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Official home of genome aligner based upon notion of Cactus graphs
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Job 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v12 is completely failed #1361

Open song984888 opened 7 months ago

song984888 commented 7 months ago

what's wrong with my result using cactus-v2.8.1?!

Input newick tree: ((((((Glycine_max,(Fragaria_vesca,(Cucumis_sativus,Juglans_nigra))),Arabidopsis_thaliana),Vitis_vinifera),(Ambrosia_artemisiifolia,Solanum_lycopersicum)),Aquilegia_coerulea),Acorus_gramineus),Amborella_trichopoda;

logFile: Enabling realtime logging in Toil Deprecated toil method. Please use "toil.lib.conversions.human2bytes()" instead." Deprecated toil method. Please use "toil.lib.conversions.human2bytes()" instead." Cactus Command: /home/songht/anaconda3/bin/cactus ./js my_run.txt ./myRun.hal --workDir ./tmp --stats --restart --logFile ./log_1713454178 --clean never Cactus Commit: 28a6e2cbecb5e954298f60d3ede2bdf7218f11d7 Repairing job: kind-progressivestep/instance-83artpm Repairing job: kind-progressive_step/instance-qthcbt_g Repairing job: kind-cactus_cons/instance-06ssc_rv Repairing job: kind-progressive_step/instance-3qncx1ct Repairing job: kind-progressive_step/instance-6hxn2lri Repairing job: kind-EncapsulatedJob/instance-dcjz9iw8 Repairing job: kind-preprocess_all/instance-2ildbr9t Repairing job: kind-progressive_step/instance-4q082cnf Repairing job: kind-progressive_workflow/instance-vkt51ano Repairing job: kind-progressive_step/instance-cowwzjc3 Repairing job: kind-Job/instance-_rga7ss3 Repairing job: kind-progressive_step/instance-pm06qz92 Running Toil version 6.0.0-0e2a07a20818e593bfdfde3cc51ca4ad809fde96 on host Z100L. Starting real-time logging. Issued job 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v7 with job batch system ID: 1 and disk: 2.4 Gi, memory: 87.1 Gi, cores: 128, accelerators: [], preemptible: False 2024-04-18 23:29:40.692017: Running the command: "cactus_consolidated --sequences Anc2 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc2.fa Anc3 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc3.fa Aquilegia_coerulea /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Aquilegia_coerulea.fa Acorus_gramineus /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Acorus_gramineus.fa --speciesTree (((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda; --logLevel INFO --alignments /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1_primary.paf --params /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.config.xml --outputFile /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.c2h --outputHalFastaFile /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.c2h.fa --outputR <...> nght/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.ref --outgroupEvents Aquilegia_coerulea Acorus_gramineus --referenceEvent Anc1 --threads 128" cactus_consolidated(Anc1): Params file: /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.config.xml cactus_consolidated(Anc1): Output file string : /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.c2h cactus_consolidated(Anc1): Output hal fasta file string : /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.c2h.fa cactus_consolidated(Anc1): Output reference fasta file string : /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.ref cactus_consolidated(Anc1): Sequence files and events: Anc2 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc2.fa Anc3 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc3.fa Aquilegia_coerulea /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Aquilegia_coerulea.fa Acorus_gramineus /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Acorus_gramineus.fa cactus_consolidated(Anc1): Alignments file: /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1_primary.paf cactus_consolidated(Anc1): Secondary alignments file: (null) cactus_consolidated(Anc1): Constraint alignments file: (null) cactus_consolidated(Anc1): Species tree: (((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda; cactus_consolidated(Anc1): Outgroup events: Aquilegia_coerulea Acorus_gramineus cactus_consolidated(Anc1): Reference event: Anc1 cactus_consolidated(Anc1): Loaded the parameters files, 0 seconds have elapsed cactus_consolidated(Anc1): Set up the cactus disk, 0 seconds have elapsed cactus_consolidated(Anc1): Constructed the first flower cactus_consolidated(Anc1): Going to build the event tree with newick string: (((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda; cactus_consolidated(Anc1): [0x45e39a] cactus_consolidated(Anc1): [0x467182] cactus_consolidated(Anc1): [0x428e65] cactus_consolidated(Anc1): [0x4029e5] cactus_consolidated(Anc1): [0x632f2a] cactus_consolidated(Anc1): [0x6347c7] cactus_consolidated(Anc1): [0x4060a5] cactus_consolidated(Anc1): ERROR: Invalid Newick tree, missing ';' Got exit code 1 (indicating failure) from job _toil_worker cactus_cons file:/home/songht/plants/Asteaceae/genomes/cactusRun_R1/js kind-cactus_cons/instance-06ssc_rv. Job failed with exit value 1: 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v7 Exit reason: None The job seems to have left a log file, indicating failure: 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v8 Log from job "kind-cactus_cons/instance-06ssc_rv" follows: =========> [2024-04-18T23:29:40+0800] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2024-04-18T23:29:40+0800] [MainThread] [I] [toil] Running Toil version 6.0.0-0e2a07a20818e593bfdfde3cc51ca4ad809fde96 on host Z100L. [2024-04-18T23:29:40+0800] [MainThread] [I] [toil.worker] Working on job 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v7 [2024-04-18T23:29:40+0800] [MainThread] [I] [toil.worker] Loaded body Job('cactus_cons' kind-cactus_cons/instance-06ssc_rv v7) from description 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v7 [2024-04-18T23:29:40+0800] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release." [2024-04-18T23:29:40+0800] [MainThread] [W] [root] Deprecated toil method. Please call "logging.getLevelName" directly. [2024-04-18T23:29:40+0800] [MainThread] [I] [cactus.shared.common] Running the command ['cactus_consolidated', '--sequences', 'Anc2 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc2.fa Anc3 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc3.fa Aquilegia_coerulea /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Aquilegia_coerulea.fa Acorus_gramineus /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Acorus_gramineus.fa', '--speciesTree', '(((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda;', '--logLevel', 'INFO', '--alignments', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1_primary.paf', '--params', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.config.xml', '--outputFile', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.c2h', '--outputHalFastaFile', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.c2h.fa', '--outputReferenceFile', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.ref', '--outgroupEvents', 'Aquilegia_coerulea Acorus_gramineus', '--referenceEvent', 'Anc1', '--threads', '128'] [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] 2024-04-18 23:29:40.692017: Running the command: "cactus_consolidated --sequences Anc2 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc2.fa Anc3 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc3.fa Aquilegia_coerulea /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Aquilegia_coerulea.fa Acorus_gramineus /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Acorus_gramineus.fa --speciesTree (((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda; --logLevel INFO --alignments /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1_primary.paf --params /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.config.xml --outputFile /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.c2h --outputHalFastaFile /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.c2h.fa --outputR <...> nght/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.ref --outgroupEvents Aquilegia_coerulea Acorus_gramineus --referenceEvent Anc1 --threads 128" [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Params file: /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.config.xml [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Output file string : /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.c2h [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Output hal fasta file string : /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.c2h.fa [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Output reference fasta file string : /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.ref [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Sequence files and events: Anc2 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc2.fa Anc3 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc3.fa Aquilegia_coerulea /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Aquilegia_coerulea.fa Acorus_gramineus /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Acorus_gramineus.fa [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Alignments file: /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1_primary.paf [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Secondary alignments file: (null) [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Constraint alignments file: (null) [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Species tree: (((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda; [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Outgroup events: Aquilegia_coerulea Acorus_gramineus [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Reference event: Anc1 [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Loaded the parameters files, 0 seconds have elapsed [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Set up the cactus disk, 0 seconds have elapsed [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Constructed the first flower [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Going to build the event tree with newick string: (((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda; [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): [0x45e39a] [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): [0x467182] [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): [0x428e65] [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): [0x4029e5] [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): [0x632f2a] [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): [0x6347c7] [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): [0x4060a5] [2024-04-18T23:29:40+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): ERROR: Invalid Newick tree, missing ';' [2024-04-18T23:29:40+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Failed job accessed files: [2024-04-18T23:29:40+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-cactus_cons/instance-um53h5z5/file-40558a44a2884207a7b0165de830c869/Anc2.ref' to path '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc2.fa' [2024-04-18T23:29:40+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-cactus_cons/instance-w1rshx4p/file-38374646d5c54a00a873442e40c22369/Anc3.ref' to path '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc3.fa' [2024-04-18T23:29:40+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-trim_unaligned_sequences/instance-x0df3mfy/file-b02364ded31843c79320adf29f052e44/tmpskxpbko6.tmp' to path '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Aquilegia_coerulea.fa' [2024-04-18T23:29:40+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-trim_unaligned_sequences/instance-x0df3mfy/file-7fb8ae40fe8f4effa667d63cdda890ef/tmpccyw9w2k.tmp' to path '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Acorus_gramineus.fa' [2024-04-18T23:29:40+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-trim_unaligned_sequences/instance-x0df3mfy/file-0103afd77f2841a6867770971c241639/tmpkiw6yxd2.tmp' to path '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.paf' Traceback (most recent call last): File "/home/songht/anaconda3/lib/python3.10/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/home/songht/anaconda3/lib/python3.10/site-packages/toil/job.py", line 2829, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/home/songht/anaconda3/lib/python3.10/site-packages/toil/job.py", line 2746, in _run return self.run(fileStore) File "/home/songht/anaconda3/lib/python3.10/site-packages/toil/job.py", line 2974, in run rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) File "/home/songht/anaconda3/lib/python3.10/site-packages/cactus/pipeline/cactus_workflow.py", line 143, in cactus_cons messages = cactus_call(check_output=True, returnStdErr=True, File "/home/songht/anaconda3/lib/python3.10/site-packages/cactus/shared/common.py", line 906, in cactus_call raise RuntimeError("{}Command {} exited {}: {}".format(sigill_msg, call, process.returncode, out)) RuntimeError: cactus_consolidated(Anc1): Command ['cactus_consolidated', '--sequences', 'Anc2 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc2.fa Anc3 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc3.fa Aquilegia_coerulea /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Aquilegia_coerulea.fa Acorus_gramineus /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Acorus_gramineus.fa', '--speciesTree', '(((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda;', '--logLevel', 'INFO', '--alignments', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1_primary.paf', '--params', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.config.xml', '--outputFile', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.c2h', '--outputHalFastaFile', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.c2h.fa', '--outputReferenceFile', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/c558/85b0/tmppn7ttpzb/Anc1.ref', '--outgroupEvents', 'Aquilegia_coerulea Acorus_gramineus', '--referenceEvent', 'Anc1', '--threads', '128'] exited 1: [2024-04-18T23:29:40+0800] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host Z100L <========= Due to failure we are reducing the remaining try count of job 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v8 with ID kind-cactus_cons/instance-06ssc_rv to 1 0 jobs are running, 0 jobs are issued and waiting to run Issued job 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v9 with job batch system ID: 2 and disk: 2.4 Gi, memory: 87.1 Gi, cores: 128, accelerators: [], preemptible: False 2024-04-18 23:29:41.534819: Running the command: "cactus_consolidated --sequences Anc2 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc2.fa Anc3 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc3.fa Aquilegia_coerulea /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Aquilegia_coerulea.fa Acorus_gramineus /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Acorus_gramineus.fa --speciesTree (((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda; --logLevel INFO --alignments /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1_primary.paf --params /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.config.xml --outputFile /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.c2h --outputHalFastaFile /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.c2h.fa --outputR <...> nght/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.ref --outgroupEvents Aquilegia_coerulea Acorus_gramineus --referenceEvent Anc1 --threads 128" cactus_consolidated(Anc1): Params file: /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.config.xml cactus_consolidated(Anc1): Output file string : /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.c2h cactus_consolidated(Anc1): Output hal fasta file string : /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.c2h.fa cactus_consolidated(Anc1): Output reference fasta file string : /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.ref cactus_consolidated(Anc1): Sequence files and events: Anc2 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc2.fa Anc3 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc3.fa Aquilegia_coerulea /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Aquilegia_coerulea.fa Acorus_gramineus /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Acorus_gramineus.fa cactus_consolidated(Anc1): Alignments file: /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1_primary.paf cactus_consolidated(Anc1): Secondary alignments file: (null) cactus_consolidated(Anc1): Constraint alignments file: (null) cactus_consolidated(Anc1): Species tree: (((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda; cactus_consolidated(Anc1): Outgroup events: Aquilegia_coerulea Acorus_gramineus cactus_consolidated(Anc1): Reference event: Anc1 cactus_consolidated(Anc1): Loaded the parameters files, 0 seconds have elapsed cactus_consolidated(Anc1): Set up the cactus disk, 0 seconds have elapsed cactus_consolidated(Anc1): Constructed the first flower cactus_consolidated(Anc1): Going to