGCAAGCTTCGCAAAGGAACGCTTGTATCTTCTGGAGATTTTAAACGTATTCGTCAA ATGTTAGACAACTTAAAATAA Cal_Anoxybacillus_B2M1_NZ_CP015435;60_0_3290 ATGCCAAAAATGAAAACTCACAGAGGCTCTGCAAAGCGTTTTAAAAAGACGGGTACTGGT AAATTGAAGCGTTCTCATGCGTTTACTAGCCACTTGTTTGCTAATAAAACTCAAAAGCAA AAACGCAAGCTTCGCAAAGGAACGCTTGTATCTTCTGGAGATTTTAAACGTATTCGTCAA ATGCTAGACAACTTAAAATAA Cal_Anoxybacillus_B7M1_NZ_CP015436;61_0_1979 ATGCCAAAAATGAAAACTCACAGAGGCTCTGCAAAGCGTTTTAAAAAGACGGGTACTGGT AAATTGAAGCGTTCTCATGCGTTTACTAGCCACTTGTTTGCTAATAAAACTCAAAAGCAA AAACGCAAGCTTCGCAAAGGAACGCTTGTATCTTCTGGAGATTTTAAACGTATTCGTCAA ATGCTAGACAACTTAAAATAA Cal_Anoxybacillus_P3H1B_NZ_LPUG01000001;62_7_603 ATGCCAAAAATGAAAACTCACAGAGGCTCTGCAAAGCGTTTTAAAAAGACGGGTACTGGT AAATTGAAGCGTTCTCATGCGTTTACTAGCCACTTGTTTGCTAATAAAACTCAAAAGCAA AAACGCAAGCTTCGCAAAGGAACGCTTGTATCTTCTGGAGATTTTAAACGTATTCGTCAA ATGTTAGACAACTTAAAATAA Cal_Anoxybacillus_PDR2_NZ_CP047158;63_0_2852 ATGCCAAAAATGAAAACTCACAGAGGCTCTGCAAAGCGTTTTAAAAAGACGGGTACTGGT AAATTGAAGCGTTCTCATGCGTTTACTAGCCACTTGTTTGCTAATAAAACTCAAAAGCAA AAACGCAAGCTTCGCAAAGGAACGCTTGTATCTTCTGGAGATTTTAAACGTATTCGTCAA ATGTTAGACAACTTAAAATAA Cal_Anoxybacillus_rupiensis_DSM_17127_NZ_JACIDF010000001;64_2_153 ATGCCAAAAATGAAAACTCACAGAGGCTCTGCAAAGCGTTTTAAAAAGACGGGTACTGGT AAATTGAAGCGTTCTCATGCGTTTACTAGCCACTTGTTTGCTAATAAAACTCAAAAGCAA AAACGCAAGCTTCGCAAAGGAACGCTTGTATCTTCTGGAGATTTTAAACGTATTCGTCAA ATGTTAGACAACTTAAAATAA Cal_Anoxybacillus_tepidamans_PS2_NZ_JHVN01000001;65_18_42 ATGCCAAAAATGAAAACTCACAGAGGCTCTGCAAAGCGCTTTAAAAAGACGGGTACTGGT AAACTTAAACGTTCTCATGCGTTTACTAGCCACTTATTTGCAAACAAAACGCAAAAGCAA AAACGCAAACTTCGCAAAGCAACGCTTGTATCTTCTGGCGACTTCAAACGCATTCGTCAA TTGCTTGACAACTTAAAATAA Cal_Anoxybacillus_UARK-01_NZ_NASY01000001;66_31_156 ATGCCAAAAATGAAAACTCACAGAGGCTCTGCAAAGCGTTTTAAAAAGACGGGTACTGGT AAATTGAAGCGTTCTCATGCGTTTACTAGCCACTTGTTTGCTAATAAAACTCAAAAGCAA AAACGCAAGCTTCGCAAAGGAACGCTTGTATCTTCTGGAGATTTTAAACGTATTCGTCAA ATGCTAGACAACTTAAAATAA Cal_A_rupensis_GAB_PacBio;67_0_1383 ATGCCAAAAATGAAAACTCACAGAGGCTCTGCAAAGCGTTTTAAAAAGACGGGTACTGGT AAATTGAAGCGTTCTCATGCGTTTACTAGCCACTTGTTTGCTAATAAAACTCAAAAGCAA AAACGCAAGCTTCGCAAAGGAACGCTTGTATCTTCTGGAGATTTTAAACGTATTCGTCAA ATGTTAGACAACTTAAAATAA Tal_Anoxybacillus_calidus_DSM_25220_NZ_JACDUU010000001;68_3_119 ATGCCAAAAATGAAAACTCACAAAGGCTCTGCAAAGCGTTTCAAAAAGACTGGTACTGGT AAATTAAAACGTTCACACGCTTTCACTAGCCACTTATTCGCGAACAAAACTCAAAAACAA AAACGTAAACTTCGTAAAGCGACACTTGTATCTTCAGGTGACTTCAAACGCATTCGTCAA TTATTAGACAACTTGAAATAA Tal_Anoxybacillus_vitaminiphilus_CGMCC_1.8979_NZ_QLMH01000001;69_2_220 ATGCCAAAAATGAAAACTCACAAAGGCTCTGCAAAGCGTTTCAAAAAGACTGGTACTGGT AAATTAAAACGTTCACACGCTTTTACTAGCCACTTATTCGCAAACAAAACACAAAAACAA AAACGCAAACTTCGTAAAGCGACACTTGTATCTTCTGGTGACTTCAAACGCATTCGTCAA TTATTGGACAACTTGAAATAA Thermolongibacillus_altinsuensis_DSM_24979_NZ_SLUL01000001;70_2_90 ATGCCAAAAATGAAAACTCACAAAGGCTCAGCAAAGCGTTTCAAAAAGACGGGTACTGGT AAATTAAAACGTTCACACGCATTTACTAGCCACTTGTTCGCAAACAAAACACAAAAACAA AAACGTAAACTTCGCAAAGCAACGCTTGTATCAAAAGGTGACTTCAAACGCATTCGTCAA TTGTTAGATAACGTAAAATAA