build the event tree with newick string: (((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda; cactus_consolidated(Anc1): [0x45e39a] cactus_consolidated(Anc1): [0x467182] cactus_consolidated(Anc1): [0x428e65] cactus_consolidated(Anc1): [0x4029e5] cactus_consolidated(Anc1): [0x632f2a] cactus_consolidated(Anc1): [0x6347c7] cactus_consolidated(Anc1): [0x4060a5] cactus_consolidated(Anc1): ERROR: Invalid Newick tree, missing ';' Got exit code 1 (indicating failure) from job _toil_worker cactus_cons file:/home/songht/plants/Asteaceae/genomes/cactusRun_R1/js kind-cactus_cons/instance-06ssc_rv. Job failed with exit value 1: 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v9 Exit reason: None The job seems to have left a log file, indicating failure: 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v11 Log from job "kind-cactus_cons/instance-06ssc_rv" follows: =========> [2024-04-18T23:29:41+0800] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2024-04-18T23:29:41+0800] [MainThread] [I] [toil] Running Toil version 6.0.0-0e2a07a20818e593bfdfde3cc51ca4ad809fde96 on host Z100L. [2024-04-18T23:29:41+0800] [MainThread] [I] [toil.worker] Working on job 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v10 [2024-04-18T23:29:41+0800] [MainThread] [I] [toil.worker] Loaded body Job('cactus_cons' kind-cactus_cons/instance-06ssc_rv v10) from description 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v10 [2024-04-18T23:29:41+0800] [MainThread] [W] [toil.statsAndLogging] Deprecated toil method that will be moved/replaced in a future release." [2024-04-18T23:29:41+0800] [MainThread] [W] [root] Deprecated toil method. Please call "logging.getLevelName" directly. [2024-04-18T23:29:41+0800] [MainThread] [I] [cactus.shared.common] Running the command ['cactus_consolidated', '--sequences', 'Anc2 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc2.fa Anc3 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc3.fa Aquilegia_coerulea /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Aquilegia_coerulea.fa Acorus_gramineus /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Acorus_gramineus.fa', '--speciesTree', '(((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda;', '--logLevel', 'INFO', '--alignments', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1_primary.paf', '--params', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.config.xml', '--outputFile', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.c2h', '--outputHalFastaFile', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.c2h.fa', '--outputReferenceFile', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.ref', '--outgroupEvents', 'Aquilegia_coerulea Acorus_gramineus', '--referenceEvent', 'Anc1', '--threads', '128'] [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] 2024-04-18 23:29:41.534819: Running the command: "cactus_consolidated --sequences Anc2 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc2.fa Anc3 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc3.fa Aquilegia_coerulea /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Aquilegia_coerulea.fa Acorus_gramineus /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Acorus_gramineus.fa --speciesTree (((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda; --logLevel INFO --alignments /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1_primary.paf --params /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.config.xml --outputFile /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.c2h --outputHalFastaFile /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.c2h.fa --outputR <...> nght/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.ref --outgroupEvents Aquilegia_coerulea Acorus_gramineus --referenceEvent Anc1 --threads 128" [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Params file: /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.config.xml [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Output file string : /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.c2h [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Output hal fasta file string : /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.c2h.fa [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Output reference fasta file string : /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.ref [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Sequence files and events: Anc2 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc2.fa Anc3 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc3.fa Aquilegia_coerulea /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Aquilegia_coerulea.fa Acorus_gramineus /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Acorus_gramineus.fa [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Alignments file: /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1_primary.paf [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Secondary alignments file: (null) [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Constraint alignments file: (null) [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Species tree: (((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda; [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Outgroup events: Aquilegia_coerulea Acorus_gramineus [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Reference event: Anc1 [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Loaded the parameters files, 0 seconds have elapsed [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Set up the cactus disk, 0 seconds have elapsed [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Constructed the first flower [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): Going to build the event tree with newick string: (((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda; [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): [0x45e39a] [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): [0x467182] [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): [0x428e65] [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): [0x4029e5] [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): [0x632f2a] [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): [0x6347c7] [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): [0x4060a5] [2024-04-18T23:29:41+0800] [MainThread] [I] [toil-rt] cactus_consolidated(Anc1): ERROR: Invalid Newick tree, missing ';' [2024-04-18T23:29:41+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Failed job accessed files: [2024-04-18T23:29:41+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-cactus_cons/instance-um53h5z5/file-40558a44a2884207a7b0165de830c869/Anc2.ref' to path '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc2.fa' [2024-04-18T23:29:41+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-cactus_cons/instance-w1rshx4p/file-38374646d5c54a00a873442e40c22369/Anc3.ref' to path '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc3.fa' [2024-04-18T23:29:41+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-trim_unaligned_sequences/instance-x0df3mfy/file-b02364ded31843c79320adf29f052e44/tmpskxpbko6.tmp' to path '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Aquilegia_coerulea.fa' [2024-04-18T23:29:41+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-trim_unaligned_sequences/instance-x0df3mfy/file-7fb8ae40fe8f4effa667d63cdda890ef/tmpccyw9w2k.tmp' to path '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Acorus_gramineus.fa' [2024-04-18T23:29:41+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-trim_unaligned_sequences/instance-x0df3mfy/file-0103afd77f2841a6867770971c241639/tmpkiw6yxd2.tmp' to path '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.paf' Traceback (most recent call last): File "/home/songht/anaconda3/lib/python3.10/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/home/songht/anaconda3/lib/python3.10/site-packages/toil/job.py", line 2829, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/home/songht/anaconda3/lib/python3.10/site-packages/toil/job.py", line 2746, in _run return self.run(fileStore) File "/home/songht/anaconda3/lib/python3.10/site-packages/toil/job.py", line 2974, in run rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) File "/home/songht/anaconda3/lib/python3.10/site-packages/cactus/pipeline/cactus_workflow.py", line 143, in cactus_cons messages = cactus_call(check_output=True, returnStdErr=True, File "/home/songht/anaconda3/lib/python3.10/site-packages/cactus/shared/common.py", line 906, in cactus_call raise RuntimeError("{}Command {} exited {}: {}".format(sigill_msg, call, process.returncode, out)) RuntimeError: cactus_consolidated(Anc1): Command ['cactus_consolidated', '--sequences', 'Anc2 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc2.fa Anc3 /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc3.fa Aquilegia_coerulea /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Aquilegia_coerulea.fa Acorus_gramineus /home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Acorus_gramineus.fa', '--speciesTree', '(((Anc2:1.0,Anc3:1.0)Anc1:1.0,Aquilegia_coerulea:1.0)Anc0:1.0,Acorus_gramineus:1.0),Amborella_trichopoda;', '--logLevel', 'INFO', '--alignments', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1_primary.paf', '--params', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.config.xml', '--outputFile', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.c2h', '--outputHalFastaFile', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.c2h.fa', '--outputReferenceFile', '/home/songht/plants/Asteaceae/genomes/cactusRun_R1/tmp/ceb31c6f8c145ec9a39e57a65c973220/d7a2/f888/tmpswzmrg1d/Anc1.ref', '--outgroupEvents', 'Aquilegia_coerulea Acorus_gramineus', '--referenceEvent', 'Anc1', '--threads', '128'] exited 1: [2024-04-18T23:29:41+0800] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host Z100L <========= Due to failure we are reducing the remaining try count of job 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v11 with ID kind-cactus_cons/instance-06ssc_rv to 0 Job 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v12 is completely failed Finished toil run with 14 failed jobs. Failed jobs at end of the run: 'progressive_step' kind-progressive_step/instance-cowwzjc3 v4 'Job' kind-Job/instance-_rga7ss3 v3 'progressive_step' kind-progressive_step/instance-pm06qz92 v4 'progressive_step' kind-progressive_step/instance-3qncx1ct v4 'cactus_cons_with_resources' kind-progressive_step_2/instance-6wqpen7l v5 'progressive_step' kind-progressive_step/instance-6hxn2lri v4 'EncapsulatedJob' kind-EncapsulatedJob/instance-dcjz9iw8 v3 'Job' kind-progressive_schedule/instance-8z5qa96i v5 'progressive_step' kind-progressivestep/instance-83artpm v3 'Job' kind-preprocess_all/instance-2ildbr9t v6 'progressive_step' kind-progressive_step/instance-qthcbt_g v4 'progressive_step' kind-progressive_step/instance-4q082cnf v3 'sanitize_fasta_headers' kind-progressive_workflow/instance-vkt51ano v5 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v12 Stopping real-time logging server. Joining real-time logging server thread.

glennhickey commented 7 months ago

Your tree looks invalid. See the newick format definition here that shows you need ()s around every split.

That said, this is still a bug in cactus in that it should be reporting ERROR: Invalid Newick tree, right away, rather than waiting so far into the pipeline.