5. I could also run prank without any errors $prank -d=rpmI.fasta -o=test

[gtonkinhill]

Hi,

As this is occurring on different genes somewhat randomly I would guess that it is caused by too many instances of Prank running at the same time causing a memory issue. It might be worth trying using only a single cpu -t 1

[luke-dt]

I'm also having a similar issue. Here's the tail of the output with the error message:

generating core genome MSAs... 100%|██████████| 4489/4489 [26:46<00:00, 2.79it/s] 2%|▏ | 108/4489 [3:01:20<153:06:48, 125.82s/it]slurmstepd: error: _is_a_lwp: open() /proc/17672/status failed: No such file or directory 3%|▎ | 120/4489 [4:07:25<228:56:23, 188.64s/it]Traceback (most recent call last): File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/bin/panaroo", line 10, in sys.exit(main()) File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/panaroo/main.py", line 483, in main generate_core_genome_alignment(G, temp_dir, args.output_dir, File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/panaroo/generate_output.py", line 296, in generate_core_genome_alignment multi_align_sequences(commands, output_dir + "aligned_gene_sequences/", File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/panaroo/generate_alignments.py", line 158, in multi_align_sequences alignment_results = Parallel(n_jobs=threads, prefer="threads")( File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/joblib/parallel.py", line 1056, in call self.retrieve() File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/joblib/parallel.py", line 935, in retrieve self._output.extend(job.get(timeout=self.timeout)) File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/multiprocessing/pool.py", line 771, in get raise self._value File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, kwds)) File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 595, in call return self.func(*args, *kwargs) File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/joblib/parallel.py", line 262, in call return [func(args, kwargs) File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/joblib/parallel.py", line 262, in return [func(*args, **kwargs) File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/panaroo/generate_alignments.py", line 148, in align_sequences stdout, stderr = command[0]() File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/Bio/Application/init.py", line 574, in call raise ApplicationError(return_code, str(self), stdout_str, stderr_str) Bio.Application.ApplicationError: Non-zero return code -11 from 'prank -d=/scratch/gdlab/ldioriot/panaroo_test/d02_panaroo-2/k_michiganensis/tmpw7v56pqd/ydfZ_1.fasta -o=ydfZ_1 -f=8 -codon' 3%|▎ | 131/4489 [4:47:17<159:17:28, 131.59s/it]

When I open ydfZ_1.fasta, it looks like a valid fasta file

[gtonkinhill]

Hi,

Do you still get this issue using a single cpu? This involves running Panaroo with the flag -t 1

[luke-dt]

I'll try that now. FWIW, the crash also generates a core dump:

(base) ldiorio-toth@htcf:/scratch/gdlab/ldioriot/panaroo_test/d02_panaroo_prank/k_michiganensis$ file core core: ELF 64-bit LSB core file x86-64, version 1 (SYSV), SVR4-style, from 'prank -d=/scratch/gdlab/ldioriot/panaroo_test/d02_panaroo_prank/k_michiganensis' (base) ldiorio-toth@htcf:/scratch/gdlab/ldioriot/panaroo_test/d02_panaroo_prank/k_michiganensis$ gdb prank core GNU gdb (Ubuntu 7.11.1-0ubuntu1~16.5) 7.11.1 Copyright (C) 2016 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-linux-gnu". Type "show configuration" for configuration details. For bug reporting instructions, please see: http://www.gnu.org/software/gdb/bugs/. Find the GDB manual and other documentation resources online at: http://www.gnu.org/software/gdb/documentation/. For help, type "help". Type "apropos word" to search for commands related to "word"... prank: No such file or directory. [New LWP 12517] Core was generated by `prank -d=/scratch/gdlab/ldioriot/panaroo_test/d02_panaroo_prank/k_michiganensis'. Program terminated with signal SIGSEGV, Segmentation fault.

0 0x000000e3ff7d96f6 in ?? ()

[luke-dt]

@gtonkinhill I tried running with the -t 1 flag and it failed again, but with a slightly different error:

writing output... generating core genome MSAs... 100%|██████████| 4489/4489 [2:48:34<00:00, 2.25s/it]
0%| | 14/4489 [6:00:04<935:08:22, 752.29s/it]Traceback (most recent call last): File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/bin/panaroo", line 10, in sys.exit(main()) File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/panaroo/main.py", line 483, in main generate_core_genome_alignment(G, temp_dir, args.output_dir, File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/panaroo/generate_output.py", line 296, in generate_core_genome_alignment multi_align_sequences(commands, output_dir + "aligned_gene_sequences/", File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/panaroo/generate_alignments.py", line 158, in multi_align_sequences alignment_results = Parallel(n_jobs=threads, prefer="threads")( File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/joblib/parallel.py", line 1046, in call while self.dispatch_one_batch(iterator): File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/joblib/parallel.py", line 861, in dispatch_one_batch self._dispatch(tasks) File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/joblib/parallel.py", line 779, in _dispatch job = self._backend.apply_async(batch, callback=cb) File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 208, in apply_async result = ImmediateResult(func) File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 572, in init self.results = batch() File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/joblib/parallel.py", line 262, in call return [func(*args, *kwargs) File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/joblib/parallel.py", line 262, in return [func(args, **kwargs) File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/panaroo/generate_alignments.py", line 148, in align_sequences stdout, stderr = command[0]() File "/opt/apps/labs/gdlab/envs/panaroo/1.2.9/lib/python3.9/site-packages/Bio/Application/init.py", line 574, in call raise ApplicationError(return_code, str(self), stdout_str, stderr_str) Bio.Application.ApplicationError: Non-zero return code -6 from 'prank -d=/scratch/gdlab/ldioriot/panaroo_test/d02_panaroo_prank_1c/k_michiganensis/tmpjvb9bwr4/ydfZ_1.fasta -o=ydfZ_1 -f=8 -codon', message "terminate called after throwing an instance of 'std::out_of_range'" 0%| | 14/4489 [6:00:16<1919:19:28, 1544.04s/it]

[gtonkinhill]

Hi,

My guess is that this might be an issue with the installation of Prank. It's a bit hard to diagnose just from the error messages. It might be worth trying to reinstall Prank. If you are able to send me a small reproducible example I would also be happy to take a look.

[luke-dt]

I'll try reinstalling prank. The panaroo installation was done in a virtual environment through conda/mamba.

Here are 10 Refseq assemblies (annotated with prokka) that failed in about an hour for me:

GCF_003940635.1_ASM394063v1_genomic GCF_003940625.1_ASM394062v1_genomic GCF_003940585.1_ASM394058v1_genomic GCF_003939685.1_ASM393968v1_genomic GCF_003936865.1_ASM393686v1_genomic GCF_003936925.1_ASM393692v1_genomic GCF_003936385.1_ASM393638v1_genomic GCF_003936325.1_ASM393632v1_genomic GCF_003936245.1_ASM393624v1_genomic GCF_003936255.1_ASM393625v1_genomic

using the following command:

panaroo \ -i ${tmpdir}/*.gff \ -o ${outdir}/${species} \ --clean-mode strict \ --core_threshold 0.99 \ -a core \ --aligner prank \ -t 12

However, I get an error with pretty much any usage of PRANK so you can probably try subsets of those genomes for quick debugging. One thing that I have noticed as it runs is that behaves normally during the first "generating core genome MSA" step. It then generates a TON of *best.fas files in the working directory (not sure if this is normal behavior) and a core dump during the second step but will keep running for a while before throwing an error and halting.

translating hits... removing by consensus... Updating output... Number of refound genes: 91 collapse gene families with refound genes... Processing depth: 1 Iteration: 1 100%|██████████| 7033/7033 [00:00<00:00, 35613.74it/s] Processing depth: 2 Iteration: 1 100%|██████████| 7033/7033 [00:00<00:00, 33503.97it/s] Iteration: 2 100%|██████████| 1/1 [00:00<00:00, 31068.92it/s] Processing depth: 3 Iteration: 1 100%|██████████| 7032/7032 [00:00<00:00, 31962.11it/s] generating core genome MSAs... 100%|██████████| 5438/5438 [16:08<00:00, 5.62it/s] <--- normal behavior 2%|▏ | 108/5359 [56:33<56:29:09, 38.73s/it] <--- core dump